# Patent

## Title
Inducing cellular immune responses to Plasmodium falciparum using peptide and nucleic acid compositions

## Abstract

This invention uses our knowledge of the mechanisms by which antigen is recognized by T cells to identify and prepare Plasmodium falciparum epitopes, and to develop epitope-based vaccines directed towards malaria. More specifically, this application communicates our discovery of pharmaceutical compositions and methods of use in the prevention and treatment of malaria. In particular, this application discloses isolated peptides comprising oligopeptides, for example the oligopeptide GVSENIFLK, or isolated peptides conjugated with T helper peptides that are used as antigens in epitope-based vaccines to prevent and/or treat malaria.

## Background
CROSS-REFERENCES TO RELATED APPLICATIONS
This application is a continuation-in-part of U.S. application Ser. No. 09/017,743, filed Feb. 3, 1998 (abandoned); and is a continuation-in-part of U.S. application Ser. No. 08/821,739, filed Mar. 20, 1997 (abandoned); and is a continuation-in-part of U.S. application Ser. No. 08/452,843, filed May 30, 1995 (abandoned); and is a continuation-in-part of U.S. application Ser. No. 08/454,033, filed May 26, 1995 (abandoned); and is a continuation-in-part of U.S. application Ser. No. 08/344,824, filed Nov. 23, 1994 (abandoned); said Ser. No. 09/017,743 (abandoned) is a continuation-in-part of U.S. application Ser. No. 08/753,615, filed Nov. 23, 1996 (abandoned); which is a continuation-in-part of U.S. application Ser. No. 08/590,298, filed Jan. 23, 1996 (abandoned); which is a continuation-in-part of said Ser. No. 08/452,843, filed May 30, 1995 (abandoned); which is a continuation-in-part of said Ser. No. 08/344,824, filed Nov. 23, 1994 (abandoned); which is a continuation-in-part of U.S. application Ser. No. 08/278,634, filed Jul. 21, 1994 (abandoned); said Ser. No. 08/821,739 (abandoned) claims the benefit of U.S. Provisional Application No. 60/013,833, filed Mar. 21, 1996 (now inactive); and is a continuation-in-part of U.S. application Ser. No. 08/451,913, filed May 26, 1995 (abandoned).
This application is related to U.S. Ser. No. 09/189,702 filed Nov. 10, 1998, now U.S. Pat. No. 7,252,829, which is a CIP of U.S. Ser. No. 08/205,713 filed Mar. 4, 1994 (abandoned), which is a CIP of Ser. No. 08/159,184 filed Nov. 29, 1993 and now abandoned, which is a CIP of Ser. No. 08/073,205 filed Jun. 4, 1993 and now abandoned, which is a CIP of Ser. No. 08/027,146 filed Mar. 5, 1993 and now abandoned. The present application is also related to U.S. Ser. No. 09/226,775 (abandoned), which is a CIP of abandoned U.S. Ser. No. 08/815,396, which claims benefit of abandoned U.S. Ser. No. 60/013,113 filed Mar. 21, 1996. Furthermore, the present application is related to U.S. Ser. No. 09/017,735 (abandoned), which is a CIP of abandoned U.S. Ser. No. 08/589,108; U.S. Ser. No. 08/454,033 (abandoned); and U.S. Ser. No. 08/349,177 (abandoned). The present application is also related to U.S. Ser. No. 09/017,524 (abandoned), U.S. Ser. No. 08/821,739 (abandoned), which claims benefit of abandoned U.S. Ser. No. 60/013,833 filed Mar. 21, 1996; and U.S. Ser. No. 08/347,610 (abandoned), which is a CIP of U.S. Ser. No. 08/159,339, now U.S. Pat. No. 6,037,135, which is a CIP of abandoned U.S. Ser. No. 08/103,396, which is a CIP of abandoned U.S. Ser. No. 08/027,746, which is a CIP of abandoned U.S. Ser. No. 07/926,666. The present application is also related to U.S. Ser. No. 09/017,743 (abandoned), which is a CIP of abandoned U.S. Ser. No. 08/590,298; and U.S. Ser. No. 08/452,843 (abandoned), which is a CIP of U.S. Ser. No. 08/344,824 (abandoned), which is a CIP of abandoned U.S. Ser. No. 08/278,634. The present application is also related to PCT application PCT/US99/12066 filed May 28, 1999 which claims benefit of provisional U.S. Ser. No. 60/087,192, filed May 29, 1998 (now inactive), and U.S. Ser. No. 09/009,953 (abandoned), which is a CIP of abandoned U.S. Ser. No. 60/036,713 and abandoned U.S. Ser. No. 60/037,432. In addition, the present application is related to U.S. Ser. No. 09/098,584 (abandoned), U.S. Ser. No. 09/239,043 now U.S. Pat. No. 6,689,363, and to Provisional U.S. Patent Application 60/117,486 filed Jan. 27, 1999 (now inactive). The present application is also related to Ser. No. 09/350,401 filed Jul. 8, 1999, and U.S. Ser. No. 09/357,737 filed Jul. 19, 1999. All of the above applications are incorporated herein by reference.


FEDERALLY SPONSORED RESEARCH AND DEVELOPMENT
This invention was funded, in part, by the United States government under grants with the National Institutes of Health. The U.S. government has certain rights in this invention.


The Substitute Sequence Listing written in file Substitute Sequence Listing 2060—0040004, 699,629 bytes, created on Mar. 14, 2003, on compact discs for application Ser. No. 09/390,061, Sette et al., Inducing Cellular Immune Responses to Plasmodium falciparum Using Peptide and Nucleic Acid Compositions, is herein incorporated-by-reference.










INDEX
















I.
Background of the Invention 


II.
Summary of the Invention


III. 
Brief Description of the Figures


IV.
Detailed Description of the Invention










A.
Definitions



B.
Stimulation of CTL and HTL responses



C.
Binding Affinity of Peptide Epitopes for HLA Molecules



D.
Peptide Epitope Binding Motifs and Supermotifs












 1.
HLA-A1 supermotif




 2.
HLA-A2 supermotif




 3.
HLA-A3 supermotif




 4.
HLA-A24 supermotif




 5.
HLA-B7 supermotif




 6.
HLA-B27 supermotif




 7.
HLA-B44 supermotif




 8.
HLA-B58 supermotif




 9.
HLA-B62 supermotif




10.
HLA-A1 motif




11.
HLA-A2.1 motif




12.
HLA-A3 motif




13.
HLA-A11 motif




14.
HLA-A24 motif




15.
HLA-DR-1-4-7 supermotif




16.
HLA-DR3 motifs










E.
Enhancing Population Coverage of the Vaccine



F.
Immune Response-Stimulating Peptide Epitope Analogs



G.
Computer Screening of Protein Sequences from Disease-




Related Antigens for Supermotif- or Motif-Containing Epitopes



H.
Preparation of Peptide Epitopes



I.
Assays to Detect T-Cell Responses



J.
Use of Peptide Epitopes for Evaluating Immune Responses



K.
Vaccine Compositions












 1.
Minigene Vaccines




 2.
Combinations of CTL Peptides with Helper Peptides










L.
Administration of Vaccines for Therapeutic or Prophylactic 




Purposes



M.
Kits








V.
Examples


VI.
Claims


VII.
Abstract









I. BACKGROUND OF THE INVENTION
Malaria, which is caused by infection with the parasite Plasmodium falciparum (PF), represents a major world health problem. Approximately 500 million people in the world are at risk from the disease, with approximately 200 million people actually harboring the parasites. An estimated 1 to 2 million deaths occur each year due to malaria. (Miller et al., Science 234:1349, 1986).
Fatal outcomes are not confined to first infections, and constant exposure is apparently a prerequisite for maintaining immunity. Naturally acquired sterile immunity is rare, if it exists at all. Accordingly, major efforts to develop an efficacious malaria vaccine have been undertaken.
Human volunteers injected with irradiated PF sporozoites are resistant to subsequent sporozoite challenges, which demonstrates that development of a malaria vaccine is indeed immunologically feasible. Furthermore, these immune individuals developed a vigorous response, including antibodies, and cytotoxic T lymphocyte (CTL) and helper T lymphocyte (HTL) components, directed against multiple antigens. Reproducing the breadth and multiplicity of this response in a vaccine, however, is a task of large proportions. The epitope approach, as described herein, may represent a solution to this challenge, in that it allows the incorporation of various antibody, CTL and HTL epitopes, from various proteins, in a single vaccine composition.
Anti-sporozoite antibodies are by themselves, in general, not completely efficacious in clearing the infection (Egan et al., Science 236:453, 1987). However, high concentrations of antibodies directed against the repeated region of the major B cell antigen of the sporozoite/circumsporozoite protein (CSP) have been shown to prevent liver cell infection in certain experimental models (Egan et al., Science 236:453, 1987; Potocnjak, P. et al., Science 207:71, 1980). The present inventors have shown that constructs encompassing CSP-repeat B cell epitopes and the optimized helper epitope PADRETM (San Diego, Calif.) are highly immunogenic, and can protect in vitro against sporozoite invasion in both mouse and human liver cells, and protect mice in vivo against live sporozoite challenge (Franke et al., Vaccine 17:1201-1205, 1999)
PF-specific CD4+ T cells also have a role in malarial immunity beyond providing help for B cell and CTL responses. Experiments by Renia et al. (Renia, et al., Proc. Natl. Acad. Sci. USA 88:7963, 1991) demonstrated that HTLs directed against the Plasmodium yoelli CS protein could in fact adoptivley transfer protection against malaria.
Considerable data implicate CTLs in protection against pre-erythrocytic-stage malaria. CD8+ CTLs can eliminate Plasmodium berghei- or Plasmodium yoelii-infected mouse hepatocytes from in vitro culture in a major histocompatibility complex (MHC)-restricted and antigen-restricted manner (Hoffman et al., Science 244:1078-1081, 1989; Weiss et al., J. Exp. Med. 171:763-773, 1990). Further, it has also been shown that the immunity that developed in mice vaccinated with irradiated sporozoites is also dependent upon the present of CD8+ T cells. These T cells accumulate in inflammatory liver infiltrates subsequent to challenge. Passive transfer of circumsporozoite (CSP)-specific CTL clones as long as three hours after inoculation of sporozoites (i.e., after the parasites have left the bloodstream and infected liver cells) were capable of protecting animals against infection (Romero et al., Nature 341:323, 1989).
It is notable that CTL-restricted responses directed against a single antigen are insufficient to protect mice with different MHC alleles, and a combination of multiple antigens was required even to protect mice from the most common laboratory strains of Plasmodium. These data indicate that a combination of epitopes form several antigens is necessary to elicit a protective CTL response.
Indirect evidence that CTLs are important in protective immunity against Pf in humans has also accumulated. It has been reported that cytotoxic CD8+ T cells can be identified in humans immunized with PF sporozoites (Moreno, et al., Int. Immunol. 3:997, 1991). Further, humans immunized with irradiated sporozoites or naturally exposed to malaria can generate a CTL response to the pre-erythrocytic-stage antigens, CSP, sporozoite surface protein 2 (SSP2), liver-stage antigen-1 (LSA-1), and exported protein-1 (Exp-1) (see, e.g. Malik et al., Proc. Natl. Acad. Sci. USA 88, 3300-3304, 1991; Doolan et al., Int. Immunol. 3:511-516, 1991; Hill et al., Nature 360:434-439, 1992). Additionally, there is evidence that the polymorphism within the CSP may be the result of selection by CTLs of parasites that express variant forms (MCutchan and Water, Immunol. Lett. 25:23-26, 1990). This is based on the observation that the variation is nonsynonymous at the nucleotide level, thereby indicating selective pressure at the protein level. The polymorphism primarily maps to identified CTL and T helper epitopes (Doolan et al., Int. Immunol. 5:27-46, 1993); and CTL responses to some of the parasite variants do not cross-react (Hill et al., supra). Finally, the MHC class I human leukocyte antigen (HLA)-Bw53 has been associated with resistance to severe malaria in The Gambia, and CTLs to a conserved epitope restricted by the HLA-Bw53 allele have been identified on P. falciparum LSA-1 (Hill et al., Nature 352:595-600, 1991; Hill et al., Nature 340:434-439, 1992). Since HLA-Bw53 is found in 15%-40% of the population of sub-Saharan Africa but in less than 1% of Caucasians and Asians, these data suggest evolutionary selection on the basis of protection against severe malaria.
Thus, antibody, and both HLA class I and class II restricted responses directed against multiple sporozoite antigens appear to be involved in generating protective immunity to malaria. Furthermore, several important antigenic epitopes against which humoral and cellular immunity is focused have already been exactly delineated.
HLA class I molecules are expressed on the surface of almost all nucleated cells. Following intracellular processing of antigens, epitopes from the antigens are presented as a complex with the HLA class I molecules on the surface of such cells. CTL recognize the peptide-HLA class I complex, which then results in the destruction of the cell bearing the HLA-peptide complex directly by the CTL and/or via the activation of non-destructive mechanisms e.g., the production of interferon.
In view of the heterogeneous immune response observed with PF infection, induction of a multi-specific cellular immune response directed simultaneously against multiple PF epitopes appears to be important for the development of an efficacious vaccine against PF. There is a need, however, to establish vaccine embodiments that elicit immune responses that correspond to responses seen in patients that clear PF infection.
The information provided in this section is intended to disclose the presently understood state of the art as of the filing date of the present application. Information is included in this section which was generated subsequent to the priority date of this application. Accordingly, information in this section is not intended, in any way, to delineate the priority date for the invention.
II. SUMMARY OF THE INVENTION
This invention applies our knowledge of the mechanisms by which antigen is recognized by T cells, for example, to develop epitope-based vaccines directed towards PF. More specifically, this application communicates our discovery of specific epitope pharmaceutical compositions and methods of use in the prevention and treatment of PF infection.
Upon development of appropriate technology, the use of epitope-based vaccines has several advantages over current vaccines, particularly when compared to the use of whole antigens in vaccine compositions. There is evidence that the immune response to whole antigens is directed largely toward variable regions of the antigen, allowing for immune escape due to mutations. The epitopes for inclusion in an epitope-based vaccine are selected from conserved regions of antigens of pathogenic organisms or tumor-associated antigens, which thereby reduces the likelihood of escape mutants. Furthermore, immunosuppressive epitopes that may be present in whole antigens can be avoided with the use of epitope-based vaccines.
An additional advantage of an epitope-based vaccine approach is the ability to combine selected epitopes (CTL and HTL), and further, to modify the composition of the epitopes, achieving, for example, enhanced immunogenicity. Accordingly, the immune response can be modulated, as appropriate, for the target disease. Similar engineering of the response is not possible with traditional approaches.
Another major benefit of epitope-based immune-stimulating vaccines is their safety. The possible pathological side effects caused by infectious agents or whole protein antigens, which might have their own intrinsic biological activity, is eliminated.
An epitope-based vaccine also provides the ability to direct and focus an immune response to multiple selected antigens from the same pathogen. Thus, patient-by-patient variability in the immune response to a particular pathogen may be alleviated by inclusion of epitopes from multiple antigens from that pathogen in a vaccine composition. A “pathogen” may be an infectious agent or a tumor associated molecule.
One of the most formidable obstacles to the development of broadly efficacious epitope-based immunotherapeutics, however, has been the extreme polymorphism of HLA molecules. To date, effective non-genetically biased coverage of a population has been a task of considerable complexity; such coverage has required that epitopes be used that are specific for HLA molecules corresponding to each individual HLA allele; impractically large numbers of epitopes would therefore have to be used in order to cover ethnically diverse populations. Thus, there has existed a need for peptide epitopes that are bound by multiple HLA antigen molecules for use in epitope-based vaccines. The greater the number of HLA antigen molecules bound, the greater the breadth of population coverage by the vaccine.
Furthermore, as described herein in greater detail, a need has existed to modulate peptide binding properties, e.g., so that peptides that are able to bind to multiple HLA antigens do so with an affinity that will stimulate an immune response. Identification of epitopes restricted by more than one HLA allele at an affinity that correlates with immunogenicity is important to provide thorough population coverage, and to allow the elicitation of responses of sufficient vigor to prevent or clear an infection in a diverse segment of the population. Such a response can also target a broad array of epitopes. The technology disclosed herein provides for such favored immune responses.
In a preferred embodiment, epitopes for inclusion in vaccine compositions of the invention are selected by a process whereby protein sequences of known antigens are evaluated for the presence of motif or supermotif-bearing epitopes. Peptides corresponding to a motif- or supermotif-bearing epitope are then synthesized and tested for the ability to bind to the HLA molecule that recognizes the selected motif. Those peptides that bind at an intermediate or high affinity i.e., an IC50 (or a KD value) of 500 nM or less for HLA class I molecules or an IC50 of 1000 nM or less for HLA class II molecules, are further evaluated for their ability to induce a CTL or HTL response. Immunogenic peptide epitopes are selected for inclusion in vaccine compositions.
Supermotif-bearing peptides may additionally be tested for the ability to bind to multiple alleles within the HLA supertype family. Moreover, peptide epitopes may be analogued to modify binding affinity and/or the ability to bind to multiple alleles within an HLA supertype.
The invention also includes embodiments comprising methods for monitoring or evaluating an immune response to PF in patient having a known HLA-type. Such methods comprise incubating a T cell sample from the patient with a peptide composition comprising an PF epitope consisting essentially of an amino acid sequence described in Tables VII to Table XX or Table XXII which binds the product of at least one HLA allele present in the patient, and detecting for the presence of a T cell that binds to the peptide. A CTL peptide epitope may, for example, be used as a component of a tetrameric complex for such an analysis.
An alternative modality for defining the peptide epitopes in accordance with the invention is to recite the physical properties, such as length; primary structure; or charge, which are correlated with binding to a particular allele-specific HLA molecule or group of allele-specific HLA molecules. A further modality for defining peptide epitopes is to recite the physical properties of an HLA binding pocket, or properties shared by several allele-specific HLA binding pockets (e.g. pocket configuration and charge distribution) and reciting that the peptide epitope fits and binds to said pocket or pockets.
As will be apparent from the discussion below, other methods and embodiments are also contemplated. Further, novel synthetic peptides produced by any of the methods described herein are also part of the invention.



III. BRIEF DESCRIPTION OF THE FIGURES
FIG. 1: FIG. 1 provides a graph of total frequency of genotypes as a function of the number of PF candidate epitopes bound by HLA-A and B molecules, in an average population.



IV. DETAILED DESCRIPTION OF THE INVENTION
The peptide epitopes and corresponding nucleic acid compositions of the present invention are useful for stimulating an immune response to PF by stimulating the production of CTL or HTL responses. The peptide epitopes, which are derived directly or indirectly from native PF protein amino acid sequences, are able to bind to HLA molecules and stimulate an immune response to PF. The complete sequence of the PF proteins to be analyzed can be obtained from Genbank. Peptide epitopes and analogs thereof can also be readily determined from sequence information that may subsequently be discovered for heretofore unknown variants of PF, as will be clear from the disclosure provided below.
The peptide epitopes of the invention have been identified in a number of ways, as will be discussed below. Also discussed in greater detail is that analog peptides have been derived and the binding activity for HLA molecules modulated by modifying specific amino acid residues to create peptide analogs exhibiting altered immunogenicity. Further, the present invention provides compositions and combinations of compositions that enable epitope-based vaccines that are capable of interacting with HLA molecules encoded by various genetic alleles to provide broader population coverage than prior vaccines.
IV.A. DEFINITIONS
The invention can be better understood with reference to the following definitions, which are listed alphabetically:
A “computer” or “computer system” generally includes: a processor; at least one information storage/retrieval apparatus such as, for example, a hard drive, a disk drive or a tape drive; at least one input apparatus such as, for example, a keyboard, a mouse, a touch screen, or a microphone; and display structure. Additionally, the computer may include a communication channel in communication with a network. Such a computer may include more or less than what is listed above.
“Cross-reactive binding” indicates that a peptide is bound by more than one HLA molecule; a synonym is degenerate binding.
A “cryptic epitope” elicits a response by immunization with an isolated peptide, but the response is not cross-reactive in vitro when intact whole protein which comprises the epitope is used as an antigen.
A “dominant epitope” is an epitope that induces an immune response upon immunization with a whole native antigen (see, e.g., Sercarz, et al., Annu. Rev. Immunol. 11:729-766, 1993). Such a response is cross-reactive in vitro with an isolated peptide epitope.
With regard to a particular amino acid sequence, an “epitope” is a set of amino acid residues which is involved in recognition by a particular immunoglobulin, or in the context of T cells, those residues necessary for recognition by T cell receptor (TCR) proteins and/or Major Histocompatibility Complex (MHC) receptors. In an immune system setting, in vivo or in vitro, an epitope is the collective features of a molecule, such as primary, secondary and tertiary peptide structure, and charge, that together form a site recognized by an immunoglobulin, TCR or HLA molecule. Throughout this disclosure epitope and peptide are often used interchangeably. It is to be appreciated, however, that isolated or purified protein or peptide molecules larger than and comprising an epitope of the invention are still within the bounds of the invention.
“Human Leukocyte Antigen” or “HLA” is a human class I or class II MHC protein (see, e.g., Stites, et al., IMMUNOLOGY, 8TH ED., Lange Publishing, Los Altos, Calif. (1994).
An “HLA supertype or family”, as used herein, describes sets of HLA molecules grouped on the basis of shared peptide-binding specificities. HLA class I molecules that share somewhat similar binding affinity for peptides bearing certain amino acid motifs are grouped into HLA supertypes. The terms HLA superfamily, HLA supertype family, HLA family, and HLA xx-like molecules (where xx denotes a particular HLA type), are synonyms.
Throughout this disclosure, results are expressed in terms of “IC50's.” IC50 is the concentration of peptide in a binding assay at which 50% inhibition of binding of a reference peptide is observed. Given the conditions in which the assays are run (i.e., limiting HLA proteins and labeled peptide concentrations), these values approximate KD values. Assays for determining binding are described in detail, e.g., in PCT publications WO 94/20127 and WO 94/03205. It should be noted that IC50 values can change, often dramatically, if the assay conditions are varied, and depending on the particular reagents used (e.g., HLA preparation, etc.). For example, excessive concentrations of HLA molecules will increase the apparent measured IC50 of a given ligand.
Alternatively, binding is expressed relative to a reference peptide. Although as a particular assay becomes more, or less, sensitive, the IC50's of the peptides tested may change somewhat, the binding relative to the reference peptide will not significantly change. For example, in an assay run under conditions such that the IC50 of the reference peptide increases 10-fold, the IC50 values of the test peptides will also shift approximately 10-fold. Therefore, to avoid ambiguities, the assessment of whether a peptide is a good, intermediate, weak, or negative binder is generally based on its IC50, relative to the IC50 of a standard peptide.
Binding may also be determined using other assay systems including those using: live cells (e.g., Ceppellini et al., Nature 339:392, 1989; Christnick et al., Nature 352:67, 1991; Busch et al., Immunol. 2:443, 1990; Hill et al., J. Immunol. 147:189, 1991; del Guercio et al., J. Immunol. 154:685, 1995), cell free systems using detergent lysates (e.g., Cerundolo et al., J. Immunol. 21:2069, 1991), immobilized purified MHC (e.g., Hill et al., J. Immunol. 152, 2890, 1994; Marshall et al., J. Immunol. 152:4946, 1994), ELISA systems (e.g., Reay et al., EMBO J. 11:2829, 1992), surface plasmon resonance (e.g., Khilko et al., J. Biol. Chem. 268:15425, 1993); high flux soluble phase assays (Hammer et al., J. Exp. Med. 180:2353, 1994), and measurement of class I MHC stabilization or assembly (e.g., Ljunggren et al., Nature 346:476, 1990; Schumacher et al., Cell 62:563, 1990; Townsend et al., Cell 62:285, 1990; Parker et al., J. Immunol. 149:1896, 1992).
As used herein, “high affinity” with respect to HLA class I molecules is defined as binding with an IC50, or KD value, of 50 nM or less; “intermediate affinity” is binding with an IC50 or KD value of between about 50 and about 500 nM. “High affinity” with respect to binding to HLA class II molecules is defined as binding with an IC50 or KD value of 100 nM or less; “intermediate affinity” is binding with an IC50 or KD value of between about 100 and about 1000 nM.
The terms “identical” or percent “identity,” in the context of two or more peptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues that are the same, when compared and aligned for maximum correspondence over a comparison window, as measured using a sequence comparison algorithm or by manual alignment and visual inspection.
An “immunogenic peptide” or “peptide epitope” is a peptide that comprises an allele-specific motif or supermotif such that the peptide will bind an HLA molecule and induce a CTL and/or HTL response. Thus, immunogenic peptides of the invention are capable of binding to an appropriate HLA molecule and thereafter inducing a cytotoxic T cell response, or a helper T cell response, to the antigen from which the immunogenic peptide is derived.
The phrases “isolated” or “biologically pure” refer to material which is substantially or essentially free from components which normally accompany the material as it is found in its native state. Thus, isolated peptides in accordance with the invention preferably do not contain materials normally associated with the peptides in their in situ environment.
“Major Histocompatibility Complex” or “MHC” is a cluster of genes that plays a role in control of the cellular interactions responsible for physiologic immune responses. In humans, the MHC complex is also known as the HLA complex. For a detailed description of the MHC and HLA complexes, see, Paul, FUNDAMENTAL IMMUNOLOGY, 3RD ED., Raven Press, New York, 1993.
The term “motif” refers to the pattern of residues in a peptide of defined length, usually a peptide of from about 8 to about 13 amino acids for a class I HLA motif and from about 6 to about 25 amino acids for a class II HLA motif, which is recognized by a particular HLA molecule. Peptide motifs are typically different for each protein encoded by each human HLA allele and differ in the pattern of the primary and secondary anchor residues.
A “negative binding residue” or “deleterious residue” is an amino acid which, if present at certain positions (typically not primary anchor positions) in a peptide epitope, results in decreased binding affinity of the peptide for the peptide's corresponding HLA molecule.
The term “peptide” is used interchangeably with “oligopeptide” in the present specification to designate a series of residues, typically L-amino acids, connected one to the other, typically by peptide bonds between the alpha-amino and carboxyl groups of adjacent amino acids. The preferred CTL-inducing peptides of the invention are 13 residues or less in length and usually consist of between about 8 and about 11 residues, preferably 9 or 10 residues. The preferred HTL-inducing peptides are less than about 50 residues in length and usually consist of between about 6 and about 30 residues, more usually between about 12 and 25, and often between about 15 and 20 residues.
“Pharmaceutically acceptable” refers to a non-toxic, inert, and physiologically compatible composition.
A “primary anchor residue” is an amino acid at a specific position along a peptide sequence which is understood to provide a contact point between the immunogenic peptide and the HLA molecule. One to three, usually two, primary anchor residues within a peptide of defined length generally defines a “motif” for an immunogenic peptide. These residues are understood to fit in close contact with peptide binding grooves of an HLA molecule, with their side chains buried in specific pockets of the binding grooves themselves. In one embodiment, for example, the primary anchor residues are located at position 2 (from the amino terminal position) and at the carboxyl terminal position of a 9-residue peptide epitope in accordance with the invention. The primary anchor positions for each motif and supermotif are set forth in Table 1. For example, analog peptides can be created by altering the presence or absence of particular residues in these primary anchor positions. Such analogs are used to modulate the binding affinity of a peptide comprising a particular motif or supermotif.
“Promiscuous recognition” is where a distinct peptide is recognized by the same T cell clone in the context of various HLA molecules. Promiscuous recognition or binding is synonymous with cross-reactive binding.
A “protective immune response” or “therapeutic immune response” refers to a CTL and/or an HTL response to an antigen derived from an infectious agent or a tumor antigen, which prevents or at least partially arrests disease symptoms or progression. The immune response may also include an antibody response which has been facilitated by the stimulation of helper T cells.
The term “residue” refers to an amino acid or amino acid mimetic incorporated into an oligopeptide by an amide bond or amide bond mimetic.
A “secondary anchor residue” is an amino acid at a position other than a primary anchor position in a peptide which may influence peptide binding. A secondary anchor residue occurs at a significantly higher frequency amongst bound peptides than would be expected by random distribution of amino acids at one position. The secondary anchor residues are said to occur at “secondary anchor positions.” A secondary anchor residue can be identified as a residue which is present at a higher frequency among high or intermediate affinity binding peptides, or a residue otherwise associated with high or intermediate affinity binding. For example, analog peptides can be created by altering the presence or absence of particular residues in these secondary anchor positions. Such analogs are used to finely modulate the binding affinity of a peptide comprising a particular motif or supermotif.
A “subdominant epitope” is an epitope which evokes little or no response upon immunization with whole antigens which comprise the epitope, but for which a response can be obtained by immunization with an isolated peptide, and this response (unlike the case of cryptic epitopes) is detected when whole protein is used to recall the response in vitro or in vivo.
A “supermotif” is a peptide binding specificity shared by HLA molecules encoded by two or more HLA alleles. Preferably, a supermotif-bearing peptide is recognized with high or intermediate affinity (as defined herein) by two or more HLA antigens.
“Synthetic peptide” refers to a peptide that is not naturally occurring, but is man-made using such methods as chemical synthesis or recombinant DNA technology.
The nomenclature used to describe peptide compounds follows the conventional practice wherein the amino group is presented to the left (the N-terminus) and the carboxyl group to the right (the C-terminus) of each amino acid residue. When amino acid residue positions are referred to in a peptide epitope they are numbered in an amino to carboxyl direction with position one being the position closest to the amino terminal end of the epitope, or the peptide or protein of which it may be a part. In the formulae representing selected specific embodiments of the present invention, the amino- and carboxyl-terminal groups, although not specifically shown, are in the form they would assume at physiologic pH values, unless otherwise specified. In the amino acid structure formulae, each residue is generally represented by standard three letter or single letter designations. The L-form of an amino acid residue is represented by a capital single letter or a capital first letter of a three-letter symbol, and the D-form for those amino acids having D-forms is represented by a lower case single letter or a lower case three letter symbol. Glycine has no asymmetric carbon atom and is simply referred to as “Gly” or G. Symbols for the amino acids are shown below.












Single 
Three 



Letter Symbol
Letter Symbol
Amino Acids







A
Ala
Alanine


C
Cys
Cysteine


D
Asp
Aspartic Acid


E
Glu
Glutamic Acid


F
Phe
Phenylalanine


G
Gly
Glycine


H
His
Histidine


I
Ile
Isoleucine


K
Lys
Lysine


L
Leu
Leucine


M
Met
Methionine


N
Asn
Asparagine


P
Pro
Proline


Q
Gln
Glutamine


R
Arg
Arginine


S
Ser
Serine


T
Thr
Threonine


V
Val
Valine


W
Trp
Tryptophan


Y
Tyr
Tyrosine









IV.B. STIMULATION OF CTL AND HTL RESPONSES
The mechanism by which T cells recognize antigens has been delineated during the past ten years. Based on our understanding of the immune system we have developed efficacious peptide epitope vaccine compositions that can induce a therapeutic or prophylactic immune response to PF in a broad population. For an understanding of the value and efficacy of the claimed compositions, a brief review of immunology-related technology is provided.
A complex of an HLA molecule and a peptidic antigen acts as the ligand recognized by HLA-restricted T cells (Buus, S. et al., Cell 47:1071, 1986; Babbitt, B. P. et al., Nature 317:359, 1985; Townsend, A. and Bodmer, H., Annu. Rev. Immunol. 7:601, 1989; Germain, R. N., Annu. Rev. Immunol. 11:403, 1993). Through the study of single amino acid substituted antigen analogs and the sequencing of endogenously bound, naturally processed peptides, critical residues that correspond to motifs required for specific binding to HLA antigen molecules have been identified and are described herein and are set forth in Tables I, II, and III (see also, e.g., Southwood, et al., J. Immunol. 160:3363, 1998; Rammensee, et al., Immunogenetics 41:178, 1995; Rammensee et al., SYFPEITHI, access via web at: http://134.2.96.221/scripts.hlaserver.dll/home.htm; Sette, A. and Sidney, J. Curr. Opin. Immunol. 10:478, 1998; Engelhard, V. H., Curr. Opin. Immunol. 6:13, 1994; Sette, A. and Grey, H. M., Curr. Opin. Immunol. 4:79, 1992; Sinigaglia, F. and Hammer, J. Curr. Biol. 6:52, 1994; Ruppert et al., Cell 74:929-937, 1993; Kondo et al., J. Immunol. 155:4307-4312, 1995; Sidney et al., J. Immunol. 157:3480-3490, 1996; Sidney et al., Human Immunol. 45:79-93, 1996; Sette, A. and Sidney, J. Immunogenetics, in press, 1999).
Furthermore, x-ray crystallographic analysis of HLA-peptide complexes has revealed pockets within the peptide binding cleft of HLA molecules which accommodate, in an allele-specific mode, residues borne by peptide ligands; these residues in turn determine the HLA binding capacity of the peptides in which they are present. (See, e.g., Madden, D. R. Annu. Rev. Immunol. 13:587, 1995; Smith, et al., Immunity 4:203, 1996; Fremont et al., Immunity 8:305, 1998; Stern et al., Structure 2:245, 1994; Jones, E. Y. Curr. Opin. Immunol. 9:75, 1997; Brown, J. H. et al., Nature 364:33, 1993; Guo, H. C. et al., Proc. Natl. Acad. Sci. USA 90:8053, 1993; Guo, H. C. et al., Nature 360:364, 1992; Silver, M. L. et al., Nature 360:367, 1992; Matsumura, M. et al., Science 257:927, 1992; Madden et al., Cell 70:1035, 1992; Fremont, D. H. et al., Science 257:919, 1992; Saper, M. A., Bjorkman, P. J. and Wiley, D. C., J. Mol. Biol. 219:277, 1991.)
Accordingly, the definition of class I and class II allele-specific HLA binding motifs, or class I or class II supermotifs allows identification of regions within a protein that have the potential of binding particular HLA antigen(s).
The present inventors have found that the correlation of binding affinity with immunogenicity, which is disclosed herein, is an important factor to be considered when evaluating candidate peptides. Thus, by a combination of motif searches and HLA-peptide binding assays, candidates for epitope-based vaccines have been identified. After determining their binding affinity, additional confirmatory work can be performed to select, amongst these vaccine candidates, epitopes with preferred characteristics in terms of population coverage, antigenicity, and immunogenicity.
Various strategies can be utilized to evaluate immunogenicity, including:
1) Evaluation of primary T cell cultures from normal individuals (see, e.g., Wentworth, P. A. et al., Mol. Immunol. 32:603, 1995; Celis, E. et al., Proc. Natl. Acad. Sci. USA 91:2105, 1994; Tsai, V. et al., J. Immunol. 158:1796, 1997; Kawashima, I. et al., Human Immunol. 59:1, 1998); This procedure involves the stimulation of peripheral blood lymphocytes (PBL) from normal subjects with a test peptide in the presence of antigen presenting cells in vitro over a period of several weeks. T cells specific for the peptide become activated during this time and are detected using, e.g., a 51Cr-release assay involving peptide sensitized target cells.
2) Immunization of HLA transgenic mice (see, e.g., Wentworth, P. A. et al., J. Immunol. 26:97, 1996; Wentworth, P. A. et al., Int. Immunol. 8:651, 1996; Alexander, J. et al., J. Immunol. 159:4753, 1997); In this method, peptides in incomplete Freund's adjuvant are administered subcutaneously to HLA transgenic mice. Several weeks following immunization, splenocytes are removed and cultured in vitro in the presence of test peptide for approximately one week. Peptide-specific T cells are detected using, e.g., a 51Cr-release assay involving peptide sensitized target cells and target cells expressing endogenously generated antigen.
3) Demonstration of recall T cell responses from immune individuals who have effectively been vaccinated, recovered from infection, and/or from chronically infected patients (see, e.g., Rehermann, B. et al., J. Exp. Med. 181:1047, 1995; Doolan, D. L. et al., Immunity 7:97, 1997; Bertoni, R. et al., J. Clin. Invest. 100:503, 1997; Threlkeld, S. C. et al., J. Immunol. 159:1648, 1997; Diepolder, H. M. et al., J. Virol. 71:6011, 1997). In applying this strategy, recall responses are detected by culturing PBL from subjects that have been naturally exposed to the antigen, for instance through infection, and thus have generated an immune response “naturally”, or from patients who were vaccinated against the infection. PBL from subjects are cultured in vitro for 1-2 weeks in the presence of test peptide plus antigen presenting cells (APC) to allow activation of “memory” T cells, as compared to “naive” T cells. At the end of the culture period, T cell activity is detected using assays for T cell activity including 51Cr release involving peptide-sensitized targets, T cell proliferation, or lymphokine release.
The following describes the peptide epitopes and corresponding nucleic acids of the invention.
IV.C. BINDING AFFINITY OF PEPTIDE EPITOPES FOR HLA MOLECULES
As indicated herein, the large degree of HLA polymorphism is an important factor to be taken into account with the epitope-based approach to vaccine development. To address this factor, epitope selection encompassing identification of peptides capable of binding at high or intermediate affinity to multiple HLA molecules is preferably utilized, most preferably these epitopes bind at high or intermediate affinity to two or more allele-specific HLA molecules.
CTL-inducing peptides of interest for vaccine compositions preferably include those that have an IC50 or binding affinity value for class I HLA molecules of 500 nM or better (i.e., the value is ≦500 nM). HTL-inducing peptides preferably include those that have an IC50 or binding affinity value for class II HLA molecules of 1000 nM or better, (i.e., the value is ≦1,000 nM). For example, peptide binding is assessed by testing the capacity of a candidate peptide to bind to a purified HLA molecule in vitro. Peptides exhibiting high or intermediate affinity are then considered for further analysis. Selected peptides are tested on other members of the supertype family. In preferred embodiments, peptides that exhibit cross-reactive binding are then used in cellular screening analyses or vaccines.
As disclosed herein, higher HLA binding affinity is correlated with greater immunogenicity. Greater immunogenicity can be manifested in several different ways. Immunogenicity corresponds to whether an immune response is elicited at all, and to the vigor of any particular response, as well as to the extent of a population in which a response is elicited. For example, a peptide might elicit an immune response in a diverse array of the population, yet in no instance produce a vigorous response. In accordance with these principles, close to 90% of high binding peptides have been found to be immunogenic, as contrasted with about 50% of the peptides which bind with intermediate affinity. Moreover, higher binding affinity peptides leads to more vigorous immunogenic responses. As a result, less peptide is required to elicit a similar biological effect if a high affinity binding peptide is used. Thus, in preferred embodiments of the invention, high affinity binding epitopes are particularly useful.
The relationship between binding affinity for HLA class I molecules and immunogenicity of discrete peptide epitopes on bound antigens has been determined for the first time in the art by the present inventors. The correlation between binding affinity and immunogenicity was analyzed in two different experimental approaches (see, e.g., Sette, et al., J. Immunol. 153:5586-5592, 1994). In the first approach, the immunogenicity of potential epitopes ranging in HLA binding affinity over a 10,000-fold range was analyzed in HLA-A*0201 transgenic mice. In the second approach, the antigenicity of approximately 100 different hepatitis B virus (HBV)-derived potential epitopes, all carrying A*0201 binding motifs, was assessed by using PBL from acute hepatitis patients. Pursuant to these approaches, it was determined that an affinity threshold value of approximately 500 nM (preferably 50 nM or less) determines the capacity of a peptide epitope to elicit a CTL response. These data are true for class I binding affinity measurements for naturally processed peptides and for synthesized T cell epitopes. These data also indicate the important role of determinant selection in the shaping of T cell responses (see, e.g., Schaeffer et al. Proc. Natl. Acad. Sci. USA 86:4649-4653, 1989).
An affinity threshold associated with immunogenicity in the context of HLA class II DR molecules has also been delineated (see, e.g., Southwood et al. J. Immunology 160:3363-3373, 1998, and U.S. Ser. No. 09/009,953 filed Jan. 21, 1998, now U.S. Pat. No. 6,413,517). In order to define a biologically significant threshold of DR binding affinity, a database of the binding affinities of 32 DR-restricted epitopes for their restricting element (i.e., the HLA molecule that binds the motif) was compiled. In approximately half of the cases (15 of 32 epitopes), DR restriction was associated with high binding affinities, i.e. binding affinity values of 100 nM or less. In the other half of the cases (16 of 32), DR restriction was associated with intermediate affinity (binding affinity values in the 100-1000 nM range). In only one of 32 cases was DR restriction associated with an IC50 of 1000 nM or greater. Thus, 1000 nM can be defined as an affinity threshold associated with immunogenicity in the context of DR molecules.
The binding affinity of peptides for HLA molecules can be determined as described in Example 1, below.
IV.D. PEPTIDE EPITOPE BINDING MOTIFS AND SUPERMOTIFS
Through the study of single amino acid substituted antigen analogs and the sequencing of endogenously bound, naturally processed peptides, critical residues required for allele-specific binding to HLA molecules have been identified. The presence of these residues correlates with binding affinity for HLA molecules. The identification of motifs and/or supermotifs that correlate with high and intermediate affinity binding is an important issue with respect to the identification of immunogenic peptide epitopes for the inclusion in a vaccine. Kast et al. (J. Immunol. 152:3904-3912, 1994) have shown that motif-bearing peptides account for 90% of the epitopes that bind to allele-specific HLA class I molecules. In this study all possible peptides of 9 amino acids in length and overlapping by eight amino acids (240 peptides), which cover the entire sequence of the E6 and E7 proteins of human papillomavirus type 16, were evaluated for binding to five allele-specific HLA molecules that are expressed at high frequency among different ethnic groups. This unbiased set of peptides allowed an evaluation of the predictive value of HLA class I motifs. From the set of 240 peptides, 22 peptides were identified that bound to an allele-specific HLA molecule with high or intermediate affinity. Of these 22 peptides, 20 (i.e. 91%) were motif-bearing. Thus, this study demonstrates the value of motifs for the identification of peptide epitopes for inclusion in a vaccine: application of motif-based identification techniques will identify about 90% of the potential epitopes in a target antigen protein sequence.
Such peptide epitopes are identified in the Tables described below.
Peptides of the present invention may also comprise epitopes that bind to MHC class II DR molecules. A greater degree of heterogeneity in both size and binding frame position of the motif, relative to the N and C termini of the peptide, exists for class II peptide ligands. This increased heterogeneity of HLA class II peptide ligands is due to the structure of the binding groove of the HLA class II molecule which, unlike its class I counterpart, is open at both ends. Crystallographic analysis of HLA class II DRB*0101-peptide complexes showed that the major energy of binding is contributed by peptide residues complexed with complementary pockets on the DRB*0101 molecules. An important anchor residue engages the deepest hydrophobic pocket (see, e.g., Madden, D. R. Ann. Rev. Immunol. 13:587, 1995) and is referred to as position 1 (P1). P1 may represent the N-terminal residue of a class II binding peptide epitope, but more typically is flanked towards the N-terminus by one or more residues. Other studies have also pointed to an important role for the peptide residue in the 6th position towards the C-terminus, relative to P1, for binding to various DR molecules.
In the past few years evidence has accumulated to demonstrate that a large fraction of HLA class I and class II molecules can be classified into a relatively few supertypes, each characterized by largely overlapping peptide binding repertoires, and consensus structures of the main peptide binding pockets. Thus, peptides of the present invention are identified by any one of several HLA-specific amino acid motifs (see, e.g., Tables I-III), or if the presence of the motif corresponds to the ability to bind several allele-specific HLA antigens, a supermotif. The HLA molecules that bind to peptides that possess a particular amino acid supermotif are collectively referred to as an HLA “supertype.”
The peptide motifs and supermotifs described below, and summarized in Tables I-III, provide guidance for the identification and use of peptide epitopes in accordance with the invention.
Examples of peptide epitopes bearing a respective supermotif or motif are included in Tables as designated in the description of each motif or supermotif below. The Tables include a binding affinity ratio listing for some of the peptide epitopes. The ratio may be converted to IC50 by using the following formula: IC50 of the standard peptide/ratio=IC50 of the test peptide (i.e., the peptide epitope). The IC50 values of standard peptides used to determine binding affinities for Class I peptides are shown in Table IV. The IC50 values of standard peptides used to determine binding affinities for Class II peptides are shown in Table V. The peptides used as standards for the binding assays described herein are examples of standards; alternative standard peptides can also be used when performing binding analyses.
To obtain the peptide epitope sequences listed in each Table, protein sequence data for four P. falciparum antigens were evaluated for the presence of the designated supermotif or motif. These antigens are: EXP-1, LSA-1, SSP2, and CSP. Nineteen sequences were available for CSP, 10 sequences were available for SSP, and one sequence each was available for EXP-1 and LSA-1. Peptide epitopes were additionally evaluated on the basis of their conservancy among the protein sequences for the PF antigens for which multiple sequences were available. A criterion for conservancy requires that the entire sequence of an HLA class I binding peptide be totally (i.e., 100%) conserved in 79% of the sequences available for a specific protein. Similarly, a criterion for conservancy requires that the entire 9-mer core region of an HLA class II binding peptide be totally conserved in 79% of the sequences available for a specific protein. The percent conservancy of the selected peptide epitopes is indicated on the Tables. The frequency, i.e. the number of sequences of the PF protein antigen in which the totally conserved peptide sequence was identified, is also shown. The “pos” (position) column in the Tables designates the amino acid position in the PF protein that corresponds to the first amino acid residue of the epitope. The “number of amino acids” indicates the number of residues in the epitope sequence.
HLA Class I Motifs Indicative of CTL Inducing Peptide Epitopes:
The primary anchor residues of the HLA class I peptide epitope supermotifs and motifs delineated below are summarized in Table I. The HLA class I motifs set out in Table I(a) are those most particularly relevant to the invention claimed here. Primary and secondary anchor positions are summarized in Table II. Allele-specific HLA molecules that comprise HLA class I supertype families are listed in Table VI. In some cases, peptide epitopes may be listed in both a motif and a supermotif Table. The relationship of a particular motif and respective supermotif is indicated in the description of the individual motifs.
IV.D.1. HLA-A1 Supermotif
The HLA-A1 supermotif is characterized by the presence in peptide ligands of a small (T or S) or hydrophobic (L, I, V, or M) primary anchor residue in position 2, and an aromatic (Y, F, or W) primary anchor residue at the C-terminal position of the epitope (see, e.g., Sette and Sidney, Immunogenetics, in press, 1999). The corresponding family of HLA molecules that bind to the A1 supermotif (i.e., the HLA-A1 supertype) is comprised of at least A*0101, A*2601, A*2602, A*2501, and A*3201 (see, e.g., DiBrino, M. et al., J. Immunol. 151:5930, 1993; DiBrino, M. et al., J. Immunol. 152:620, 1994; Kondo, A. et al., Immunogenetics 45:249, 1997). Other allele-specific HLA molecules predicted to be members of the A1 supertype are shown in Table VI. Peptides binding to each of the individual HLA proteins can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the supermotif.
Representative peptide epitopes that comprise the A1 supermotif are set forth on the attached Table VII.
IV.D.2. HLA-A2 Supermotif
Primary anchor specificities for allele-specific HLA-A2.1 molecules (see, e.g., Falk et al., Nature 351:290-296, 1991; Hunt et al., Science 255:1261-1263, 1992; Parker et al., J. Immunol. 149:3580-3587, 1992; Ruppert et al., Cell 74:929-937, 1993) and cross-reactive binding among HLA-A2 and -A28 molecules have been described. (See, e.g., Fruci et al., Human Immunol. 38:187-192, 1993; Tanigaki et al., Human Immunol. 39:155-162, 1994; Del Guercio et al., J. Immunol. 154:685-693, 1995; Kast et al., J. Immunol. 152:3904-3912, 1994 for reviews of relevant data.) These primary anchor residues define the HLA-A2 supermotif; which presence in peptide ligands corresponds to the ability to bind several different HLA-A2 and -A28 molecules. The HLA-A2 supermotif comprises peptide ligands with L, I, V, M, A, T, or Q as a primary anchor residue at position 2 and L, I, V, M, A, or T as a primary anchor residue at the C-terminal position of the epitope.
The corresponding family of HLA molecules (i.e., the HLA-A2 supertype that binds these peptides) is comprised of at least: A*0201, A*0202, A*0203, A*0204, A*0205, A*0206, A*0207, A*0209, A*0214, A*6802, and A*6901. Other allele-specific HLA molecules predicted to be members of the A2 supertype are shown in Table VI. As explained in detail below, binding to each of the individual allele-specific HLA molecules can be modulated by substitutions at the primary anchor and/or secondary anchor positions, preferably choosing respective residues specified for the supermotif.
Representative peptide epitopes that comprise an A2 supermotif are set forth on the attached Table VIII. The motifs comprising the primary anchor residues V, A, T, or Q at position 2 and L, I, V, A, or T at the C-terminal position are those most particularly relevant to the invention claimed herein.
IV.D.3. HLA-A3 Supermotif
The HLA-A3 supermotif is characterized by the presence in peptide ligands of A, L, I, V, M, S, or, T as a primary anchor at position 2, and a positively charged residue, R or K, at the C-terminal position of the epitope, e.g., in position 9 of 9-mers (see, e.g., Sidney et al., Hum. Immunol. 45:79, 1996). Exemplary members of the corresponding family of HLA molecules (the HLA-A3 supertype) that bind the A3 supermotif include at least A*0301, A*1101, A*3101, A*3301, and A*6801. Other allele-specific HLA molecules predicted to be members of the A3 supertype are shown in Table VI. As explained in detail below, peptide binding to each of the individual allele-specific HLA proteins can be modulated by substitutions of amino acids at the primary and/or secondary anchor positions of the peptide, preferably choosing respective residues specified for the supermotif.
Representative peptide epitopes that comprise the A3 supermotif are set forth on the attached Table IX.
IV.D.4. HLA-A24 Supermotif
The HLA-A24 supermotif is characterized by the presence in peptide ligands of an aromatic (F, W, or Y) or hydrophobic aliphatic (L, I, V, M, or T) residue as a primary anchor in position 2, and Y, F, W, L, I, or M as primary anchor at the C-terminal position of the epitope (see, e.g., Sette and Sidney, Immunogenetics, in press, 1999). The corresponding family of HLA molecules that bind to the A24 supermotif (i.e., the A24 supertype) includes at least A*2402, A*3001, and A*2301. Other allele-specific HLA molecules predicted to be members of the A24 supertype are shown in Table VI. Peptide binding to each of the allele-specific HLA molecules can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the supermotif.
Representative peptide epitopes that comprise the A24 supermotif are set forth on the attached Table X.
IV.D.5. HLA-B7 Supermotif
The HLA-B7 supermotif is characterized by peptides bearing proline in position 2 as a primary anchor, and a hydrophobic or aliphatic amino acid (L, I, V, M, A, F, W, or Y) as the primary anchor at the C-terminal position of the epitope. The corresponding family of HLA molecules that bind the B7 supermotif (i.e., the HLA-B7 supertype) is comprised of at least twenty six HLA-B proteins including: B*0702, B*0703, B*0704, B*0705, B*1508, B*3501, B*3502, B*3503, B*3504, B*3505, B*3506, B*3507, B*3508, B*5101, B*5102, B*5103, B*5104, B*5105, B*5301, B*5401, B*5501, B*5502, B*5601, B*5602, B*6701, and B*7801 (see, e.g., Sidney, et al., J. Immunol. 154:247, 1995; Barber, et al., Curr. Biol. 5:179, 1995; Hill, et al., Nature 360:434, 1992; Rammensee, et al., Immunogenetics 41:178, 1995 for reviews of relevant data). Other allele-specific HLA molecules predicted to be members of the B7 supertype are shown in Table VI. As explained in detail below, peptide binding to each of the individual allele-specific HLA proteins can be modulated by substitutions at the primary and/or secondary anchor positions of the peptide, preferably choosing respective residues specified for the supermotif.
Representative peptide epitopes that comprise the B7 supermotif are set forth on the attached Table XI.
IV.D.6. HLA-B27 Supermotif
The HLA-B27 supermotif is characterized by the presence in peptide ligands of a positively charged (R, H, or K) residue as a primary anchor at position 2, and a hydrophobic (F, Y, L, W, M, I, A, or V) residue as a primary anchor at the C-terminal position of the epitope (see, e.g., Sidney and Sette, Immunogenetics, in press, 1999). Exemplary members of the corresponding family of HLA molecules that bind to the B27 supermotif (i.e., the B27 supertype) include at least B*1401, B*1402, B*1509, B*2702, B*2703, B*2704, B*2705, B*2706, B*3801, B*3901, B*3902, and B*7301. Other allele-specific HLA molecules predicted to be members of the B27 supertype are shown in Table VI. Peptide binding to each of the allele-specific HLA molecules can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the supermotif.
Representative peptide epitopes that comprise the B27 supermotif are set forth on the attached Table XII.
IV.D.7. HLA-B44 Supermotif
The HLA-B44 supermotif is characterized by the presence in peptide ligands of negatively charged (D or E) residues as a primary anchor in position 2, and hydrophobic residues (F, W, Y, L, I, M, V, or A) as a primary anchor at the C-terminal position of the epitope (see, e.g., Sidney et al., Immunol. Today 17:261, 1996). Exemplary members of the corresponding family of HLA molecules that bind to the B44 supermotif (i.e., the B44 supertype) include at least: B*1801, B*1802, B*3701, B*4001, B*4002, B*4006, B*4402, B*4403, and B*4006. Peptide binding to each of the allele-specific HLA molecules can be modulated by substitutions at primary and/or secondary anchor positions; preferably choosing respective residues specified for the supermotif.
IV.D.8. HLA-B58 Supermotif
The HLA-B58 supermotif is characterized by the presence in peptide ligands of a small aliphatic residue (A, S, or T) as a primary anchor residue at position 2, and an aromatic or hydrophobic residue (F, W, Y, L, I, V, M, or A) as a primary anchor residue at the C-terminal position of the epitope (see, e.g., Sidney and Sette, Immunogenetics, in press, 1999 for reviews of relevant data). Exemplary members of the corresponding family of HLA molecules that bind to the B58 supermotif (i.e., the B58 supertype) include at least: B*1516, B*1517, B*5701, B*5702, and B*5801. Other allele-specific HLA molecules predicted to be members of the B58 supertype are shown in Table VI. Peptide binding to each of the allele-specific HLA molecules can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the supermotif.
Representative peptide epitopes that comprise the B58 supermotif are set forth on the attached Table XIII.
IV.D.9. HLA-B62 Supermotif
The HLA-B62 supermotif is characterized by the presence in peptide ligands of the polar aliphatic residue Q or a hydrophobic aliphatic residue (L, V, M, I, or P) as a primary anchor in position 2, and a hydrophobic residue (F, W, Y, M, I, V, L, or A) as a primary anchor at the C-terminal position of the epitope (see, e.g., Sidney and Sette, Immunogenetics, in press, 1999). Exemplary members of the corresponding family of HLA molecules that bind to the B62 supermotif (i.e., the B62 supertype) include at least: B*1501, B*1502, B*1513, and B5201. Other allele-specific HLA molecules predicted to be members of the B62 supertype are shown in Table VI. Peptide binding to each of the allele-specific HLA molecules can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the supermotif.
Representative peptide epitopes that comprise the B62 supermotif are set forth on the attached Table XIV.
IV.D.10. HLA-A1 Motif
The HLA-A1 motif is characterized by the presence in peptide ligands of T, S, or M as a primary anchor residue at position 2 and the presence of Y as a primary anchor residue at the C-terminal position of the epitope. An alternative allele-specific A1 motif is characterized by a primary anchor residue at position 3 rather than position 2. This motif is characterized by the presence of D, E, A, or S as a primary anchor residue in position 3, and a Y as a primary anchor residue at the C-terminal position of the epitope (see, e.g., DiBrino et al., J. Immunol., 152:620, 1994; Kondo et al., Immunogenetics 45:249, 1997; and Kubo et al., J. Immunol. 152:3913, 1994 for reviews of relevant data). Peptide binding to HLA A1 can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the motif.
Representative peptide epitopes that comprise either A1 motif are set forth on the attached Table XV. Those epitopes comprising T, S, or M at position 2 and Y at the C-terminal position are also included in the listing of HLA-A1 supermotif-bearing peptide epitopes listed in Table VII, as these residues are a subset of the A1 supermotif primary anchors.
IV.D.11. HLA-A*0201 Motif
An HLA-A2*0201 motif was determined to be characterized by the presence in peptide ligands of L or M as a primary anchor residue in position 2, and L or V as a primary anchor residue at the C-terminal position of a 9-residue peptide (see, e.g., Falk et al., Nature 351:290-296, 1991) and was further found to comprise an I at position 2 and I or A at the C-terminal position of a nine amino acid peptide (see, e.g., Hunt et al., Science 255:1261-1263, Mar. 6, 1992; Parker et al., J. Immunol. 149:3580-3587, 1992). The A*0201 allele-specific motif has also been defined by the present inventors to additionally comprise V, A, T, or Q as a primary anchor residue at position 2, and M or T as a primary anchor residue at the C-terminal position of the epitope (see, e.g., Kast et al., J. Immunol. 152:3904-3912, 1994). Thus, the HLA-A*0201 motif comprises peptide ligands with L, I, V, M, A, T, or Q as primary anchor residues at position 2 and L, I, V, M, A, or T as a primary anchor residue at the C-terminal position of the epitope. The preferred and tolerated residues that characterize the primary anchor positions of the HLA-A*0201 motif are identical to the residues describing the A2 supermotif. (For reviews of relevant data, see, e.g., Del Guercio et al., J. Immunol. 154:685-693, 1995; Ruppert et al., Cell 74:929-937, 1993; Sidney et al., Immunol. Today 17:261-266, 1996; Sette and Sidney, Curr. Opin. in Immunol. 10:478-482, 1998). Secondary anchor residues that characterize the A*0201 motif have additionally been defined (see, e.g., Ruppert et al., Cell 74:929-937, 1993). These are shown in Table II. Peptide binding to HLA-A*0201 molecules can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the motif.
Representative peptide epitopes that comprise an A*0201 motif are set forth on the attached Table VIII. The A*0201 motifs comprising the primary anchor residues V, A, T, or Q at position 2 and L, I, V, A, or T at the C-terminal position are those most particularly relevant to the invention claimed herein
IV.D.12. HLA-A3 Motif
The HLA-A3 motif is characterized by the presence in peptide ligands of L, M, V, I, S, A, T, F, C, G, or D as a primary anchor residue at position 2, and the presence of K, Y, R, H, F, or A as a primary anchor residue at the C-terminal position of the epitope (see, e.g., DiBrino et al., Proc. Natl. Acad. Sci USA 90:1508, 1993; and Kubo et al., J. Immunol. 152:3913-3924, 1994). Peptide binding to HLA-A3 can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the motif.
Representative peptide epitopes that comprise the A3 motif are set forth on the attached Table XVI. Those peptide epitopes that also comprise the A3 supermotif are also listed in Table IX. The A3 supermotif primary anchor residues comprise a subset of the A3- and A11-allele specific motif primary anchor residues.
IV.D.13. HLA-A11 Motif
The HLA-A11 motif is characterized by the presence in peptide ligands of V, T, M, L, I, S, A, G, N, C, D, or F as a primary anchor residue in position 2, and K, R, Y, or H as a primary anchor residue at the C-terminal position of the epitope (see, e.g., Zhang et al., Proc. Natl. Acad. Sci USA 90:2217-2221, 1993; and Kubo et al., J. Immunol. 152:3913-3924, 1994). Peptide binding to HLA-A11 can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the motif.
Representative peptide epitopes that comprise the A11 motif are set forth on the attached Table XVII; peptide epitopes comprising the A3 allele-specific motif are also present in this Table because of the extensive overlap between the A3 and A11 motif primary anchor specificities. Further, those peptide epitopes that comprise the A3 supermotif are also listed in Table IX.
IV.D.14. HLA-A24 Motif
The HLA-A24 motif is characterized by the presence in peptide ligands of Y, F, W, or M as a primary anchor residue in position 2, and F, L, I, or W as a primary anchor residue at the C-terminal position of the epitope (see, e.g., Kondo et al., J. Immunol. 155:4307-4312, 1995; and Kubo et al., J. Immunol. 152:3913-3924, 1994). Peptide binding to HLA-A24 molecules can be modulated by substitutions at primary and/or secondary anchor positions; preferably choosing respective residues specified for the motif.
Representative peptide epitopes that comprise the A24 motif are set forth on the attached Table XVIII. These epitopes are also listed in Table X, which sets forth HLA-A24-supermotif-bearing peptide epitopes, as the primary anchor residues characterizing the A24 allele-specific motif comprise a subset of the A24 supermotif primary anchor residues.
Motifs Indicative of Class II HTL Inducing Peptide Epitopes
The primary and secondary anchor residues of the HLA class II peptide epitope supermotifs and motifs delineated below are summarized in Table III.
IV.D.15. HLA DR-1-4-7 Supermotif
Motifs have also been identified for peptides that bind to three common HLA class II allele-specific HLA molecules: HLA DRB1*0401, DRB1*0101, and DRB1*0701 (see, e.g., the review by Southwood et al. J. Immunology 160:3363-3373, 1998). Collectively, the common residues from these motifs delineate the HLA DR-1-4-7 supermotif. Peptides that bind to these DR molecules carry a supermotif characterized by a large aromatic or hydrophobic residue (Y, F, W, L, I, V, or M) as a primary anchor residue in position 1, and a small, non-charged residue (S, T, C, A, P, V, I, L, or M) as a primary anchor residue in position 6 of a 9-mer core region. Allele-specific secondary effects and secondary anchors for each of these HLA types have also been identified (Southwood et al., supra). These are set forth in Table III. Peptide binding to HLA-DRB1*0401, DRB1*0101, and/or DRB1*0701 can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the supermotif.
Conserved 9-mer core regions (i.e., sequences that are 100% conserved in at least 79% of the PF antigen protein sequences used for the analysis), comprising the DR-1-4-7 supermotif, wherein position 1 of the supermotif is at position 1 of the nine-residue core, are set forth in Table XIXa. Respective exemplary peptide epitopes of 15 amino acid residues in length, each of which comprise a conserved nine residue core, are also shown in section “a” of the Table. Cross-reactive binding data for exemplary 15-residue supermotif-bearing peptides are shown in Table XIXb.
IV.D.16. HLA DR3 Motifs
Two alternative motifs (i.e., submotifs) characterize peptide epitopes that bind to HLA-DR3 molecules (see, e.g., Geluk et al., J. Immunol. 152:5742, 1994). In the first motif (submotif DR3A) a large, hydrophobic residue (L, I, V, M, F, or Y) is present in anchor position 1 of a 9-mer core, and D is present as an anchor at position 4, towards the carboxyl terminus of the epitope. As in other class II motifs, core position 1 may or may not occupy the peptide N-terminal position.
The alternative DR3 submotif provides for lack of the large, hydrophobic residue at anchor position 1, and/or lack of the negatively charged or amide-like anchor residue at position 4, by the presence of a positive charge at position 6 towards the carboxyl terminus of the epitope. Thus, for the alternative allele-specific DR3 motif (submotif DR3B): L, I, V, M, F, Y, A, or Y is present at anchor position 1; D, N, Q, E, S, or T is present at anchor position 4; and K, R, or H is present at anchor position 6. Peptide binding to HLA-DR3 can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the motif.
Conserved 9-mer core regions (i.e., those sequences that are 100% conserved in at least 79% of the PF antigen protein sequences used for the analysis) corresponding to a nine residue sequence comprising the DR3A submotif (wherein position 1 of the motif is at position 1 of the nine residue core) are set forth in Table XXa. Respective exemplary peptide epitopes of 15 amino acid residues in length, each of which comprise a conserved nine residue core, are also shown in Table XXa. Table XXb shows binding data of exemplary DR3 submotif A-bearing peptides.
Conserved 9-mer core regions (i.e., those that are 100% conserved in at least 79% conserved in the PF antigen protein sequences used for the analysis) comprising the DR3B submotif and respective exemplary 15-mer peptides comprising the DR3 submotif-B epitope are set forth in Table XXc. Table XXd shows binding data of exemplary DR3 submotif B-bearing peptides.
Each of the HLA class I or class II peptide epitopes set out in the Tables herein are deemed singly to be an inventive aspect of this application. Further, it is also an inventive aspect of this application that each peptide epitope may be used in combination with any other peptide epitope.
IV.E. ENHANCING POPULATION COVERAGE OF THE VACCINE
Vaccines that have broad population coverage are preferred because they are more commercially viable and generally applicable to the most people. Broad population coverage can be obtained using the peptides of the invention (and nucleic acid compositions that encode such peptides) through selecting peptide epitopes that bind to HLA alleles which, when considered in total, are present in most of the population. Table XXI lists the overall frequencies of the HLA class I supertypes in various ethnicities (Table XXIa) and the combined population coverage achieved by the A2-, A3-, and B7-supertypes (Table XXIb). The A2-, A3-, and B7 supertypes are each present on the average of over 40% in each of these five major ethnic groups. Coverage in excess of 80% is achieved with a combination of these supermotifs. These results suggest that effective and non-ethnically biased population coverage is achieved upon use of a limited number of cross-reactive peptides. Although the population coverage reached with these three main peptide specificities is high, coverage can be expanded to reach 95% population coverage and above, and more easily achieve truly multispecific responses upon use of additional supermotif or allele-specific motif bearing peptides.
The B44-, A1-, and A24-supertypes are present, on average, in a range from 25% to 40% in these major ethnic populations (Table XXIa). While less prevalent overall, the B27-, B58-, and B62 supertypes are each present with a frequency >25% in at least one major ethnic group (Table XXIa). Table XXIb summarizes the estimated prevalence of combinations of HLA supertypes that have been identified in five major ethnic groups. The incremental coverage obtained by the inclusion of A1-, A24-, and B44-supertypes with the A2, A3, and B7 coverage and coverage obtained with all of the supertypes described herein, is shown.
The data presented herein, together with the previous definition of the A2-, A3-, and B7-supertypes, indicates that all antigens, with the possible exception of A29, B8, and B46, can be classified into a total of nine HLA supertypes. By including epitopes from the six most frequent supertypes, an average population coverage of 99% is obtained for five major ethnic groups.
IV.F. IMMUNE RESPONSE-STIMULATING PEPTIDE ANALOGS
In general, CTL and HTL responses are not directed against all possible epitopes. Rather, they are restricted to a few “immunodominant” determinants (Zinkernagel, et al., Adv. Immunol. 27:5159, 1979; Bennink, et al., J. Exp. Med. 168:19351939, 1988; Rawle, et al., J. Immunol. 146:3977-3984, 1991). It has been recognized that immunodominance (Benacerraf, et al., Science 175:273-279, 1972) could be explained by either the ability of a given epitope to selectively bind a particular HLA protein (determinant selection theory) (Vitiello, et al., J. Immunol. 131:1635, 1983); Rosenthal, et al., Nature 267:156-158, 1977), or to be selectively recognized by the existing TCR (T cell receptor) specificities (repertoire theory) (Klein, J., IMMUNOLOGY, THE SCIENCE OF SELFNONSELF DISCRIMINATION, John Wiley & Sons, New York, pp. 270-310, 1982). It has been demonstrated that additional factors, mostly linked to processing events, can also play a key role in dictating, beyond strict immunogenicity, which of the many potential determinants will be presented as immunodominant (Sercarz, et al., Annu. Rev. Immunol. 
11:729-766, 1993).
The concept of dominance and subdominance is relevant to immunotherapy of both infectious diseases and cancer. For example, in the course of chronic infectious disease, recruitment of subdominant epitopes can be important for successful clearance of the infection, especially if dominant CTL or HTL specificities have been inactivated by functional tolerance, suppression, mutation of viruses and other mechanisms (Franco, et al., Curr. Opin. Immunol. 7:524-531, 1995). In the case of cancer and tumor antigens, CTLs recognizing at least some of the highest binding affinity peptides might be functionally inactivated. Lower binding affinity peptides are preferentially recognized at these times, and may therefore be preferred in therapeutic or prophylactic anti-cancer vaccines.
In particular, it has been noted that a significant number of epitopes derived from known non-viral tumor associated antigens (TAA) bind HLA class I with intermediate affinity (IC50 in the 50-500 nM range). For example, it has been found that 8 of 15 known TAA peptides recognized by tumor infiltrating lymphocytes (TIL) or CTL bound in the 50-500 nM range. (These data are in contrast with estimates that 90% of known viral antigens were bound by HLA class I molecules with IC50 of 50 nM or less, while only approximately 10% bound in the 50-500 nM range (Sette, et al., J. Immunol., 153:558-5592, 1994). In the cancer setting this phenomenon is probably due to elimination or functional inhibition of the CTL recognizing several of the highest binding peptides, presumably because of T cell tolerization events.
Without intending to be bound by theory, it is believed that because T cells to dominant epitopes may have been clonally deleted, selecting subdominant epitopes may allow existing T cells to be recruited, which will then lead to a therapeutic or prophylactic response. However, the binding of HLA molecules to subdominant epitopes is often less vigorous than to dominant ones. Accordingly, there is a need to be able to modulate the binding affinity of particular immunogenic epitopes for one or more HLA molecules, and thereby to modulate the immune response elicited by the peptide, for example to prepare analog peptides which elicit a more vigorous response. This ability would greatly enhance the usefulness of peptide epitope-based vaccines and therapeutic agents.
Although peptides with suitable cross-reactivity among all alleles of a superfamily are identified by the screening procedures described above, cross-reactivity is not always as complete as possible, and in certain cases procedures to increase cross-reactivity of peptides can be useful; moreover, such procedures can also be used to modify other properties of the peptides such as binding affinity or peptide stability. Having established the general rules that govern cross-reactivity of peptides for HLA alleles within a given motif or supermotif, modification (i.e., analoging) of the structure of peptides of particular interest in order to achieve broader (or otherwise modified) HLA binding capacity can be performed. More specifically, peptides which exhibit the broadest cross-reactivity patterns, can be produced in accordance with the teachings herein. The present concepts related to analog generation are set forth in greater detail in U.S. Ser. No. 09/226,775 filed Jan. 6, 1999, now abandoned.
In brief, the strategy employed utilizes the motifs or supermotifs which correlate with binding to certain HLA molecules. The motifs or supermotifs are defined by having primary anchors, and in many cases secondary anchors. Analog peptides can be created by substituting amino acid residues at primary anchor, secondary anchor, or at primary and secondary anchor positions. Generally, analogs are made for peptides that already bear a motif or supermotif. Preferred secondary anchor residues of supermotifs and motifs that have been defined for HLA class I and class II binding peptides are shown in Tables II and III, respectively.
For a number of the motifs or supermotifs in accordance with the invention, residues are defined which are deleterious to binding to allele-specific HLA molecules or members of HLA supertypes that bind the respective motif or supermotif (Tables II and III). Accordingly, removal of such residues that are detrimental to binding can be performed in accordance with the present invention. For example, in the case of the A3 supertype, when all peptides that have such deleterious residues are removed from the population of peptides used for the analysis, the incidence of cross-reactivity increased from 22% to 37% (see, e.g., Sidney, J. et al., Hu. Immunol. 45:79, 1996). Thus, one strategy to improve the cross-reactivity of peptides within a given supermotif is simply to delete one or more of the deleterious residues present within a peptide and substitute a small “neutral” residue such as Ala (that may not influence T cell recognition of the peptide). An enhanced likelihood of cross-reactivity is expected if, together with elimination of detrimental residues within a peptide, “preferred” residues associated with high affinity binding to an allele-specific HLA molecule or to multiple HLA molecules within a superfamily are inserted.
To ensure that an analog peptide, when used as a vaccine, actually elicits a CTL response to the native epitope in vivo (or, in the case of class II epitopes, elicits helper T cells that cross-react with the wild type peptides), the analog peptide may be used to immunize T cells in vitro from individuals of the appropriate HLA allele. Thereafter, the immunized cells' capacity to induce lysis of wild type peptide sensitized target cells is evaluated. It will be desirable to use as antigen presenting cells, cells that have been either infected, or transfected with the appropriate genes, or, in the case of class II epitopes only, cells that have been pulsed with whole protein antigens, to establish whether endogenously produced antigen is also recognized by the relevant T cells.
Another embodiment of the invention is to create analogs of weak binding peptides. Class I binding peptides exhibiting binding affinities of 500-5000 nM, and carrying an acceptable but suboptimal primary anchor residue at one or both positions can be “fixed” by substituting preferred anchor residues in accordance with the respective supertype. The analog peptides can then be tested for crossbinding activity.
Another embodiment for generating effective peptide analogs involves the substitution of residues that have an adverse impact on peptide stability or solubility in, e.g., a liquid environment. This substitution may occur at any position of the peptide epitope. For example, a cysteine (C) can be substituted out in favor of α-amino butyric acid. Due to its chemical nature, cysteine has the propensity to form disulfide bridges and sufficiently alter the peptide structurally so as to reduce binding capacity. Substituting α-amino butyric acid for C not only alleviates this problem, but actually improves binding and crossbinding capability in certain instances (see, e.g., the review by Sette et al., In: Persistent Viral Infections, Eds. R. Ahmed and I. Chen, John Wiley & Sons, England, 1999). Substitution of cysteine with α-amino butyric acid may occur at any residue of a peptide epitope, i.e. at either anchor or non-anchor positions.
Representative analog peptides are set forth in Table XXII. The Table indicates the length and sequence of the analog peptide as well as the motif or supermotif, if appropriate. The information in the “Fixed Nomenclature” column indicates the residues substituted at the indicated position numbers for the respective analog.
IV.G. COMPUTER SCREENING OF PROTEIN SEQUENCES FROM DISEASE-RELATED ANTIGENS FOR SUPERMOTIF- OR MOTIF-BEARING PEPTIDES
In order to identify supermotif- or motif-bearing epitopes in a target antigen, a native protein sequence, e.g., a tumor-associated antigen, or sequences from an infectious organism, or a donor tissue for transplantation, is screened using a means for computing, such as an intellectual calculation or a computer, to determine the presence of a supermotif or motif within the sequence. The information obtained from the analysis of native peptide can be used directly to evaluate the status of the native peptide or may be utilized subsequently to generate the peptide epitope.
Computer programs that allow the rapid screening of protein sequences for the occurrence of the subject supermotifs or motifs are encompassed by the present invention; as are programs that permit the generation of analog peptides. These programs are implemented to analyze any identified amino acid sequence or operate on an unknown sequence and simultaneously determine the sequence and identify motif-bearing epitopes thereof; analogs can be simultaneously determined as well. Generally, the identified sequences will be from a pathogenic organism or a tumor-associated peptide. For example, the target molecules considered herein include, without limitation, the EXP1, LSA1, SSP2, and CSP1 proteins of PF.
In cases where the sequence of multiple variants of the same target protein are available, peptides may also be selected on the basis of their conservancy. A presently preferred criterion for conservancy defines that the entire sequence of an HLA class I binding peptide or the entire 9-mer core of a class II binding peptide, be totally (i.e., 100%) conserved in at least 79% of the sequences evaluated for a specific protein. This definition of conservancy has been employed herein; although, as appreciated by those in the art, lower or higher degrees of conservancy can be employed as appropriate for a given antigenic target.
It is important that the selection criteria utilized for prediction of peptide binding are as accurate as possible, to correlate most efficiently with actual binding. Prediction of peptides that bind, for example, to HLA-A*0201, on the basis of the presence of the appropriate primary anchors, is positive at about a 30% rate (see, e.g., Ruppert, J. et al. Cell 74:929, 1993). However, by extensively analyzing peptide-HLA binding data disclosed herein, data in related patent applications, and data in the art, the present inventors have developed a number of allele-specific polynomial algorithms that dramatically increase the predictive value over identification on the basis of the presence of primary anchor residues alone. These algorithms take into account not only the presence or absence of primary anchors, but also consider the positive or deleterious presence of secondary anchor residues (to account for the impact of different amino acids at different positions). The algorithms are essentially based on the premise that the overall affinity (or AG) of peptide-HLA interactions can be approximated as a linear polynomial function of the type:

ΔG=a1i×a2i×a3i . . . ×ani 

where aji is a coefficient that represents the effect of the presence of a given amino acid (j) at a given position (i) along the sequence of a peptide of n amino acids. An important assumption of this method is that the effects at each position are essentially independent of each other. This assumption is justified by studies that demonstrated that peptides are bound to HLA molecules and recognized by T cells in essentially an extended conformation. Derivation of specific algorithm coefficients has been described, for example, in Gulukota, K. et al., J. Mol. Biol. 267:1258, 1997.

Additional methods to identify preferred peptide sequences, which also make use of specific motifs, include the use of neural networks and molecular modeling programs (see, e.g., Milik et al., Nature Biotechnology 16:753, 1998; Altuvia et al., Hum. Immunol. 58:1, 1997; Altuvia et al, J. Mol. Biol. 249:244, 1995; Buus, S. Curr. Opin. Immunol. 11:209-213, 1999; Brusic, V. et al., Bioinformatics 14:121-130, 1998; Parker et al., J. Immunol. 152:163, 1993; Meister et al., Vaccine 13:581, 1995; Hammer et al., J. Exp. Med. 180:2353, 1994; Sturniolo et al., Nature Biotechnol. 17:555 1999).
For example, it has been shown that in sets of A*0201 motif-bearing peptides containing at least one preferred secondary anchor residue while avoiding the presence of any deleterious secondary anchor residues, 69% of the peptides will bind A*0201 with an IC50 less than 500 nM (Ruppert, J. et al. Cell 74:929, 1993). These algorithms are also flexible in that cut-off scores may be adjusted to select sets of peptides with greater or lower predicted binding properties, as desired.
In utilizing computer screening to identify peptide epitopes, a protein sequence or translated sequence may be analyzed using software developed to search for motifs, for example the “FINDPATTERNS’ program (Devereux, et al. Nucl. Acids Res. 12:387-395, 1984) or MotifSearch 1.4 software program (D. Brown, San Diego, Calif.) to identify potential peptide sequences containing appropriate HLA binding motifs. The identified peptides can be scored using customized polynomial algorithms to predict their capacity to bind specific HLA class I or class II alleles. As appreciated by one of ordinary skill in the art, a large array of computer programming software and hardware options are available in the relevant art which can be employed to implement the motifs of the invention in order to evaluate (e.g., without limitation, to identify epitopes, identify epitope concentration per peptide length, or to generate analogs) known or unknown peptide sequences.
In accordance with the procedures described above, PF peptide epitopes and analogs thereof that are able to bind HLA supertype groups or allele-specific HLA molecules have been identified (Tables VII-XX; Table XXII).
IV.H. PREPARATION OF PEPTIDE EPITOPES
Peptides in accordance with the invention can be prepared synthetically, by recombinant DNA technology or chemical synthesis, or from natural sources such as native tumors or pathogenic organisms. Peptide epitopes may be synthesized individually or as polyepitopic peptides. Although the peptide will preferably be substantially free of other naturally occurring host cell proteins and fragments thereof, in some embodiments the peptides may be synthetically conjugated to native fragments or particles.
The peptides in accordance with the invention can be a variety of lengths, and either in their neutral (uncharged) forms or in forms which are salts. The peptides in accordance with the invention are either free of modifications such as glycosylation, side chain oxidation, or phosphorylation; or they contain these modifications, subject to the condition that modifications do not destroy the biological activity of the peptides as described herein.
Desirably, the peptide epitope will be as small as possible while still maintaining substantially all of the immunologic activity of the native protein. When possible, it may be desirable to optimize HLA class I binding peptide epitopes of the invention to a length of about 8 to about 13 amino acid residues, preferably 9 to 10. HLA class II binding peptide epitopes may be optimized to a length of about 6 to about 30 amino acids in length, preferably to between about 13 and about 20 residues. Preferably, the peptide epitopes are commensurate in size with endogenously processed pathogen-derived peptides or tumor cell peptides that are bound to the relevant HLA molecules.
The identification and preparation of peptides of other lengths can also be carried out using the techniques described herein. Moreover, it is preferred to identify native peptide regions that contain a high concentration of class I and/or class II epitopes. Such a sequence is generally selected on the basis that it contains the greatest number of epitopes per amino acid length. It is to be appreciated that epitopes can be present in a frame-shifted manner, e.g. a 10 amino acid long peptide could contain two 9 amino acid long epitopes and one 10 amino acid long epitope; upon intracellular processing, each epitope can be exposed and bound by an HLA molecule upon administration of such a peptide. This larger, preferably multi-epitopic, peptide can be generated synthetically, recombinantly, or via cleavage from the native source.
The peptides of the invention can be prepared in a wide variety of ways. For the preferred relatively short size, the peptides can be synthesized in solution or on a solid support in accordance with conventional techniques. Various automatic synthesizers are commercially available and can be used in accordance with known protocols. (See, for example, Stewart & Young, SOLID PHASE PEPTIDE SYNTHESIS, 2D. ED., Pierce Chemical Co., 1984). Further, individual peptide epitopes can be joined using chemical ligation to produce larger peptides that are still within the bounds of the invention.
Alternatively, recombinant DNA technology can be employed wherein a nucleotide sequence which encodes an immunogenic peptide of interest is inserted into an expression vector, transformed or transfected into an appropriate host cell and cultivated under conditions suitable for expression. These procedures are generally known in the art, as described generally in Sambrook et al., MOLECULAR CLONING, A LABORATORY MANUAL, Cold Spring Harbor Press, Cold Spring Harbor, N.Y. (1989). Thus, recombinant polypeptides which comprise one or more peptide sequences of the invention can be used to present the appropriate T cell epitope.
The nucleotide coding sequence for peptide epitopes of the preferred lengths contemplated herein can be synthesized by chemical techniques, for example, the phosphotriester method of Matteucci, et al., J. Am. Chem. Soc. 103:3185 (1981). Peptide analogs can be made simply by substituting the appropriate and desired nucleic acid base(s) for those that encode the native peptide sequence; exemplary nucleic acid substitutions are those that encode an amino acid defined by the motifs/supermotifs herein. The coding sequence can then be provided with appropriate linkers and ligated into expression vectors commonly available in the art, and the vectors used to transform suitable hosts to produce the desired fusion protein. A number of such vectors and suitable host systems are now available. For expression of the fusion proteins, the coding sequence will be provided with operably linked start and stop codons, promoter and terminator regions and usually a replication system to provide an expression vector for expression in the desired cellular host. For example, promoter sequences compatible with bacterial hosts are provided in plasmids containing convenient restriction sites for insertion of the desired coding sequence. The resulting expression vectors are transformed into suitable bacterial hosts. Of course, yeast, insect or mammalian cell hosts may also be used, employing suitable vectors and control sequences.
IV.I. ASSAYS TO DETECT T-CELL RESPONSES
Once HLA binding peptides are identified, they can be tested for the ability to elicit a T-cell response. The preparation and evaluation of motif-bearing peptides are described in PCT publications WO 94/20127 and WO 94/03205. Briefly, peptides comprising epitopes from a particular antigen are synthesized and tested for their ability to bind to the appropriate HLA proteins. These assays may involve evaluating the binding of a peptide of the invention to purified HLA class I molecules in relation to the binding of a radioiodinated reference peptide. Alternatively, cells expressing empty class I molecules (i.e. lacking peptide therein) may be evaluated for peptide binding by immunofluorescent staining and flow microfluorimetry. Other assays that may be used to evaluate peptide binding include peptide-dependent class I assembly assays and/or the inhibition of CTL recognition by peptide competition. Those peptides that bind to the class I molecule, typically with an affinity of 500 nM or less, are further evaluated for their ability to serve as targets for CTLs derived from infected or immunized individuals, as well as for their capacity to induce primary in vitro or in vivo CTL responses that can give rise to CTL populations capable of reacting with selected target cells associated with a disease. Corresponding assays are used for evaluation of HLA class II binding peptides. HLA class II motif-bearing peptides that are shown to bind, typically at an affinity of 1000 nM or less, are further evaluated for the ability to stimulate HTL responses.
Conventional assays utilized to detect T cell responses include proliferation assays, lymphokine secretion assays, direct cytotoxicity assays, and limiting dilution assays. For example, antigen-presenting cells that have been incubated with a peptide can be assayed for the ability to induce CTL responses in responder cell populations. Antigen-presenting cells can be normal cells such as peripheral blood mononuclear cells or dendritic cells. Alternatively, mutant non-human mammalian cell lines that are deficient in their ability to load class I molecules with internally processed peptides and that have been transfected with the appropriate human class I gene, may be used to test for the capacity of the peptide to induce in vitro primary CTL responses.
Peripheral blood mononuclear cells (PBMCs) may be used as the responder cell source of CTL precursors. The appropriate antigen-presenting cells are incubated with peptide, after which the peptide-loaded antigen-presenting cells are then incubated with the responder cell population under optimized culture conditions. Positive CTL activation can be determined by assaying the culture for the presence of CTLs that kill radio-labeled target cells, both specific peptide-pulsed targets as well as target cells expressing endogenously processed forms of the antigen from which the peptide sequence was derived.
More recently, a method has been devised which allows direct quantification of antigen-specific CTLs by staining with Fluorescein-labelled HLA tetrameric complexes (Altman, J. D. et al., Proc. Natl. Acad. Sci. USA 90:10330, 1993; Altman, J. D. et al., Science 274:94, 1996). Other relatively recent technical developments include staining for intracellular lymphokines, and interferon release assays or ELISPOT assays. Tetramer staining, intracellular lymphokine staining and ELISPOT assays all appear to be at least 10-fold more sensitive than more conventional assays (Lalvani, A. et al., J. Exp. Med. 186:859, 1997; Dunbar, P. R. et al., Curr. Biol. 8:413, 1998; Murali-Krishna, K. et al., Immunity 8:177, 1998).
HTL activation may also be assessed using such techniques known to those in the art such as T cell proliferation and secretion of lymphokines, e.g. IL-2 (see, e.g. Alexander et al., Immunity 1:751-761, 1994).
Alternatively, immunization of HLA transgenic mice can be used to determine immunogenicity of peptide epitopes. Several transgenic mouse models including mice with human A2.1, A11 (which can additionally be used to analyze HLA-A3 epitopes), and B7 alleles have been characterized and others (e.g., transgenic mice for HLA-A1 and A24) are being developed. HLA-DR1 and HLA-DR3 mouse models have also been developed. Additional transgenic mouse models with other HLA alleles may be generated as necessary. Mice may be immunized with peptides emulsified in Incomplete Freund's Adjuvant and the resulting T cells tested for their capacity to recognize peptide-pulsed target cells and target cells transfected with appropriate genes. CTL responses may be analyzed using cytotoxicity assays described above. Similarly, HTL responses may be analyzed using such assays as T cell proliferation or secretion of lymphokines Exemplary immunogenic peptide epitopes are set out in Table XXIII.
IV.J. USE OF PEPTIDE EPITOPES AS DIAGNOSTIC AGENTS AND FOR EVALUATING IMMUNE RESPONSES
HLA class I and class II binding peptides as described herein can be used, in one embodiment of the invention, as reagents to evaluate an immune response. The immune response to be evaluated may be induced by using as an immunogen any agent that may result in the production of antigen-specific CTLs or HTLs that recognize and bind to the peptide epitope(s) to be employed as the reagent. The peptide reagent need not be used as the immunogen. Assay systems that may be used for such an analysis include relatively recent technical developments such as tetramers, staining for intracellular lymphokines and interferon release assays, or ELISPOT assays.
For example, a peptide of the invention may be used in a tetramer staining assay to assess peripheral blood mononuclear cells for the presence of antigen-specific CTLs following exposure to a pathogen or immunogen. The HLA-tetrameric complex is used to directly visualize antigen-specific CTLs (see, e.g., Ogg et al., Science 279:2103-2106, 1998; and Altman et al., Science 174:94-96, 1996) and determine the frequency of the antigen-specific CTL population in a sample of peripheral blood mononuclear cells. A tetramer reagent using a peptide of the invention may be generated as follows: A peptide that binds to an HLA molecule is refolded in the presence of the corresponding HLA heavy chain and β2-microglobulin to generate a trimolecular complex. The complex is biotinylated at the carboxyl terminal end of the heavy chain at a site that was previously engineered into the protein. Tetramer formation is then induced by the addition of streptavidin. By means of fluorescently labeled streptavidin, the tetramer can be used to stain antigen-specific cells. The cells may then be identified, for example, by flow cytometry. Such an analysis may be used for diagnostic or prognostic purposes.
Peptides of the invention may also be used as reagents to evaluate immune recall responses. (see, e.g., Bertoni et al., J. Clin. Invest. 100:503-513, 1997 and Penna et al., J. Exp. Med. 174:1565-1570, 1991.) For example, patient PBMC samples from individuals infected with PF may be analyzed for the presence of antigen-specific CTLs or HTLs using specific peptides. A blood sample containing mononuclear cells may be evaluated by cultivating the PBMCs and stimulating the cells with a peptide of the invention. After an appropriate cultivation period, the expanded cell population may be analyzed, for example, for CTL or for HTL activity.
The peptides may also be used as reagents to evaluate the efficacy of a vaccine. PBMCs obtained from a patient vaccinated with an immunogen may be analyzed using, for example, either of the methods described above. The patient is HLA typed, and peptide epitope reagents that recognize the allele-specific molecules present in that patient are selected for the analysis. The immunogenicity of the vaccine is indicated by the presence of PF epitope-specific CTLs and/or HTLs in the PBMC sample.
The peptides of the invention may also be used to make antibodies, using techniques well known in the art (see, e.g. CURRENT PROTOCOLS IN IMMUNOLOGY, Wiley/Greene, NY; and Antibodies A Laboratory Manual Harlow, Harlow and Lane, Cold Spring Harbor Laboratory Press, 1989), which may be useful as reagents to diagnose PF infection. Such antibodies include those that recognize a peptide in the context of an HLA molecule, i.e., antibodies that bind to a peptide-MHC complex.
IV.K. VACCINE COMPOSITIONS
Vaccines that contain an immunogenically effective amount of one or more peptides as described herein are a further embodiment of the invention. Once appropriately immunogenic epitopes have been defined, they can be sorted and delivered by various means, herein referred to as “vaccine” compositions. Such vaccine compositions can include, for example, lipopeptides (e.g., Vitiello, A. et al., J. Clin. Invest. 95:341, 1995), peptide compositions encapsulated in poly(DL-lactide-co-glycolide) (“PLG”) microspheres (see, e.g., Eldridge, et al., Molec. Immunol. 28:287-294, 1991: Alonso et al., Vaccine 12:299-306, 1994; Jones et al., Vaccine 13:675-681, 1995), peptide compositions contained in immune stimulating complexes (ISCOMS) (see, e.g., Takahashi et al., Nature 344:873-875, 1990; Hu et al., Clin Exp Immunol. 113:235-243, 1998), multiple antigen peptide systems (MAPs) (see e.g., Tam, J. P., Proc. Natl. Acad. Sci. U.S.A. 85:5409-5413, 1988; Tam, J. P., J. Immunol. Methods 196:17-32, 1996), viral delivery vectors (Perkus, M. E. et al., In: Concepts in vaccine development, Kaufmann, S. H. E., ed., p. 379, 1996; Chakrabarti, S. et al., Nature 320:535, 1986; Hu, S. L. et al., Nature 320:537, 1986; Kieny, M.-P. et al., AIDS Bio/Technology 4:790, 1986; Top, F. H. et al., J. Infect. Dis. 124:148, 1971; Chanda, P. K. et al., Virology 175:535, 1990), particles of viral or synthetic origin (e.g., Kofler, N. et al., J. Immunol. Methods. 192:25, 1996; Eldridge, J. H. et al., Sem. Hematol. 30:16, 1993; Falo, L. D., Jr. et al., Nature Med. 7:649, 1995), adjuvants (Warren, H. S., Vogel, F. R., and Chedid, L. A. Annu. Rev. Immunol. 4:369, 1986; Gupta, R. K. et al., Vaccine 11:293, 1993), liposomes (Reddy, R. et al., J. Immunol. 148:1585, 1992; Rock, K. L., Immunol. Today 17:131, 1996), or, naked or particle absorbed cDNA (Ulmer, J. B. et al., Science 259:1745, 1993; Robinson, H. L., Hunt, L. A., and Webster, R. G., Vaccine 11:957, 1993; Shiver, J. W. et al., In: Concepts in vaccine development, Kaufmann, S. H. E., ed., p. 423, 1996; Cease, K. B., and Berzofsky, J. A., Annu. Rev. Immunol. 12:923, 1994 and Eldridge, J. H. et al., Sem. Hematol. 30:16, 1993). Toxin-targeted delivery technologies, also known as receptor mediated targeting, such as those of Avant Immunotherapeutics, Inc. (Needham, Mass.) may also be used.
Furthermore, vaccines in accordance with the invention encompass compositions of one or more of the claimed peptide(s). The peptide(s) can be individually linked to its own carrier; alternatively, the peptide(s) can exist as a homopolymer or heteropolymer of active peptide units. Such a polymer has the advantage of increased immunological reaction and, where different peptide epitopes are used to make up the polymer, the additional ability to induce antibodies and/or CTLs that react with different antigenic determinants of the pathogenic organism or tumor-related peptide targeted for an immune response. The composition may be a naturally occurring region of an antigen or may be prepared, e.g., recombinantly or by chemical synthesis.
Furthermore, useful carriers that can be used with vaccines of the invention are well known in the art, and include, e.g., thyroglobulin, albumins such as human serum albumin, tetanus toxoid, polyamino acids such as poly L-lysine, poly L-glutamic acid, influenza, hepatitis B virus core protein, and the like. The vaccines can contain a physiologically tolerable (i.e., acceptable) diluent such as water, or saline, preferably phosphate buffered saline. The vaccines also typically include an adjuvant. Adjuvants such as incomplete Freund's adjuvant, aluminum phosphate, aluminum hydroxide, or alum are examples of materials well known in the art. Additionally, as disclosed herein, CTL responses can be primed by conjugating peptides of the invention to lipids, such as tripalmitoyl-S-glycerylcysteinlyseryl-serine (P3CSS).
As disclosed in greater detail herein, upon immunization with a peptide composition in accordance with the invention, via injection, aerosol, oral, transdermal, transmucosal, intrapleural, intrathecal, or other suitable routes, the immune system of the host responds to the vaccine by producing large amounts of CTLs and/or HTLs specific for the desired antigen. Consequently, the host becomes at least partially immune to later infection, or at least partially resistant to developing an ongoing chronic infection, or derives at least some therapeutic benefit when the antigen was tumor-associated.
In some instances it may be desirable to combine the class I peptide vaccines of the invention with vaccines which induce or facilitate neutralizing antibody responses to the target antigen of interest, particularly to surface antigens. A preferred embodiment of such a composition comprises class I and class II epitopes in accordance with the invention. An alternative embodiment of such a composition comprises a class I and/or class II epitope in accordance with the invention, along with a PADRETM (Epimmune, San Diego, Calif.) molecule (described, for example, in U.S. Pat. No. 5,736,142). Furthermore, any of these embodiments can be administered as a nucleic acid mediated modality.
The vaccine compositions of the invention may also be used in combination with antiviral drugs such as interferon-α.
For therapeutic or prophylactic immunization purposes, the peptides of the invention can also be expressed by viral or bacterial vectors. Examples of expression vectors include attenuated viral hosts, such as vaccinia or fowlpox. This approach involves the use of vaccinia virus, for example, as a vector to express nucleotide sequences that encode the peptides of the invention. Upon introduction into an acutely or chronically infected host or into a non-infected host, the recombinant vaccinia virus expresses the immunogenic peptide, and thereby elicits a host CTL and/or HTL response. Vaccinia vectors and methods useful in immunization protocols are described in, e.g., U.S. Pat. No. 4,722,848. Another vector is BCG (Bacille Calmette Guerin). BCG vectors are described in Stover et al., Nature 351:456-460 (1991). A wide variety of other vectors useful for therapeutic administration or immunization of the peptides of the invention, e.g. adeno and adeno-associated virus vectors, retroviral vectors, Salmonella typhi vectors, detoxified anthrax toxin vectors, and the like, will be apparent to those skilled in the art from the description herein.
Antigenic peptides are used to elicit a CTL and/or HTL response ex vivo, as well. Ex vivo administration is described, for example, in application U.S. Ser. No. 09/016,361 filed Jan. 30, 1998, now abandoned. The resulting CTL or HTL cells, can be used to treat chronic infections, or tumors in patients that do not respond to other conventional forms of therapy, or will not respond to a therapeutic vaccine peptide or nucleic acid in accordance with the invention. Ex vivo CTL or HTL responses to a particular antigen (infectious or tumor-associated antigen) are induced by incubating in tissue culture the patient's, or genetically compatible, CTL or HTL precursor cells together with a source of antigen-presenting cells (APC), such as dendritic cells, and the appropriate immunogenic peptide. After an appropriate incubation time (typically about 14 weeks), in which the precursor cells are activated and expanded into effector cells, the cells are infused back into the patient, where they will destroy (CTL) or facilitate destruction (HTL) of their specific target cell (an infected cell or a tumor cell). Transfected dendritic cells may also be used as antigen presenting cells. Alternatively, dendritic cells are transfected, e.g., with a minigene construct in accordance with the invention, in order to elicit immune responses. Minigenes will be discussed in greater detail in a following section.
Vaccine compositions may also be administered in vivo in combination with dendritic cell mobilization whereby loading of dendritic cells occurs in vivo.
DNA or RNA encoding one or more of the peptides of the invention can also be administered to a patient. This approach is described, for instance, in Wolff et. al., Science 247:1465 (1990) as well as U.S. Pat. Nos. 5,580,859; 5,589,466; 5,804,566; 5,739,118; 5,736,524; 5,679,647; WO 98/04720; and in more detail below. Examples of DNA-based delivery technologies include “naked DNA”, facilitated (bupivicaine, polymers, peptide-mediated) delivery, cationic lipid complexes, and particle-mediated (“gene gun”) or pressure-mediated delivery (see, e.g., U.S. Pat. No. 5,922,687).
Preferably, the following principles are utilized when selecting an array of epitopes for inclusion in a polyepitopic composition for use in a vaccine, or for selecting discrete epitopes to be included in a vaccine and/or to be encoded by nucleic acids such as a minigene. Exemplary epitopes that may be utilized in a vaccine to treat or prevent PF infection are set out in Tables XXXIII and XXXIV. The multiple epitopes to be incorporated in a given vaccine composition may be, but need not be, contiguous in sequence in the native antigen from which the epitopes are derived.
It is preferred that each of the following principles are balanced in order to make the selection.
1.) Epitopes are selected which, upon administration, mimic immune responses that have been observed to be correlated with PF clearance. For HLA Class I this includes 3-4 epitopes that come from at least one antigen of PF. For HLA Class II a similar rationale is employed; again 3-4 epitopes are selected from at least one PF antigen (see e.g., Rosenberg et al., Science 278:1447-1450).
2.) Epitopes are selected that have the requisite binding affinity established to be correlated with immunogenicity: for HLA Class I an IC50 of 500 nM or less, or for Class II an IC50 of 1000 nM or less.
3.) Sufficient supermotif bearing-peptides, or a sufficient array of allele-specific motif-bearing peptides, are selected to give broad population coverage. For example, it is preferable to have at least 80% population coverage. A Monte Carlo analysis, a statistical evaluation known in the art, can be employed to assess the breadth, or redundancy of, population coverage.
4.) When selecting epitopes from cancer-related antigens it is often preferred to select analogs because the patient may have developed tolerance to the native epitope. When selecting epitopes for infectious disease-related antigens it is preferable to select either native or analoged epitopes. Of particular relevance for infectious disease vaccines (but for cancer-related vaccines as well), are epitopes referred to as “nested epitopes.” Nested epitopes occur where at least two epitopes overlap in a given peptide sequence. A peptide comprising “transcendent nested epitopes” is a peptide that has both HLA class I and HLA class II epitopes in it.
When providing nested epitopes, it is preferable to provide a sequence that has the greatest number of epitopes per provided sequence. Preferably, one avoids providing a peptide that is any longer than the amino terminus of the amino terminal epitope and the carboxyl terminus of the carboxyl terminal epitope in the peptide. When providing a longer peptide sequence, such as a sequence comprising nested epitopes, it is important to screen the sequence in order to insure that it does not have pathological or other deleterious biological properties.
5.) When creating a minigene, as disclosed in greater detail in the following section, an objective is to generate the smallest peptide possible that encompasses the epitopes of interest. The principles employed are similar, if not the same as those employed when selecting a peptide comprising nested epitopes. Furthermore, upon determination of the nucleic acid sequence to be provided as a minigene, the peptide encoded thereby is analyzed to determine whether any “junctional epitopes” have been created. A junctional epitope is an actual binding epitope, as predicted, e.g., by motif analysis, that only exists because two discrete peptide sequences are encoded directly next to each other. Junctional epitopes are generally to be avoided because the recipient may generate an immune response to that non-native epitope. Of particular concern is a junctional epitope that is a “dominant epitope.” A dominant epitope may lead to such a zealous response that immune responses to other epitopes are diminished or suppressed.
IV.K.1. Minigene Vaccines
A growing body of experimental evidence demonstrates that a number of different approaches are available which allow simultaneous delivery of multiple epitopes. Nucleic acids encoding the peptides of the invention are a particularly useful embodiment of the invention. Epitopes for inclusion in a minigene are preferably selected according to the guidelines set forth in the previous section. A preferred means of administering nucleic acids encoding the peptides of the invention uses minigene constructs encoding a peptide comprising one or multiple epitopes of the invention. The use of multi-epitope minigenes is described below and in, e.g., application U.S. Ser. No. 09/311,784, now U.S. Pat. No. 6,534,482; Ishioka et al., J. Immunol. 162:3915-3925, 1999; An, L. and Whitton, J. L., J. Virol. 71:2292, 1997; Thomson, S. A. et al., J. Immunol. 157:822, 1996; Whitton, J. L. et al., J. Virol. 67:348, 1993; Hanke, R. et al., Vaccine 16:426, 1998. For example, a multi-epitope DNA plasmid encoding nine dominant HLA-A*0201- and A11-restricted epitopes derived from the polymerase, envelope, and core proteins of HBV and human immunodeficiency virus (HIV), the PADRETM universal HTL epitope, and an endoplasmic reticulum-translocating signal sequence was engineered. Immunization of HLA transgenic mice with this plasmid construct resulted in strong CTL induction responses against the nine epitopes tested, similar to those observed with a lipopeptide of known immunogenicity in humans, and significantly greater than immunization in oil-based adjuvants. Moreover, the immunogenicity of DNA-encoded epitopes in vivo correlated with the in vitro responses of specific CTL lines against target cells transfected with the DNA plasmid. Thus, these data show that the minigene served to both: 1.) generate a CTL response and 2.) that the induced CTLs recognized cells expressing the encoded epitopes. A similar approach may be used to develop minigenes encoding PF epitopes.
For example, to create a DNA sequence encoding the selected epitopes (minigene) for expression in human cells, the amino acid sequences of the epitopes may be reverse translated. A human codon usage table can be used to guide the codon choice for each amino acid. These epitope-encoding DNA sequences may be directly adjoined, so that when translated, a continuous polypeptide sequence is created. To optimize expression and/or immunogenicity, additional elements can be incorporated into the minigene design. Examples of amino acid sequences that can be reverse translated and included in the minigene sequence include: HLA class I epitopes, HLA class II epitopes, a ubiquitination signal sequence, and/or an endoplasmic reticulum targeting signal. In addition, HLA presentation of CTL and HTL epitopes may be improved by including synthetic (e.g. poly-alanine) or naturally-occurring flanking sequences adjacent to the CTL or HTL epitopes; these larger peptides comprising the epitope(s) are within the scope of the invention.
The minigene sequence may be converted to DNA by assembling oligonucleotides that encode the plus and minus strands of the minigene. Overlapping oligonucleotides (30-100 bases long) may be synthesized, phosphorylated, purified and annealed under appropriate conditions using well known techniques. The ends of the oligonucleotides can be joined, for example, using T4 DNA ligase. This synthetic minigene, encoding the epitope polypeptide, can then be cloned into a desired expression vector.
Standard regulatory sequences well known to those of skill in the art are preferably included in the vector to ensure expression in the target cells. Several vector elements are desirable: a promoter with a down-stream cloning site for minigene insertion; a polyadenylation signal for efficient transcription termination; an E. coli origin of replication; and an E. coli selectable marker (e.g. ampicillin or kanamycin resistance). Numerous promoters can be used for this purpose, e.g., the human cytomegalovirus (hCMV) promoter. See, e.g., U.S. Pat. Nos. 5,580,859 and 5,589,466 for other suitable promoter sequences.
Additional vector modifications may be desired to optimize minigene expression and immunogenicity. In some cases, introns are required for efficient gene expression, and one or more synthetic or naturally-occurring introns could be incorporated into the transcribed region of the minigene. The inclusion of mRNA stabilization sequences and sequences for replication in mammalian cells may also be considered for increasing minigene expression.
Once an expression vector is selected, the minigene is cloned into the polylinker region downstream of the promoter. This plasmid is transformed into an appropriate E. coli strain, and DNA is prepared using standard techniques. The orientation and DNA sequence of the minigene, as well as all other elements included in the vector, are confirmed using restriction mapping and DNA sequence analysis. Bacterial cells harboring the correct plasmid can be stored as a master cell bank and a working cell bank.
In addition, immunostimulatory sequences (ISSs or CpGs) appear to play a role in the immunogenicity of DNA vaccines. These sequences may be included in the vector, outside the minigene coding sequence, if desired to enhance immunogenicity.
In some embodiments, a bi-cistronic expression vector which allows production of both the minigene-encoded epitopes and a second protein (included to enhance or decrease immunogenicity) can be used. Examples of proteins or polypeptides that could beneficially enhance the immune response if co-expressed include cytokines (e.g., IL-2, IL-12, GM-CSF), cytokine-inducing molecules (e.g., LeIF), costimulatory molecules, or for HTL responses, pan-DR binding proteins (PADRETM, Epimmune, San Diego, Calif.). HTL epitopes can be joined to intracellular targeting signals and expressed separately from expressed CTL epitopes; this allows direction of the HTL epitopes to a cell compartment different than that of the CTL epitopes. If required, this could facilitate more efficient entry of HTL epitopes into the HLA class II pathway, thereby improving HTL induction. In contrast to HTL or CTL induction, specifically decreasing the immune response by co-expression of immunosuppressive molecules (e.g. TGF-β) may be beneficial in certain diseases.
Therapeutic quantities of plasmid DNA can be produced for example, by fermentation in E. coli, followed by purification. Aliquots from the working cell bank are used to inoculate growth medium, and grown to saturation in shaker flasks or a bioreactor according to well known techniques. Plasmid DNA can be purified using standard bioseparation technologies such as solid phase anion-exchange resins supplied by QIAGEN, Inc. (Valencia, Calif.). If required, supercoiled DNA can be isolated from the open circular and linear forms using gel electrophoresis or other methods.
Purified plasmid DNA can be prepared for injection using a variety of formulations. The simplest of these is reconstitution of lyophilized DNA in sterile phosphate-buffer saline (PBS). This approach, known as “naked DNA,” is currently being used for intramuscular (IM) administration in clinical trials. To maximize the immunotherapeutic effects of minigene DNA vaccines, an alternative method for formulating purified plasmid DNA may be desirable. A variety of methods have been described, and new techniques may become available. Cationic lipids can also be used in the formulation; in addition, glycolipids, fusogenic liposomes, peptides and compounds referred to collectively as protective, interactive, non-condensing compounds (PINC) can also be complexed to purified plasmid DNA to influence variables such as stability, intramuscular dispersion, or trafficking to specific organs or cell types (see, e.g., as described by WO 93/24640; Mannino & Gould-Fogerite, BioTechniques 6(7): 682 (1988); U.S. Pat. No. 5,279,833; WO 91/06309; and Felgner, et al., Proc. Nat'l Acad. Sci. USA 84:7413 (1987).
Target cell sensitization can be used as a functional assay for expression and HLA class I presentation of minigene-encoded CTL epitopes. For example, the plasmid DNA is introduced into a mammalian cell line that is suitable as a target for standard CTL chromium release assays. The transfection method used will be dependent on the final formulation. Electroporation can be used for “naked” DNA, whereas cationic lipids allow direct in vitro transfection. A plasmid expressing green fluorescent protein (GFP) can be co-transfected to allow enrichment of transfected cells using fluorescence activated cell sorting (FACS). These cells are then chromium-51 (51Cr) labeled and used as target cells for epitope-specific CTL lines; cytolysis, detected by 51Cr release, indicates both production of, and HLA presentation of, minigene-encoded CTL epitopes. Expression of HTL epitopes may be evaluated in an analogous manner using assays to assess HTL activity.
In vivo immunogenicity is a second approach for functional testing of minigene DNA formulations. Transgenic mice expressing appropriate human HLA proteins are immunized with the DNA product. The dose and route of administration are formulation dependent (e.g., IM for DNA in PBS, intraperitoneal (IP) for lipid-complexed DNA). Twenty-one days after immunization, splenocytes are harvested and restimulated for 1 week in the presence of peptides encoding each epitope being tested. Thereafter, for CTL effector cells, assays are conducted for cytolysis of peptide-loaded, 51Cr-labeled target cells using standard techniques. Lysis of target cells that were sensitized by HLA loaded with peptide epitopes, corresponding to minigene-encoded epitopes, demonstrates DNA vaccine function for in vivo induction of CTLs. Immunogenicity of HTL epitopes is evaluated in transgenic mice in an analogous manner.
Alternatively, the nucleic acids can be administered using ballistic delivery as described, for instance, in U.S. Pat. No. 5,204,253. Using this technique, particles comprised solely of DNA are administered. In a further alternative embodiment, DNA can be adhered to particles, such as gold particles.
IV.K.2. Combinations of CTL Peptides with Helper Peptides
Vaccine compositions comprising the peptides of the present invention, or analogs thereof, which have immunostimulatory activity may be modified to provide desired attributes, such as improved serum half life, or to enhance immunogenicity.
For instance, the ability of a peptide to induce CTL activity can be enhanced by linking the peptide to a sequence which contains at least one epitope that is capable of inducing a T helper cell response. The use of T helper epitopes in conjunction with CTL epitopes to enhance immunogenicity is illustrated, for example, in applications U.S. Ser. No. 08/197,484, now U.S. Pat. No. 6,419,931, and U.S. Ser. No. 08/464,234, now abandoned.
Particularly preferred CTL epitope/HTL epitope conjugates are linked by a spacer molecule. The spacer is typically comprised of relatively small, neutral molecules, such as amino acids or amino acid mimetics, which are substantially uncharged under physiological conditions. The spacers are typically selected from, e.g., Ala, Gly, or other neutral spacers of nonpolar amino acids or neutral polar amino acids. It will be understood that the optionally present spacer need not be comprised of the same residues and thus may be a hetero- or homo-oligomer. When present, the spacer will usually be at least one or two residues, more usually three to six residues. Alternatively, the CTL peptide may be linked to the T helper peptide without a spacer.
The CTL peptide epitope may be linked to the T helper peptide epitope either directly or via a spacer either at the amino or carboxy terminus of the CTL peptide. The amino terminus of either the immunogenic peptide or the T helper peptide may be acylated. The HTL peptide epitopes used in the invention can be modified in the same manner as CTL peptides. For instance, they may be modified to include D-amino acids or be conjugated to other molecules such as lipids, proteins, sugars and the like.
In certain embodiments, the T helper peptide is one that is recognized by T helper cells present in the majority of the population. This can be accomplished by selecting amino acid sequences that bind to many, most, or all of the HLA class II molecules. These are known as “loosely HLA-restricted” or “promiscuous” T helper sequences. Examples of amino acid sequences that are promiscuous include sequences from antigens such as tetanus toxoid at positions 830-843 (QYIKANSKFIGITE; SEQ ID NO: 3799), Plasmodium falciparum CS protein at positions 378-398 (DIEKKIAKMEKASSVFNVVNS; SEQ ID NO: 3800), and Streptococcus 18 kD protein at positions 116 (GAVDSILGGVATYGAA; SEQ ID NO: 3801). Other examples include peptides bearing a DR 1-4-7 supermotif, or either of the DR3 motifs.
Alternatively, it is possible to prepare synthetic peptides capable of stimulating T helper lymphocytes, in a loosely HLA-restricted fashion, using amino acid sequences not found in nature (see, e.g., PCT publication WO 95/07707). These synthetic compounds called Pan-DR-binding epitopes (e.g., PADRETM, Epimmune, Inc., San Diego, Calif.) are designed to most preferrably bind most HLA-DR (human HLA class II) molecules. For instance, a pan-DR-binding epitope peptide having the formula: aKXVWANTLKAAa (SEQ ID NO: 3802), where “X” is either cyclohexylalanine, phenylalanine, or tyrosine, and a is either D-alanine or L-alanine, has been found to bind to most HLA-DR alleles, and to stimulate the response of T helper lymphocytes from most individuals, regardless of their HLA type. An alternative of a pan-DR binding epitope comprises all “L” natural amino acids and can be provided in the form of nucleic acids that encode the epitope.
HTL peptide epitopes can also be modified to alter their biological properties. For example, peptides comprising HTL epitopes can contain D-amino acids to increase their resistance to proteases and thus extend their serum half-life. Also, the epitope peptides of the invention can be conjugated to other molecules such as lipids, proteins or sugars, or any other synthetic compounds, to increase their biological activity. Specifically, the T helper peptide can be conjugated to one or more palmitic acid chains at either the amino or carboxyl termini.
In some embodiments it may be desirable to include in the pharmaceutical compositions of the invention at least one component which primes cytotoxic T cells. Lipids have been identified as agents capable of priming CTL in vivo against viral antigens. For example, palmitic acid residues can be attached to the ε- and α-amino groups of a lysine residue and then linked, e.g., via one or more linking residues such as Gly, Gly-Gly-, Ser, Ser-Ser, or the like, to an immunogenic peptide. The lipidated peptide can then be administered either directly in a micelle or particle, incorporated into a liposome, or emulsified in an adjuvant, e.g., incomplete Freund's adjuvant. In a preferred embodiment, a particularly effective immunogenic comprises palmitic acid attached to ε- and α-amino groups of Lys, which is attached via linkage, e.g., Ser-Ser, to the amino terminus of the immunogenic peptide.
As another example of lipid priming of CTL responses, E. coli lipoproteins, such as tripalmitoyl-S-glycerylcysteinlyseryl-serine (P3CSS) can be used to prime virus specific CTL when covalently attached to an appropriate peptide. (See, e.g., Deres, et al., Nature 342:561, 1989). Peptides of the invention can be coupled to P3CSS, for example, and the lipopeptide administered to an individual to specifically prime a CTL response to the target antigen. Moreover, because the induction of neutralizing antibodies can also be primed with P3CSS-conjugated epitopes, two such compositions can be combined to more effectively elicit both humoral and cell-mediated responses to infection.
As noted herein, additional amino acids can be added to the termini of a peptide to provide for ease of linking peptides one to another, for coupling to a carrier support or larger peptide, for modifying the physical or chemical properties of the peptide or oligopeptide, or the like. Amino acids such as tyrosine, cysteine, lysine, glutamic or aspartic acid, or the like, can be introduced at the C- or N-terminus of the peptide or oligopeptide, particularly class I peptides. However, it is to be noted that modification at the carboxyl terminus of a CTL epitope may, in some cases, alter binding characteristics of the peptide. In addition, the peptide or oligopeptide sequences can differ from the natural sequence by being modified by terminal-NH2 acylation, e.g., by alkanoyl (C1-C20) or thioglycolyl acetylation, terminal-carboxyl amidation, e.g., ammonia, methylamine, etc. In some instances these modifications may provide sites for linking to a support or other molecule.
IV.L. ADMINISTRATION OF VACCINES FOR THERAPEUTIC OR PROPHYLACTIC PURPOSES
The peptides of the present invention and pharmaceutical and vaccine compositions of the invention are useful for administration to mammals, particularly humans, to treat and/or prevent malaria. Vaccine compositions containing the peptides of the invention are administered to an individual susceptible to, or otherwise at risk for, malaria or to a patient infected with PF to elicit an immune response against PF antigens and thus enhance the patient's own immune response capabilities. In therapeutic applications, peptide and/or nucleic acid compositions are administered to a patient in an amount sufficient to elicit an effective CTL and/or HTL response to the PF antigen and to cure or at least partially arrest or slow symptoms and/or complications. An amount adequate to accomplish this is defined as “therapeutically effective dose.” Amounts effective for this use will depend on, e.g., the particular composition administered, the manner of administration, the stage and severity of the disease being treated, the weight and general state of health of the patient, and the judgment of the prescribing physician.
The vaccine compositions of the invention may also be used purely as prophylactic agents. The level of expected exposure (e.g., a traveler versus a resident of an area where malaria is endemic) determines the magnitude of response that is desired to be achieved by the vaccination. Therefore, some vaccination regimens may employ higher doses of the vaccine compositions, or more doses may be administered.
Generally the dosage for an initial prophylactic immunization generally occurs in a unit dosage range where the lower value is about 1, 5, 50, 500, or 1000 μg and the higher value is about 10,000; 20,000; 30,000; or 50,000 μg. Dosage values for a human typically range from about 500 μg to about 50,000 μg per 70 kilogram patient. This is followed by boosting dosages of between about 1.0 μg to about 50,000 μg of peptide administered at defined intervals from about four weeks to six months after the initial administration of vaccine. The immunogenicity of the vaccine may be assessed by measuring the specific activity of CTL and HTL obtained from a sample of the patient's blood.
As noted above, peptides comprising CTL and/or HTL epitopes of the invention induce immune responses when presented by HLA molecules and contacted with a CTL or HTL specific for an epitope comprised by the peptide. The manner in which the peptide is contacted with the CTL or HTL is not critical to the invention. For instance, the peptide can be contacted with the CTL or HTL either in vivo or in vitro. If the contacting occurs in vivo, the peptide itself can be administered to the patient, or other vehicles, e.g., DNA vectors encoding one or more peptides, viral vectors encoding the peptide(s), liposomes and the like, can be used, as described herein.
For pharmaceutical compositions, the immunogenic peptides of the invention, or DNA encoding them, are generally administered to an individual who has not been infected with PF. The peptides or DNA encoding them can be administered individually or as fusions of one or more peptide sequences.
The pharmaceutical compositions may also be used to treat individuals already infected with PF. Patients can be treated with the immunogenic peptide epitopes separately or in conjunction with other treatments, as appropriate.
For therapeutic use, administration should generally begin at the first diagnosis of PF infection. This is followed by boosting doses until at least symptoms are substantially abated and for a period thereafter. Loading doses followed by boosting doses may be required.
The peptide or other compositions used for prophylaxis or the treatment of PF infection can be used, e.g., in persons who are not manifesting symptoms of disease but who act as a disease vector. In this context, it is generally important to provide an amount of the peptide epitope delivered by a mode of administration sufficient to effectively stimulate a cytotoxic T cell response; compositions which stimulate helper T cell responses can also be given in accordance with this embodiment of the invention.
The dosage for an initial therapeutic immunization generally occurs in a unit dosage range where the lower value is about 1, 5, 50, 500, or 1000 μg and the higher value is about 10,000; 20,000; 30,000; or 50,000 μg. Dosage values for a human typically range from about 500 μg to about 50,000 μg per 70 kilogram patient. Boosting dosages of between about 1.0 μg to about 50000 μg of peptide pursuant to a boosting regimen over weeks to months may be administered depending upon the patient's response and condition as determined by measuring the specific activity of CTL and HTL obtained from the patient's blood. The peptides and compositions of the present invention may be employed in serious disease states, that is, life-threatening or potentially life threatening situations. In such cases, as a result of the minimal amounts of extraneous substances and the relative nontoxic nature of the peptides in preferred compositions of the invention, it is possible and may be felt desirable by the treating physician to administer substantial excesses of these peptide compositions relative to these stated dosage amounts.
Thus, for treatment of a chronically infected individual, a representative dose is in the range disclosed above. Initial doses followed by boosting doses at established intervals, e.g., from four weeks to six months, may be required, possibly for a prolonged period of time to effectively immunize an individual. Administration should continue until at least clinical symptoms or laboratory tests indicate that the PF infection has been eliminated or substantially abated and for a period thereafter. The dosages, routes of administration, and dose schedules are adjusted in accordance with methodologies known in the art.
The pharmaceutical compositions for therapeutic treatment are intended for parenteral, topical, oral, intrathecal, or local administration. Preferably, the pharmaceutical compositions are administered parentally, e.g., intravenously, subcutaneously, intradermally, or intramuscularly. Thus, the invention provides compositions for parenteral administration which comprise a solution of the immunogenic peptides dissolved or suspended in an acceptable carrier, preferably an aqueous carrier. A variety of aqueous carriers may be used, e.g., water, buffered water, 0.8% saline, 0.3% glycine, hyaluronic acid and the like. These compositions may be sterilized by conventional, well known sterilization techniques, or may be sterile filtered. The resulting aqueous solutions may be packaged for use as is, or lyophilized, the lyophilized preparation being combined with a sterile solution prior to administration. The compositions may contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions, such as pH-adjusting and buffering agents, tonicity adjusting agents, wetting agents, preservatives, and the like, for example, sodium acetate, sodium lactate, sodium chloride, potassium chloride, calcium chloride, sorbitan monolaurate, triethanolamine oleate, etc.
The concentration of peptides of the invention in the pharmaceutical formulations can vary widely, i.e., from less than about 0.1%, usually at or at least about 2% to as much as 20% to 50% or more by weight, and will be selected primarily by fluid volumes, viscosities, etc., in accordance with the particular mode of administration selected.
A human unit dose form of the peptide composition is typically included in a pharmaceutical composition that comprises a human unit dose of an acceptable carrier, preferably an aqueous carrier, and is administered in a volume of fluid that is known by those of skill in the art to be used for administration of such compositions to humans (see, e.g., Remington's Pharmaceutical Sciences, 17th Edition, A. Gennaro, Editor, Mack Publishing Co., Easton, Pa., 1985).
The peptides of the invention may also be administered via liposomes, which serve to target the peptides to a particular tissue, such as lymphoid tissue, or to target selectively to infected cells, as well as to increase the half-life of the peptide composition. Liposomes include emulsions, foams, micelles, insoluble monolayers, liquid crystals, phospholipid dispersions, lamellar layers and the like. In these preparations, the peptide to be delivered is incorporated as part of a liposome, alone or in conjunction with a molecule which binds to a receptor prevalent among lymphoid cells, such as monoclonal antibodies which bind to the CD45 antigen, or with other therapeutic or immunogenic compositions. Thus, liposomes either filled or decorated with a desired peptide of the invention can be directed to the site of lymphoid cells, where the liposomes then deliver the peptide compositions. Liposomes for use in accordance with the invention are formed from standard vesicle-forming lipids, which generally include neutral and negatively charged phospholipids and a sterol, such as cholesterol. The selection of lipids is generally guided by consideration of, e.g., liposome size, acid lability and stability of the liposomes in the blood stream. A variety of methods are available for preparing liposomes, as described in, e.g., Szoka, et al., Ann. Rev. Biophys. Bioeng. 9:467 (1980), and U.S. Pat. Nos. 4,235,871, 4,501,728, 4,837,028, and 5,019,369.
For targeting cells of the immune system, a ligand to be incorporated into the liposome can include, e.g., antibodies or fragments thereof specific for cell surface determinants of the desired immune system cells. A liposome suspension containing a peptide may be administered intravenously, locally, topically, etc. in a dose which varies according to, inter alia, the manner of administration, the peptide being delivered, and the stage of the disease being treated.
For solid compositions, conventional nontoxic solid carriers may be used which include, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharin, talcum, cellulose, glucose, sucrose, magnesium carbonate, and the like. For oral administration, a pharmaceutically acceptable nontoxic composition is formed by incorporating any of the normally employed excipients, such as those carriers previously listed, and generally 10-95% of active ingredient, that is, one or more peptides of the invention, and more preferably at a concentration of 25%-75%.
For aerosol administration, the immunogenic peptides are preferably supplied in finely divided form along with a surfactant and propellant. Typical percentages of peptides are 0.01%-20% by weight, preferably 1%-10%. The surfactant must, of course, be nontoxic, and preferably soluble in the propellant. Representative of such agents are the esters or partial esters of fatty acids containing from 6 to 22 carbon atoms, such as caproic, octanoic, lauric, palmitic, stearic, linoleic, linolenic, olesteric and oleic acids with an aliphatic polyhydric alcohol or its cyclic anhydride. Mixed esters, such as mixed or natural glycerides may be employed. The surfactant may constitute 0.1%-20% by weight of the composition, preferably 0.25-5%. The balance of the composition is ordinarily propellant. A carrier can also be included, as desired, as with, e.g., lecithin for intranasal delivery.
IV.M. KITS
The peptide and nucleic acid compositions of this invention can be provided in kit form together with instructions for vaccine administration. Typically the kit would include desired peptide compositions in a container, preferably in unit dosage form and instructions for administration. An alternative kit would include a minigene construct with desired nucleic acids of the invention in a container, preferably in unit dosage form together with instructions for administration. Lymphokines such as IL-2 or IL-12 may also be included in the kit. Other kit components that may also be desirable include, for example, a sterile syringe, booster dosages, and other desired excipients.
The invention will be described in greater detail by way of specific examples. The following examples are offered for illustrative purposes, and are not intended to limit the invention in any manner. Those of skill in the art will readily recognize a variety of non-critical parameters that can be changed or modified to yield alternative embodiments in accordance with the invention.
V. EXAMPLES
The following examples illustrate identification, selection, and use of immunogenic Class I and Class II peptide epitopes for inclusion in vaccine compositions.
Example 1
HLA Class I and Class II Binding Assays
The following example of peptide binding to HLA molecules demonstrates quantification of binding affinities of HLA class I and class II peptides. Binding assays can be performed with peptides that are either motif-bearing or not motif-bearing.
Epstein-Barr virus (EBV)-transformed homozygous cell lines, fibroblasts, CIR, or 721.22 transfectants were used as sources of HLA class I molecules. These cells were maintained in vitro by culture in RPMI 1640 medium supplemented with 2 mM L-glutamine (GIBCO, Grand Island, N.Y.), 50 μM 2-ME, 100 μg/ml of streptomycin, 100 U/ml of penicillin (Irvine Scientific) and 10% heat-inactivated FCS (Irvine Scientific, Santa Ana, Calif.). Cells were grown in 225-cm2 tissue culture flasks or, for large-scale cultures, in roller bottle apparatuses. The specific cell lines routinely used for purification of MHC class I and class II molecules are listed in Table XXIV.
Cell lysates were prepared and HLA molecules purified in accordance with disclosed protocols (Sidney et al., Current Protocols in Immunology 18.3.1 (1998); Sidney, et al., J. Immunol. 154:247 (1995); Sette, et al., Mol. Immunol. 31:813 (1994)). Briefly, cells were lysed at a concentration of 108 cells/ml in 50 mM Tris-HCl, pH 8.5, containing 1% Nonidet P-40 (Fluka Biochemika, Buchs, Switzerland), 150 mM NaCl, 5 mM EDTA, and 2 mM PMSF. Lysates were cleared of debris and nuclei by centrifugation at 15,000×g for 30 min.
HLA molecules were purified from lysates by affinity chromatography. Lysates prepared as above were passed twice through two pre-columns of inactivated Sepharose CL4-B and protein A-Sepharose. Next, the lysate was passed over a column of Sepharose CL-4B beads coupled to an appropriate antibody. The antibodies used for the extraction of HLA from cell lysates are listed in Table XXV. The anti-HLA column was then washed with 10-column volumes of 10 mM Tris-HCL, pH 8.0, in 1% NP-40, PBS, 2-column volumes of PBS, and 2-column volumes of PBS containing 0.4% n-octylglucoside. Finally, MHC molecules were eluted with 50 mM diethylamine in 0.15M NaCl containing 0.4% n-octylglucoside, pH 11.5. A 1/25 volume of 2.0M Tris, pH 6.8, was added to the eluate to reduce the pH to  ̃8.0. Eluates were then be concentrated by centrifugation in Centriprep 30 concentrators at 2000 rpm (Amicon, Beverly, Mass.). Protein content was evaluated by a BCA protein assay (Pierce Chemical Co., Rockford, Ill.) and confirmed by SDS-PAGE.
A detailed description of the protocol utilized to measure the binding of peptides to Class I and Class II MHC has been published (Sette et al., Mol. Immunol. 31:813, 1994; Sidney et al., in Current Protocols in Immunology, Margulies, Ed., John Wiley & Sons, New York, Section 18.3, 1998). Briefly, purified MHC molecules (5 to 500 nM) were incubated with various unlabeled peptide inhibitors and 1-10 nM 125I-radiolabeled probe peptides for 48 h in PBS containing 0.05% Nonidet P-40 (NP40) (or 20% w/v digitonin for H-2 IA assays) in the presence of a protease inhibitor cocktail. The final concentrations of protease inhibitors (each from CalBioChem, La Jolla, Calif.) were 1 mM PMSF, 1.3 nM 1.10 phenanthroline, 73 μM pepstatin A, 8 mM EDTA, 6 mM N-ethylmaleimide (for Class II assays), and 200 μM N alpha-p-tosyl-L-lysine chloromethyl ketone (TLCK). All assays were performed at pH 7.0 with the exception of DRB1*0301, which was performed at pH 4.5, and DRB1*1601 (DR2w21β1) and DRB4*0101 (DRw53), which were performed at pH 5.0. pH was adjusted as described elsewhere (see Sidney et al., in Current Protocols in Immunology, Margulies, Ed., John Wiley & Sons, New York, Section 18.3, 1998).
Following incubation, MHC-peptide complexes were separated from free peptide by gel filtration on 7.8 mm×15 cm TSK200 columns (TosoHaas 16215, Montgomeryville, Pa.), eluted at 1.2 mls/min with PBS pH 6.5 containing 0.5% NP40 and 0.1% NaN3. Because the large size of the radiolabeled peptide used for the DRB1*1501 (DR2w2β1) assay makes separation of bound from unbound peaks more difficult under these conditions, all DRB1*1501 (DR2w2β1) assays were performed using a 7.8 mm×30 cm TSK2000 column eluted at 0.6 mls/min. The eluate from the TSK columns was passed through a Beckman 170 radioisotope detector, and radioactivity was plotted and integrated using a Hewlett-Packard 3396A integrator, and the fraction of peptide bound was determined.
Radiolabeled peptides were iodinated using the chloramine-T method. Representative radiolabeled probe peptides utilized in each assay, and its assay specific IC50 nM, are summarized in Tables IV and V. Typically, in preliminary experiments, each MHC preparation was titered in the presence of fixed amounts of radiolabeled peptides to determine the concentration of HLA molecules necessary to bind 10-20% of the total radioactivity. All subsequent inhibition and direct binding assays were performed using these HLA concentrations.
Since under these conditions [label]<[HLA] and IC50≧[HLA], the measured IC50 values are reasonable approximations of the true KD values. Peptide inhibitors are typically tested at concentrations ranging from 120 μg/ml to 1.2 ng/ml, and are tested in two to four completely independent experiments. To allow comparison of the data obtained in different experiments, a relative binding figure is calculated for each peptide by dividing the IC50 of a positive control for inhibition by the IC50 for each tested peptide (typically unlabeled versions of the radiolabeled probe peptide). For database purposes, and inter-experiment comparisons, relative binding values are compiled. These values can subsequently be converted back into IC50 nM values by dividing the IC50 nM of the positive controls for inhibition by the relative binding of the peptide of interest. This method of data compilation has proven to be the most accurate and consistent for comparing peptides that have been tested on different days, or with different lots of purified MHC.
Because the antibody used for HLA-DR purification (LB3.1) is α-chain specific, β1 molecules are not separated from β3 (and/or β4 and β5) molecules. The β1 specificity of the binding assay is obvious in the cases of DRB1*0101 (DR1), DRB1*0802 (DR8w2), and DRB1*0803 (DR8w3), where no β3 is expressed. It has also been demonstrated for DRB1*0301 (DR3) and DRB3*0101 (DR52a), DRB1*0401 (DR4w4), DRB1*0404 (DR4w14), DRB1*0405 (DR4w15), DRB1*1101 (DR5), DRB1*1201 (DR5w12), DRB1*1302 (DR6w19) and DRB1*0701 (DR7). The problem of β chain specificity for DRB1*1501 (DR2w2β1), DRB5*0101 (DR2w2β2), DRB1*1601 (DR2w21β1), DRB5*0201 (DR51Dw21), and DRB4*0101 (DRw53) assays is circumvented by the use of fibroblasts. Development and validation of assays with regard to DRβ molecule specificity have been described previously (see, e.g., Southwood et al., J. Immunol. 160:3363-3373, 1998).
Binding assays as outlined above may be used to analyze supermotif and/or motif-bearing epitopes as, for example, described in Example 2.
Example 2
Identification of Conserved HLA Supermotif- and Motif-Bearing CTL Candidate Epitopes
Vaccine compositions of the invention may include multiple epitopes that comprise multiple HLA supermotifs or motifs to achieve broad population coverage. This example illustrates the identification of supermotif- and motif-bearing epitopes for the inclusion in such a vaccine composition. Additional experimental details that may be relevant to this example are found in Doolan, D. L. et al., Immunity 7:97, 1997. Calculation of population coverage was performed using the strategy described below.
Computer Searches and Algorithms for Identification of Supermotif and/or Motif-Bearing Epitopes
Computer searches for epitopes bearing HLA Class I or Class II supermotifs or motifs were performed as follows. All translated PF protein sequences were analyzed using a text string search software program, e.g., MotifSearch 1.4 (D. Brown, San Diego) to identify potential peptide sequences containing appropriate HLA binding motifs; alternative programs are readily produced in accordance with information in the art in view of the motif/supermotif disclosure herein. Furthermore, such calculations can be made mentally. Identified A2-, A3-, and DR-supermotif sequences were scored using polynomial algorithms to predict their capacity to bind to specific HLA-Class I or Class II molecules. These polynomial algorithms take into account both extended and refined motifs (that is, to account for the impact of different amino acids at different positions), and are essentially based on the premise that the overall affinity (or AG) of peptide-HLA molecule interactions can be approximated as a linear polynomial function of the type:

“ΔG”=a1i×a2i×a3i×ani 

where aji is a coefficient which represents the effect of the presence of a given amino acid (j) at a given position (i) along the sequence of a peptide of n amino acids. The crucial assumption of this method is that the effects at each position are essentially independent of each other (i.e., independent binding of individual side-chains). When residue j occurs at position i in the peptide, it is assumed to contribute a constant amount ji to the free energy of binding of the peptide irrespective of the sequence of the rest of the peptide. This assumption is justified by studies from our laboratories that demonstrated that peptides are bound to MHC and recognized by T cells in essentially an extended conformation (data omitted herein).

The method of derivation of specific algorithm coefficients has been described in Gulukota et al., J. Mol. Biol. 267:1258-126, 1997; (see also Sidney et al., Human Immunol. 45:79-93, 1996; and Southwood et al., J. Immunol. 160:3363-3373, 1998). Briefly, for all i positions, anchor and non-anchor alike, the geometric mean of the average relative binding (ARB) of all peptides carrying j is calculated relative to the remainder of the group, and used as the estimate off. For Class II peptides, if multiple alignments are possible, only the highest scoring alignment is utilized, following an iterative procedure. To calculate an algorithm score of a given peptide in a test set, the ARB values corresponding to the sequence of the peptide are multiplied. If this product exceeds a chosen threshold, the peptide is predicted to bind. Appropriate thresholds are chosen as a function of the degree of stringency of prediction desired.
Selection of HLA-A2 Supertype Cross-Reactive Peptides
Complete protein sequences from PF antigens were aligned, then scanned, utilizing motif identification software, to identify conserved 9- and 10-mer sequences containing the HLA-A*0201-motif main anchor specificity. Following conservancy determination and algorithm analysis to take into account the influence of secondary anchors, 53 peptides containing the HLA-A*0201 of potential interest were identified and tested for their capacity to bind to purified HLA-A*0201 molecules in vitro. Fifteen peptides bound A*0201 with IC50 values 500 nM.
Fourteen of these peptides were subsequently tested for immunogenicity as described below. Of these, 5 scored positive both in primary in vitro CTL responses and in HLA transgenic mice.
The five immunogenic peptides were then tested for the capacity to bind to additional A2-supertype molecules (A*0202, A*0203, A*0206, and A*6802). The peptide SSP214-23, which was immunogenic in primary human CTL cultures and contains the SSP214-22 epitope (rather than SSP214-22 itself), was included in the analysis. In addition, the peptide Exp-183, which was positive in the murine CTL assays and the peptide CSP425 and SSP2230, were also analyzed for cross-reactive binding. As shown in Table XXVI, all eight of these peptides were found to be A2-supertype cross-reactive binders with six of these binding to three or more A2 supertype alleles.
Selection of HLA-A3 Supermotif-Bearing Epitopes
The PF protein sequences scanned above were also examined for the presence of conserved peptides with the HLA-A3 supermotif primary anchors. Further analysis using the A03 and A11 algorithms (see, e.g., Gulukota et al, J. Mol. Biol. 267:1258-1267, 1997 and Sidney et al, Human Immunol. 45:79-93, 1996) identified 203 conserved 9- or 10-mer motif-containing peptide sequences that scored high in either or both algorithms. Of these candidates, twenty five peptides were identified that bound A3 and/or A11 with binding affinities of ≦500 nM. These peptides were then tested for binding cross-reactivity to the other common A3-supertype alleles (A*3101, A*3301, and A*6801). Seven of them bound at least three of the five HLA-A3-supertype molecules tested. An eighth peptide, LSA-111 was also considered for further study because it bound strongly to two of the A3 supertype alleles and weakly to the other two A3 supertype alleles. (Table XXVII)
In summary, eight HLA-A3 supertype cross-reactive binding peptides derived from conserved regions of PF proteins were identified.
Selection of HLA-B7 Supermotif Bearing Epitopes
When the same PF target antigen protein sequences were also analyzed for the presence of conserved 9- or 10-mer peptides with the HLA-B7-supermotif, 26 sequences were identified. Of these 26, 24 corresponding peptides were synthesized and tested for binding to HLA-B*0702, the most common B7-supertype allele (i.e., the prototype B7 supertype allele). Four of the peptides bound B*0702 with IC50 of ≦500 nM. These four peptides were then tested for binding to other common B7-supertype molecules (B*3501, B*51, B*5301, and B*5401). As shown in Table XXVIII, one peptide was capable of to four of the five B7 supertype alleles; another was found to bind three of the five alles.
Selection of A1 and A24 Motif-Bearing Epitopes
To further increase population coverage, HLA-A1 and -A24 epitopes can also be incorporated into potential vaccine constructs.
An analysis of the protein sequence data from the PF target antigens utilized above identified 40 A1- and 81 A24-motif-containing conserved sequences. Testing for binding to the appropriate HLA molecule (i.e., A1 or A24) was performed on a subset of those peptides. Four A1-motif peptides and four A24-motif peptides, shown in Table Table XXIX, were found to have binding capacities of 500 nM or less for the appropriate allele-specific HLA molecule.
Example 3
Confirmation of Immunogenicity
Evaluation of A*0201 Immunogenicity
It has been shown that CTL induced in A*0201/Kb transgenic mice exhibit specificity similar to CTL induced in the human system (see, e.g., Vitiello et al., J. Exp. Med. 173:1007-1015, 1991; Wentworth et al., Eur. J. Immunol. 26:97-101, 1996). Accordingly, these mice were used to evaluate the immunogenicity of the fourteen conserved A*0201 motif-bearing high affinity binding peptides identified in Example 2 above.
CTL induction in transgenic mice following peptide immmunization has been described (Vitiello et al., J. Exp. Med. 173:1007-1015, 1991; Alexander et al.; J. Immunol. 159:4753-4761, 1997). In these studies, mice were injected subcutaneously at the base of the tail with each peptide (50 μg/mouse) emulsified in IFA in the presence of an excess of an IAb-restricted helper peptide (140 μg/mouse) (HBV core 128-140, Sette et al., J. Immunol. 153:5586-5592, 1994). Eleven days after injection, splenocytes were incubated in the presence of peptide-loaded syngenic LPS blasts. After six days, cultures were assayed for cytotoxic activity using peptide-pulsed targets. The data indicated that 5 of the 14 peptides were capable of inducing primary CTL responses in A*0201/Kb transgenic mice. (For these studies, a peptide was considered positive if it induced CTL (L.U. 30/106 cells ≧2 in at least two transgenic animals (Wentworth et al., Eur. J. Immunol. 26:97-101, 1996).
The fourteen peptides that bound to HLA-A*0201 with good affinity were also tested for immunogenicity with PBMCs from at least four malaria-naïve human donors. The induction of primary CTL responses in vitro with PBMCs from normal naïve humans requires a brief treatment of the antigen-presenting cells with acidic buffer and subsequent neutralization in the presence of excess B2-microglobulin and exogenous peptide (Wentworth et al., supra). By ensuring that the majority of the HLA class I molecules are occupied by exogenous peptide, these steps are essential for the induction of primary CTL responses. Such responses cannot be induced using methods developed for the induction of recall CTL responses. A peptide was considered positive if yielding more than 2 LU30/106 cells (lytic units 20% per 104 cells, where one lytic unit corresponds to the number of effector cells required to induce 30% 51Cr release from 10,000 target cells during a 6 hr assay.) or 15% peptide-specific lysis, respectively, in at least two different primary CTL cultures. The five peptides that were positive in HLA transgenic mice were also shown to induce primary CTL responses.
The HLA-A2 cross-reactive binding peptides were tested for their ability to elicit in vitro recall responses from PBMCs of six volunteers, each of whom had an HLA-A*0201 allele, immunized with irradiated sporozoites. The results demonstrated that all of the A2-binding peptides were recognized in association with HLA-A*0201.
In addition to investigating whether the peptides could be recognized as CTL epitopes, the ability of the peptides to induce specific cytokine responses was also measured. In particular, induction of interferon-γ and TNF-α were measured, both of which have been implicated in protective immunity against malaria. PBMC from irradiated sporozoite-immunized volunteers and PBMC from naturally exposed individuals were tested. The results indicate that significant peptide-induced cytokine responses were observed for all of the A2 supermotif-bearing peptides. (See Doolan et al., Immunity 7:97-112, 1997.)
Evaluation of A*03/A11 Immunogenicity
The immunogenicity of the eight supermotif-bearing peptides was also evaluated in recall responses using PBMC from volunteers bearing HLA-A3 supertype alleles who had previously been immunized with irradiated sporozoites. All the peptides were recognized in association with both A3 and A33. The fraction of individuals responding to each peptide varied for the supertype overall from 50% for one of the peptides to 100% for three of the peptides.
Immunogenicity was also evaluated using PBMCs of semi-immune or nonimmune individuals naturally exposed to malaria. In this population, recall CTL responses (percentage specific lysis greater than 10%) were detected for five of the eight A3-binding peptides.
Immunogenicity of A3 supermotif-bearing peptides can also be evaluated in transgenic mice that bear a human HLA-A11 allele using methodology analogous to that for immunogenicity studies using HLA-A2.1 transgenic mice.
Evaluation of B7 Immunogenicity
Immunogenicity of two B7 supermotif-bearing peptides, SSP2539 and the HLA-B-restricted peptide Pfs1677 was also examined in individuals who had been exposed to PF, either through immunization or natural exposure, as described for the evaluation of A2- and A3-supermotif-bearing peptides.
Both peptides were found to be capable of inducing CTL responses. The two peptides were recognized as CTL epitopes in the context of three of the five B7 supertype alleles.
Example 4
Implementation of the Extended Supermotif to Improve the Binding Capacity of Native Epitopes by Creating Analogs
HLA motifs and supermotifs (comprising primary and/or secondary residues) are useful in the identification and preparation of highly cross-reactive native peptides, as demonstrated herein. Moreover, the definition of HLA motifs and supermotifs also allows one to engineer highly cross-reactive epitopes by identifying residues within a native peptide sequence which can be analogued, or “fixed” to confer upon the peptide certain characteristics, e.g. greater cross-reactivity within the group of HLA molecules that comprise a supertype, and/or greater binding affinity for some or all of those HLA molecules. Examples of analog peptides that exhibit modulated binding affinity are set forth in this example.
Analoging at Primary Anchor Residues
The primary anchor residues are analogued to modulate binding activity. For example, peptide engineering strategies are implemented to further increase the cross-reactivity of the A3-supertype candidate epitopes identified above. On the basis of the data disclosed, e.g., in related and U.S. Ser. No. 09/226,775, now abandoned, the main anchors of A3-supermotif-bearing peptides are altered, for example, to introduce a preferred V, S, or M at position 2.
To analyze the cross-reactivity of the analog peptides, each engineered analog is initially tested for binding to the prototype A3 supertype alleles A3 and A11; then, if binding capacity is maintained, for additional A3-supertype cross-reactivity.
Similarly, analogs of HLA-A2 supermotif-bearing epitopes may also be generated. For example, peptides binding to A2-supertype molecules may be engineered at primary anchor residues to possess a preferred residue (L, I, V, or M) at position 2 and/or a preferred I or V as a position 9 primary anchor residue.
The analog peptides are then tested for the ability to bind the A2 supermotif prototype allele, A*0201. Those peptides that demonstrate 500 nM binding capacity are then tested for A2-supertype cross-reactivity.
Similarly to the A2- and A3-motif bearing peptides, peptide binding to B7-supertype alleles may be improved, where possible, to achieve increased cross-reactive binding. B7 supermotif-bearing peptides may, for example, be engineered to possess a preferred residue (V, I, L, or F) at the C-terminal primary anchor position, as demonstrated by Sidney et al. (J. Immunol. 157:3480-3490, 1996).
Analoging at Secondary Anchor Residues
Moreover, HLA supermotifs are of value in engineering highly cross-reactive peptides and/or peptides that bind HLA molecules with increased affinity by identifying particular residues at secondary anchor positions that are associated with such properties. For example, the binding capacity of an analog of the B7 supermotif-bearing peptide Pf SSP2126, representing a discreet single amino acid substitution at position one, is analyzed. The peptide may be substituted with an F at position 1, rather than and L. The peptide, which binds to 3 of 5 B7 supertype alles, is then analyzed for the ability to bind all five B7-supertype molecules with a good affinity.
Because so few B7-supertype cross-reactive epitopes were identified in the initial binding screen, results from previous binding evaluations may be analyzed to identify conserved (8-, 9-, 10-, or 11-mer) peptides which bind, minimally, 3/5 B7 supertype molecules with weak affinity (IC50 of 500 nM-5 μM). This analysis identifies additional candidate peptides that can be analogued. These peptides are tested for enhanced binding affinity and B7-supertype cross-reactivity.
Engineered analogs with sufficiently improved binding capacity or cross-reactivity are tested as described in Example 2 for the ability of the peptide to induce CTL responses using PBMC from individuals who had previously been exposed to Pf antigens. Immunogenicity may also be studied in HLA-B7-transgenic mice, following for example, IFA immunization or lipopeptide immunization.
In conclusion, these data demonstrate that by the use of even single amino acid substitutions, it is possible to increase the binding affinity and/or cross-reactivity of peptide ligands for HLA supertype molecules.
Example 5
Identification of Conserved Pf-Derived Sequences with HLA-DR Binding Motifs
Peptide epitopes bearing an HLA class II supermotif or motif may also be identified as outlined below using methodology similar to that described in Examples 1-3.
Selection of HLA-DR-Supermotif-Bearing Epitopes
To identify PF-derived, HLA class II HTL epitopes, the protein sequences from the same four PF antigens used for the identification of HLA Class I supermotif/motif sequences were analyzed for the presence of sequences bearing an HLA-DR-motif or supermotif. Specifically, 15-mer sequences were selected comprising a DR-supermotif, further comprising a 9-mer core, and three-residue N- and C-terminal flanking regions (15 amino acids total). It was also required that the 9-mer core sequence be 100% conserved in at least 79% of the sequences analyzed.
The conserved, PF-derived peptides identified above were tested for their binding capacity for various common HLA-DR molecules. All peptides were initially tested for binding to the DR molecules in the primary panel: DR1, DR4w4, and DR7. Peptides binding at least 2 of these 3 DR molecules were then tested for binding to DR2w2β1, DR2w2β2, DR6w19, and DR9 molecules in secondary assays. Finally, peptides binding at least 2 of the 4 secondary panel DR molecules, and thus cumulatively at least 4 of 7 different DR molecules, were screened for binding to DR4w15, DR5w11, and DR8w2 molecules in tertiary assays. Peptides binding at least 7 of the 10 DR molecules comprising the primary, secondary, and tertiary screening assays were considered cross-reactive DR binders. The composition of these screening panels, and the phenotypic frequency of associated antigens, are shown in Table XXX.
In conclusion, 8 cross-reactive DR-binding peptides derived from 6 independent regions were identified that bind 7 or more HLA DR alleles. Five other peptides were also identified that bound between 4 and 6 DR alleles (Table XXXI).
Selection of Conserved DR3 Motif Peptides
Because HLA-DR3 is an allele that is prevalent in Caucasian, Black, and Hispanic populations, DR3 binding capacity is an important criterion in the selection of HTL epitopes. However, data generated previously indicated that DR3 only rarely cross-reacts with other DR alleles (Sidney et al., J. Immunol. 149:2634-2640, 1992; Geluk et al., J. Immunol. 152:5742-5748, 1994; Southwood et al., J. Immunol. 160:3363-3373, 1998). This is not entirely surprising in that the DR3 peptide-binding motif appears to be distinct from the specificity of most other DR alleles.
To efficiently identify peptides that bind DR3, target proteins were analyzed for conserved sequences carrying one of the two DR3 specific binding motifs reported by Geluk et al. (J. Immunol. 152:5742-5748, 1994). Peptides containing a DR3 motif were then synthesized and tested for their DR3 binding capacity. Three peptides were found to bind DR3 with an affinity of 1 μM or less (Table XXXI), and thereby qualify as HLA class II high affinity binders. On of these peptides was also identified above as a cross-reactive DR binding peptide.
DR3 binding epitopes identified in this manner that are found to induce immunological responses as in Example 6 below may then be included in vaccine compositions with DR supermotif-bearing peptide epitopes.
Example 6
Immunogenicity of PF-Derived HTL Epitopes
The immunogenicity of the HLA class II binding epitopes identified in Example 5 was evaluated in a study testing PBMC from either healthy volunteers previously immunized with an irradiated sporozoite vaccine, and thereby immune to malaria, or PBMC from naturally exposed individuals from the Irian Java (Indonesia) region where malaria is highly endemic. Vigorous responses were seen in volunteers vaccinated with whole irradiate sporozoites. All peptides were recognized in at least one immune individual, but not in either of the two individuals for which pre-immunization sample were available. All individuals recognized at least two, and up to nine different epitopes.
In the case of Irian Java population, PBMC from over 100 different individuals were screened for reactivity. Proliferation and secretion of various lymphokines has been measured. The results demonstrate that also in this semi-immune chronically exposed population, all peptides are recognized, with the percentage of individuals yielding positive responses ranging from 7% to 29% for IFN-γ, 36% to 51% for TNF-α and 12% to 2% for proliferative responses (Table XXII.
In conclusion, the immunogenicity of class II epitopes derived from conserved regions of the PF genome has been demonstrated.
Example 7
Calculation of Phenotypic Frequencies of HLA-Supertypes in Various Ethnic Backgrounds to Determine Breadth of Population Coverage
This example illustrates the assessment of the breadth of population coverage of a vaccine composition comprised of multiple epitopes comprising multiple supermotifs and/or motifs.
In order to analyze population coverage, gene frequencies of HLA alleles were determined. Gene frequencies for each HLA allele were calculated from antigen or allele frequencies utilizing the binomial distribution formulae gf=1−(SQRT(1−af)) (see, e.g., Sidney et al., Human Immunol. 45:79-93, 1996). To obtain overall phenotypic frequencies, cumulative gene frequencies were calculated, and the cumulative antigen frequencies derived by the use of the inverse formula [af=1−(1−Cgf)2].
Where frequency data was not available at the level of DNA typing, correspondence to the serologically defined antigen frequencies was assumed. To obtain total potential supertype population coverage no linkage disequilibrium was assumed, and only alleles confirmed to belong to each of the supertypes were included (minimal estimates). Estimates of total potential coverage achieved by inter-loci combinations were made by adding to the A coverage the proportion of the non-A covered population that could be expected to be covered by the B alleles considered (e.g., total=A+B*(1−A)). Confirmed members of the A3-like supertype are A3, A11, A31, A*3301, and A*6801. Although the A3-like supertype may also include A34, A66, and A*7401, these alleles were not included in overall frequency calculations. Likewise, confirmed members of the A2-like supertype family are A*0201, A*0202, A*0203, A*0204, A*0205, A*0206, A*0207, A*6802, and A*6901. Finally, the B7-like supertype-confirmed alleles are: B7, B*3501-03, B51, B*5301, B*5401, B*5501-2, B*5601, B*6701, and B*7801 (potentially also B*1401, B*3504-06, B*4201, and B*5602).
Population coverage achieved by combining the A2-, A3- and B7-supertypes is approximately 86% in five major ethnic groups (see Table XXI). Coverage may be extended by including peptides bearing the A1 and A24 motifs. On average, A1 is present in 12% and A24 in 29% of the population across five different major ethnic groups (Caucasian, North American Black, Chinese, Japanese, and Hispanic). Together, these alleles are represented with an average frequency of 39% in these same ethnic populations. The total coverage across the major ethnicities when A1 and A24 are combined with the coverage of the A2-, A3- and B7-supertype alleles is >95%. An analogous approach can be used to estimate population coverage achieved with combinations of class II motif-bearing epitopes.
Summary of Candidate HLA Class I and Class II Epitopes
In summary, on the basis of the data presented in the above examples, candidate peptide epitopes derived from conserved regions of PF have been identified (Table XXXIII). These include eight HLA-A2 supermotif-bearing epitopes, eight HLA-A3 supermotif-bearing epitopes, and two HLA-B7 supermotif-bearing epitope, each capable of binding to multiple A2-, A3-, or B7-supertype molecules, and immunogenic in HLA transgenic mice or antigenic for human PBL. In addition four A1 motif-bearing and four A24 motif-bearing epitopes are also include candidate CTL epitopes for inclusion in a vaccine composition.
With these 26 CTL epitopes (as disclosed herein and from the art), average population coverage, (i.e., recognition of at least one PF epitope), is predicted to be, on average, greater than 95% (range of 90.6%-99.1%), in five major ethnic populations. The potential redundancy of coverage afforded by these epitopes can be estimated using the game theory Monte Carlo simulation analysis, which is known in the art (see e.g., Osborne, M. J. and Rubinstein, A. “A course in game theory” MIT Press, 1994). As shown in FIG. 1, it is estimated that 90% of the individuals in a population comprised of the Caucasian, North American Black, Japanese, Chinese, and Hispanic ethnic groups would recognize 8 or more of the candidate epitopes described herein.
A list of PF-derived HTL epitopes that would be preferred for use in the design of minigene constructs or other vaccine formulations is summarized in Table XXXIV. As shown, 13 different peptide-binding regions have been identified which bind multiple HLA-DR molecules or bind HLA-DR3.
It is estimated that each of 10 common DR molecules recognizing the DR supermotif, and DR3, are covered by a minimum of 2 epitopes. Correspondingly, the total estimated population coverage represented by this panel of epitopes is, on average, in excess of 94% in each of the 5 major ethnic populations (Table XXXV).
Example 8
Recognition of Generation of Endogenous Processed Antigens after Priming
This example determines that CTL induced by native or analogued peptide epitopes identified and selected as described in Examples 1-6 recognize endogenously synthesized, i.e., native antigens.
Effector cells isolated from transgenic mice that are immunized with peptide epitopes as in Example 3, for example HLA-A2 supermotif-bearing epitopes, are re-stimulated in vitro using peptide-coated stimulator cells. Six days later, effector cells are assayed for cytotoxicity and the cell lines that contain peptide-specific cytotoxic activity are further re-stimulated. An additional six days later, these cell lines are tested for cytotoxic activity on 51Cr labeled Jurkat-A2.1/Kb target cells in the absence or presence of peptide, and also tested on 51Cr labeled target cells bearing the endogenously synthesized antigen, i.e. cells that are stably transfected with PF expression vectors.
The result will demonstrate that CTL lines obtained from animals primed with peptide epitope recognize endogenously synthesized PF antigen. The choice of transgenic mouse model to be used for such an analysis depends upon the epitope(s) that is being evaluated. In addition to HLA-A*0201/Kb transgenic mice, several other transgenic mouse models including mice with human A11, which may also be used to evaluate A3 epitopes, and B7 alleles have been characterized and others (e.g., transgenic mice for HLA-A1 and A24) are being developed. HLA-DR1 and HLA-DR3 mouse models have also been developed, which may be used to evaluate HTL epitopes.
Example 9
Activity of CTL-HTL Conjugated Epitopes in Transgenic Mice
This example illustrates the induction of CTLs and HTLs in transgenic mice by use of a PF CTL/HTL peptide conjugate whereby the vaccine composition comprises peptides administered to a PF-infected patient or an individual at risk for malaria. The peptide composition can comprise multiple CTL and/or HTL epitopes. This analysis demonstrates enhanced immunogenicity that can be achieved by inclusion of one or more HTL epitopes in a vaccine composition. Such a peptide composition can comprise a lipidated HTL epitope conjugated to a preferred CTL epitope containing, for example, at least one CTL epitope selected from Tables VII-XVIII, or an analog of that epitope. The HTL epitope is, for example, selected from Table XIX or XX.
Lipopeptide preparation: Lipopeptides are prepared by coupling the appropriate fatty acid to the amino terminus of the resin bound peptide. A typical procedure is as follows: A dichloromethane solution of a four-fold excess of a pre-formed symmetrical anhydride of the appropriate fatty acid is added to the resin and the mixture is allowed to react for two hours. The resin is washed with dichloromethane and dried. The resin is then treated with trifluoroacetic acid in the presence of appropriate scavengers [e.g. 5% (v/v) water] for 60 minutes at 20° C. After evaporation of excess trifluoroacetic acid, the crude peptide is washed with diethyl ether, dissolved in methanol and precipitated by the addition of water. The peptide is collected by filtration and dried.
Immunization procedures: Immunization of transgenic mice is performed as described (Alexander et al., J. Immunol. 159:4753-4761, 1997). For example, A2/Kb mice, which are transgenic for the human HLA A2.1 allele and are useful for the assessment of the immunogenicity of HLA-A*0201 motif- or HLA-A2 supermotif-bearing epitopes, are primed subcutaneously (base of the tail) with 0.1 ml of peptide conjugate formulated in saline, or DMSO/saline. Seven days after priming, splenocytes obtained from these animals are restimulated with syngenic irradiated LPS-activated lymphoblasts coated with peptide.
Cell lines: Target cells for peptide-specific cytotoxicity assays are Jurkat cells transfected with the HLA-A2.1/Kb chimeric gene (e.g., Vitiello et al., J. Exp. Med. 173:1007, 1991)
In vitro CTL activation: One week after priming, spleen cells (30×106 cells/flask) are co-cultured at 37° C. with syngeneic, irradiated (3000 rads), peptide coated lymphoblasts (10×106 cells/flask) in 10 ml of culture medium/T25 flask. After six days, effector cells are harvested and assayed for cytotoxic activity.
Assay for cytotoxic activity: Target cells (1.0 to 1.5×106) are incubated at 37° C. in the presence of 200 μl of 51Cr. After 60 minutes, cells are washed three times and resuspended in R10 medium. Peptide is added where required at a concentration of 1 μg/ml. For the assay, 104 51Cr-labeled target cells are added to different concentrations of effector cells (final volume of 200 μl) in U-bottom 96-well plates. After a 6 hour incubation period at 37° C., a 0.1 ml aliquot of supernatant is removed from each well and radioactivity is determined in a Micromedic automatic gamma counter. The percent specific lysis is determined by the formula: percent specific release=100×(experimental release−spontaneous release)/(maximum release−spontaneous release). To facilitate comparison between separate CTL assays run under the same conditions, % 51Cr release data is expressed as lytic units/106 cells. One lytic unit is arbitrarily defined as the number of effector cells required to achieve 30% lysis of 10,000 target cells in a 6 hour 51Cr release assay. To obtain specific lytic units/106, the lytic units/106 obtained in the absence of peptide is subtracted from the lytic units/106 obtained in the presence of peptide. For example, if 30% 51Cr release is obtained at the effector (E): target (T) ratio of 50:1 (i.e., 5×105 effector cells for 10,000 targets) in the absence of peptide and 5:1 (i.e., 5×104 effector cells for 10,000 targets) in the presence of peptide, the specific lytic units would be: [(1/50,000)−(1/500,000)]×106=18 LU.
The results are analyzed to assess the magnitude of the CTL responses of animals injected with the immunogenic CTL/HTL conjugate vaccine preparation and are compared to the magnitude of the CTL response achieved using the CTL epitope as outlined in Example 3. Analyses similar to this may be performed to evaluate the immunogenicity of peptide conjugates containing multiple CTL epitopes and/or multiple HTL epitopes. In accordance with these procedures it is found that a CTL response is induced, and concomitantly that an HTL response is induced, upon administration of such compositions.
Example 10
Selection of CTL and HTL Epitopes for Inclusion in a PF-Specific Vaccine
This example illustrates the procedure for the selection of peptide epitopes for vaccine compositions of the invention. The peptides in the composition may be in the form of a nucleic acid sequence, either single or one or more sequences (i.e., minigene) that encodes peptide(s), or may be single and/or polyepitopic peptides.
The following principles are utilized when selecting an array of epitopes for inclusion in a vaccine composition. Each of the following principles are balanced in order to make the selection.
1.) Epitopes are selected which, upon administration, mimic immune responses that have been observed to be correlated with PF clearance. For HLA Class I this includes 3-4 epitopes that come from at least one antigen of PF. In other words, it has been observed that patients who spontaneously clear PF generate an immune response to at least 3 epitopes on at least one PF antigen. For HLA Class II a similar rationale is employed; again 3-4 epitopes are selected from at least one PF antigen.
2.) Epitopes are selected that have the requisite binding affinity established to be correlated with immunogenicity: for HLA Class I an IC50 of 500 nM or less, or for Class II an IC50 of 1000 nM or less.
3.) Sufficient supermotif bearing peptides, or a sufficient array of allele-specific motif bearing peptides, are selected to give broad population coverage. For example, epitopes are selected to provide at least 80% population coverage. A Monte Carlo analysis, a statistical evaluation known in the art and discussed herein, can be employed to assess breadth, or redundancy, of population coverage.
4.) When selecting epitopes for PF antigens it may be preferable to select native epitopes. Therefore, of particular relevance for infectious disease vaccines, are epitopes referred to as “nested epitopes.” Nested epitopes occur where at least two epitopes overlap in a given peptide sequence. A peptide comprising “transcendent nested epitopes” is a peptide that has both HLA class I and HLA class II epitopes in it.
When providing nested epitopes, a sequence that has the greatest number of epitopes per provided sequence is provided. A limitation on this principle is to avoid providing a peptide that is any longer than the amino terminus of the amino terminal epitope and the carboxyl terminus of the carboxyl terminal epitope in the peptide. When providing a longer peptide sequence, such as a sequence comprising nested epitopes, the sequence is screened in order to insure that it does not have pathological or other deleterious biological properties.
5.) When creating a minigene, as disclosed in greater detail in Example 11, an objective is to generate the smallest peptide possible that encompasses the epitopes of interest. The principles employed are similar, if not the same as those employed when selecting a peptide comprising nested epitopes. Additionally, however, upon determination of the nucleic acid sequence to be provided as a minigene, the peptide encoded thereby is analyzed to determine whether any “junctional epitopes” have been created. A junctional epitope is an actual binding epitope, as predicted, e.g., by motif analysis. Junctional epitopes are generally to be avoided because the recipient may generate an immune response to that epitope, which is not present in a native PF protein sequence. Of particular concern is a junctional epitope that is a “dominant epitope.” A dominant epitope may lead to such a zealous response that immune responses to other epitopes are diminished or suppressed.
Peptide epitopes for inclusion in vaccine compositions are, for example, selected from those listed in Tables XXXIII and XXXIV. A vaccine composition comprised of selected peptides, when administered, is safe, efficacious, and elicits an immune response similar in magnitude of an immune response that clears an acute PF infection.
Example 11
Construction of Minigene Multi-Epitope DNA Plasmids
This example describes the design and construction of a minigene expression plasmid. Minigene plasmids may, of course, contain various configurations of CTL and/or HTL epitopes or epitope analogs as described herein. Expression plasmids have been constructed and evaluated as described, for example, in U.S. Ser. No. 09/311,784 filed May 13, 1999, now U.S. Pat. No. 6,534,482, and in Ishioka et al., J. Immunol. 162:3915-3925, 1999.
A minigene expression plasmid may include multiple CTL and HTL peptide epitopes. In the present example, HLA-A2, -A3, -B7 supermotif-bearing peptide epitopes and HLA-A1 and -A24 motif-bearing peptide epitopes are used in conjunction with DR supermotif-bearing epitopes and/or DR3 epitopes. Preferred epitopes are identified, for example, in Tables XXXIII and XXXIV. HLA class I supermotif or motif-bearing peptide epitopes derived from multiple PF antigens, e.g., EXP-1, SSP2, CSP and LSA-1, are selected such that multiple supermotifs/motifs are represented to ensure broad population coverage. Similarly, HLA class II epitopes are selected from multiple PF antigens to provide broad population coverage, i.e. both HLA DR-1-4-7 supermotif-bearing epitopes and HLA DR-3 motif-bearing epitopes are selected for inclusion in the minigene construct. The selected CTL and HTL epitopes are then incorporated into a minigene for expression in an expression vector.
This example illustrates the methods to be used for construction of such a minigene-bearing expression plasmid. Other expression vectors that may be used for minigene compositions are available and known to those of skill in the art.
The minigene DNA plasmid contains a consensus Kozak sequence and a consensus murine kappa Ig-light chain signal sequence followed by CTL and/or HTL epitopes selected in accordance with principles disclosed herein. The sequence encodes an open reading frame fused to the Myc and His antibody epitope tag coded for by the pcDNA 3.1 Myc-His vector.
Overlapping oligonucleotides, for example eight oligonucleotides, averaging approximately 70 nucleotides in length with 15 nucleotide overlaps, are synthesized and HPLC-purified. The oligonucleotides encode the selected peptide epitopes as well as appropriate linker nucleotides, Kozak sequence, and signal sequence. The final multiepitope minigene is assembled by extending the overlapping oligonucleotides in three sets of reactions using PCR. A Perkin/Elmer 9600 PCR machine is used and a total of 30 cycles are performed using the following conditions: 95° C. for 15 sec, annealing temperature (5° below the lowest calculated Tm of each primer pair) for 30 sec, and 72° C. for 1 min.
For the first PCR reaction, 5 μg of each of two oligonucleotides are annealed and extended: Oligonucleotides 1+2, 3+4, 5+6, and 7+8 are combined in 100 μl reactions containing Pfu polymerase buffer (1×=10 mM KCL, 10 mM (NH4)2SO4, 20 mM Tris-chloride, pH 8.75, 2 mM MgSO4, 0.1% Triton X-100, 100 μg/ml BSA), 0.25 mM each dNTP, and 2.5 U of Pfu polymerase. The full-length dimer products are gel-purified, and two reactions containing the product of 1+2 and 3+4, and the product of 5+6 and 7+8 are mixed, annealed, and extended for 10 cycles. Half of the two reactions are then mixed, and 5 cycles of annealing and extension carried out before flanking primers are added to amplify the full length product for 25 additional cycles. The full-length product is gel-purified and cloned into pCR-blunt (Invitrogen) and individual clones are screened by sequencing.
Example 12
The Plasmid Construct and the Degree to which it Induces Immunogenicity
The degree to which the plasmid construct prepared using the methodology outlined in Example 11 is able to induce immunogenicity is evaluated through in vivo injections into mice and subsequent in vitro assessment of CTL and HTL activity, which are analysed using cytotoxicity and proliferation assays, respectively, as detailed e.g., in U.S. Ser. No. 09/311,784 filed May 13, 1999, now U.S. Pat. No. 6,534,482, and Alexander et al., Immunity 1:751-761, 1994. To assess the capacity of the pMin minigene construct to induce CTLs in vivo, HLA-A11/Kb transgenic mice, for example, are immunized intramuscularly with 100 μg of naked cDNA. As a means of comparing the level of CTLs induced by cDNA immunization, a control group of animals is also immunized with an actual peptide composition that comprises multiple epitopes synthesized as a single polypeptide as they would be encoded by the minigene.
Splenocytes from immunized animals are stimulated twice with each of the respective compositions (peptide epitopes encoded in the minigene or the polyepitopic peptide), then assayed for peptide-specific cytotoxic activity in a 51Cr release assay. The results indicate the magnitude of the CTL response directed against the A3-restricted epitope, thus indicating the in vivo immunogenicity of the minigene vaccine and polyepitopic vaccine. It is, therefore, found that the minigene elicits immune responses directed toward the HLA-A3 supermotif peptide epitopes as does the polyepitopic peptide vaccine. A similar analysis is also performed using other HLA-A2 and HLA-B7 transgenic mouse models to assess CTL induction by HLA-A2 and HLA-B7 motif or supermotif epitopes.
To assess the capacity of a class II epitope encoding minigene to induce HTLs in vivo, I-Ab restricted mice, for example, are immunized intramuscularly with 100 μg of plasmid DNA. As a means of comparing the level of HTLs induced by DNA immunization, a group of control animals is also immunized with an actual peptide composition emulsified in complete Freund's adjuvant.
CD4+ T cells, i.e. HTLs, are purified from splenocytes of immunized animals and stimulated with each of the respective compositions (peptides encoded in the minigene). The HTL response is measured using a 3H-thymidine incorporation proliferation assay, (see, e.g., Alexander et al., Immunity 1:751-761, 1994). the results indicate the magnitude of the HTL response, thus demonstrating the in vivo immunogenicity of the minigene.
DNA minigenes, constructed as described in Example 11, may also be evaluated as a vaccine in combination with a boosting agent using a prime boost protocol. The boosting agent may consist of recombinant protein (e.g., Barnett et al., Aids Res. and Human Reotroviruses 14, Supplement 3:S299-S309, 1998) or recombinant vaccinia, for example, expressing a minigene or DNA encoding the complete protein of interest (see, e.g., Hanke et al., Vaccine 16:439-445, 1998; Sedegah et al., Proc. Natl. Acad. Sci USA 95:7648-53, 1998; Hanke and McMichael, Immunol. Letters 66:177-181, 1999; and Robinson et al., Nature Med. 5:526-34, 1999).
For example, the efficacy of the DNA minigene may be evaluated in transgenic mice. In this example, A2.1/Kb transgenic mice are immunized IM with 100 μg of the DNA minigene encoding the immunogenic peptides. After an incubation period (ranging from 3-9 weeks), the mice are boosted IP with 107 pfu/mouse of a recombinant vaccinia virus expressing the same sequence encoded by the DNA minigene. Control mice are immunized with 100 μg of DNA or recombinant vaccinia without the minigene sequence, or with DNA encoding the minigene, but without the vaccinia boost. After an additional incubation period of two weeks, splenocytes from the mice are immediately assayed for peptide-specific activity in an ELISPOT assay. Additionally, splenocytes are stimulated in vitro with the A2-restricted peptide epitopes encoded in the minigene and recombinant vaccinia, then assayed for peptide-specific activity in an IFN-γ ELISA. It is found that the minigene utilized in a prime-boost mode elicits greater immune responses toward the HLA-A2 supermotif peptides than with DNA alone. Such an analysis is also performed using other HLA-A11 and HLA-B7 transgenic mouse models to assess CTL induction by HLA-A3 and HLA-B7 motif or supermotif epitopes.
Example 13
Peptide Composition for Prophylactic Uses
Vaccine compositions of the present invention are used to prevent PF infection in persons who are at risk for such infection. For example, a polyepitopic peptide epitope composition (or a nucleic acid comprising the same) containing multiple CTL and HTL epitopes such as those selected in Examples 9 and/or 10, which are also selected to target greater than 80% of the population, is administered to individuals at risk for PF infection. The composition is provided as a single lipidated polypeptide that encompasses multiple epitopes. The vaccine is administered in an aqueous carrier comprised of Freunds Incomplete Adjuvant. The dose of peptide for the initial immunization is from about 1 to about 50,000 μg, generally 100-5,000 μg, for a 70 kg patient. The initial administration of vaccine is followed by booster dosages at 4 weeks followed by evaluation of the magnitude of the immune response in the patient, by techniques that determine the presence of epitope-specific CTL populations in a PBMC sample. Additional booster doses are administered as required. The composition is found to be both safe and efficacious as a prophylaxis against PF infection.
Alternatively, the polyepitopic peptide composition can be administered as a nucleic acid in accordance with methodologies known in the art and disclosed herein.
Example 14
Polyepitopic Vaccine Compositions Derived from Native PF Sequences
A native PF polyprotein sequence is screened, preferably using computer algorithms defined for each class I and/or class II supermotif or motif, to identify “relatively short” regions of the polyprotein that comprise multiple epitopes and is preferably less in length than an entire native antigen. This relatively short sequence that contains multiple distinct, even overlapping, epitopes is selected and used to generate a minigene construct. The construct is engineered to express the peptide, which corresponds to the native protein sequence. The “relatively short” peptide is generally less than 250 amino acids in length, often less than 100 amino acids in length, preferably less than 75 amino acids in length, and more preferably less than 50 amino acids in length. The protein sequence of the vaccine composition is selected because it has maximal number of epitopes contained within the sequence, i.e., it has a high concentration of epitopes. As noted herein, epitope motifs may be nested or overlapping (i.e., frame shifted relative to one another). For example, with frame shifted overlapping epitopes, two 9-mer epitopes and one 10-mer epitope can be present in a 10 amino acid peptide. Such a vaccine composition is administered for therapeutic or prophylactic purposes.
The vaccine composition will preferably include, for example, three CTL epitopes and at least one HTL epitope from PF. This polyepitopic native sequence is administered either as a peptide or as a nucleic acid sequence which encodes the peptide. Alternatively, an analog can be made of this native sequence, whereby one or more of the epitopes comprise substitutions that alter the cross-reactivity and/or binding affinity properties of the polyepitopic peptide.
The embodiment of this example provides for the possibility that an as yet undiscovered aspect of immune system processing will apply to the native nested sequence and thereby facilitate the production of therapeutic or prophylactic immune response-inducing vaccine compositions. Additionally such an embodiment provides for the possibility of motif-bearing epitopes for an HLA makeup that is presently unknown. Furthermore, this embodiment (absent analogs) directs the immune response to multiple peptide sequences that are actually present in native PF antigens thus avoiding the need to evaluate any junctional epitopes. Lastly, the embodiment provides an economy of scale when producing nucleic acid vaccine compositions.
Related to this embodiment, computer programs can be derived in accordance with principles in the art, which identify in a target sequence, the greatest number of epitopes per sequence length.
Example 15
Polyepitopic Vaccine Compositions Directed To Multiple Diseases
The PF peptide epitopes of the present invention are used in conjunction with peptide epitopes from target antigens related to one or more other diseases, to create a vaccine composition that is useful for the prevention or treatment of PF as well as the one or more other disease(s). Examples of the other diseases include, but are not limited to, HIV, HCV, and HBV.
For example, a polyepitopic peptide composition comprising multiple CTL and HTL epitopes that target greater than 98% of the population may be created for administration to individuals at risk for both PF and HIV infection. The composition can be provided as a single polypeptide that incorporates the multiple epitopes from the various disease-associated sources, or can be administered as a composition comprising one or more discrete epitopes.
Example 16
Use of Peptides to Evaluate an Immune Response
Peptides of the invention may be used to analyze an immune response for the presence of specific CTL or HTL populations directed to PF. Such an analysis may be performed in a manner as that described by Ogg et al., Science 279:2103-2106, 1998. In the following example, peptides in accordance with the invention are used as a reagent for diagnostic or prognostic purposes, not as an immunogen.
In this example highly sensitive human leukocyte antigen tetrameric complexes (“tetramers”) are used for a cross-sectional analysis of, for example, PF HLA-A*0201-specific CTL frequencies from HLA A*0201-positive individuals at different stages of infection or following immunization using an PF peptide containing an A*0201 motif. Tetrameric complexes are synthesized as described (Musey et al., N. Engl. J. Med. 337:1267, 1997). Briefly, purified HLA heavy chain (A*0201 in this example) and β2-microglobulin are synthesized by means of a prokaryotic expression system. The heavy chain is modified by deletion of the transmembrane-cytosolic tail and COOH-terminal addition of a sequence containing a BirA enzymatic biotinylation site. The heavy chain, β2-microglobulin, and peptide are refolded by dilution. The 45-kD refolded product is isolated by fast protein liquid chromatography and then biotinylated by BirA in the presence of biotin (Sigma, St. Louis, Mo.), adenosine 5′triphosphate and magnesium. Streptavidin-phycoerythrin conjugate is added in a 1:4 molar ratio, and the tetrameric product is concentrated to 1 mg/ml. The resulting product is referred to as tetramer-phycoerythrin.
For the analysis of patient blood samples, approximately one million PBMCs are centrifuged at 300 g for 5 minutes and resuspended in 50 μl of cold phosphate-buffered saline. Tri-color analysis is performed with the tetramer-phycoerythrin, along with anti-CD8-Tricolor, and anti-CD38. The PBMCs are incubated with tetramer and antibodies on ice for 30 to 60 min and then washed twice before formaldehyde fixation. Gates are applied to contain >99.98% of control samples. Controls for the tetramers include both A*0201-negative individuals and A*0201-positive uninfected donors. The percentage of cells stained with the tetramer is then determined by flow cytometry. The results indicate the number of cells in the PBMC sample that contain epitope-restricted CTLs, thereby readily indicating the extent of immune response to the PF epitope, and thus the stage of infection with PF, the status of exposure to PF, or exposure to a vaccine that elicits a protective or therapeutic response.
Example 17
Use of Peptide Epitopes to Evaluate Recall Responses
The peptide epitopes of the invention are used as reagents to evaluate T cell responses, such as acute or recall responses, in patients. Such an analysis may be performed on patients who have recovered from infection, who are chronically infected with PF, or who have been vaccinated with a PF vaccine.
For example, the class I restricted CTL response of persons who have been vaccinated may be analyzed. The vaccine may be any PF vaccine. PBMC are collected from vaccinated individuals and HLA typed. Appropriate peptide epitopes of the invention that are preferably highly conserved and, optimally, bear supermotifs to provide cross-reactivity with multiple HLA supertype family members, are then used for analysis of samples derived from individuals who bear that HLA type.
PBMC from vaccinated individuals are separated on Ficoll-Histopaque density gradients (Sigma Chemical Co., St. Louis, Mo.), washed three times in HBSS (GIBCO Laboratories), resuspended in RPMI-1640 (GIBCO Laboratories) supplemented with L-glutamine (2 mM), penicillin (50 U/ml), streptomycin (50 μg/ml), and Hepes (10 mM) containing 10% heat-inactivated human AB serum (complete RPMI) and plated using microculture formats. A synthetic peptide comprising an epitope of the invention is added at 10 μg/ml to each well and HBV core 128-140 epitope is added at 1 μg/ml to each well as a source of T cell help during the first week of stimulation.
In the microculture format, 4×105 PBMC are stimulated with peptide in 8 replicate cultures in 96-well round bottom plate in 100 μl/well of complete RPMI. On days 3 and 10, 100 ml of complete RPMI and 20 U/ml final concentration of rIL-2 are added to each well. On day 7 the cultures are transferred into a 96-well flat-bottom plate and restimulated with peptide, rIL-2 and 105 irradiated (3,000 rad) autologous feeder cells. The cultures are tested for cytotoxic activity on day 14. A positive CTL response requires two or more of the eight replicate cultures to display greater than 10% specific 51Cr release, based on comparison with uninfected control subjects as previously described (Rehermann, et al., Nature Med. 2:1104, 1108, 1996; Rehermann et al., J. Clin. Invest. 97:1655-1665, 1996; and Rehermann et al. J. Clin. Invest. 98:1432-1440, 1996).
Target cell lines are autologous and allogeneic EBV-transformed B-LCL that are either purchased from the American Society for Histocompatibility and Immunogenetics (ASHI, Boston, Mass.) or established from the pool of patients as described (Guilhot, et al. J. Virol. 66:2670-2678, 1992).
Cytotoxicity assays are performed in the following manner. Target cells consist of either allogeneic HLA-matched or autologous EBV-transformed B lymphoblastoid cell line that are incubated overnight with the synthetic peptide epitope of the invention at 10 μM, and labeled with 100 μCi of 51Cr (Amersham Corp., Arlington Heights, Ill.) for 1 hour after which they are washed four times with HBSS.
Cytolytic activity is determined in a standard 4-h, split well 51Cr release assay using U-bottomed 96 well plates containing 3,000 targets/well. Stimulated PBMC are tested at effector/target (E/T) ratios of 20-50:1 on day 14. Percent cytotoxicity is determined from the formula: 100×[(experimental release-spontaneous release)/maximum release-spontaneous release)]. Maximum release is determined by lysis of targets by detergent (2% Triton X-100; Sigma Chemical Co., St. Louis, Mo.). Spontaneous release is <25% of maximum release for all experiments.
The results of such an analysis indicate the extent to which HLA-restricted CTL populations have been stimulated by previous exposure to PF or a PF vaccine.
The class II restricted HTL responses may also be analyzed. Purified PBMC are cultured in a 96-well flat bottom plate at a density of 1.5×105 cells/well and are stimulated with 10 μg/ml synthetic peptide, whole antigen, or PHA. Cells are routinely plated in replicates of 4-6 wells for each condition. After seven days of culture, the medium is removed and replaced with fresh medium containing 10 U/ml IL-2. Two days later, 1 μCi 3H-thymidine is added to each well and incubation is continued for an additional 18 hours. Cellular DNA is then harvested on glass fiber mats and analyzed for 3H-thymidine incorporation. Antigen-specific T cell proliferation is calculated as the ratio of 3H-thymidine incorporation in the presence of antigen divided by the 3H-thymidine incorporation in the absence of antigen.
Example 18
Induction of CTL Responses Using a Prime Boost Protocol
A prime boost protocol similar in its underlying principle to that used to evaluated the efficacy of a DNA vaccine in transgenic mice, which was described in Example 12, may also be used for the administration of the vaccine to humans. Such a vaccine regimen is includes an initial administration of, for example, naked DNA followed by a boost using recombinant virus encoding the vaccine, or recombinant protein/polypeptide or a peptides mixture administered in an adjuvant.
For example, the initial immunization may be performed using an expression vector, such as that constructed in Example 11, in the form of naked DNA administered IM (or SC or ID) in the amounts of 0.5-5, typically 100 g, at multiple sites. The DNA (0.1 to 1000 mg) can also be administered using a gene gun. Following an incubation period of 3-4 weeks, a booster dose is then administered. The booster can be recombinant fowlpox virus administered at a dose of 5-107 to 5×109 pfu. Alternative recombinant virus, such as MVA, canarypox, adenovirus, and adeno-associated viruses can also be used for the booster, or the polyepitopic protein or a mixture of the peptides can be administered. For evaluation of vaccine efficacy, patient blood samples will be obtained before immunization as well as at intervals following administration of the initial vaccine and booster doses of the vaccine. Peripheral blood mononuclear cells are isolated from fresh heparinized blood by Ficoll-Hypaque density gradient centrifugation, aliquoted in freezing media and stored frozen. Samples are assayed for CTL and HTL activity.
Analysis of the results will indicate that a magnitude of sufficient response to achieve protective immunity against Pf is generated.
Example 19
Induction of Specific CTL Response in Humans
A human clinical trial to evaluate an immunogenic composition comprising CTL and HTL epitopes of the invention is set up as an IND Phase I, dose escalation study and carried out as a randomized, double-blind, placebo-controlled trial in patients are not infected with Pf. Such a trial is designed, for example, as follows:
A total of about 27 subjects are enrolled and divided into 3 groups:
Group I: 3 subjects are injected with placebo and 6 subjects are injected with 5 μg of peptide composition;
Group II: 3 subjects are injected with placebo and 6 subjects are injected with 50 μg peptide composition;
Group III: 3 subjects are injected with placebo and 6 subjects are injected with 500 μg of peptide composition.
After 4 weeks following the first injection, all subjects receive a booster inoculation at the same dosage.
The endpoints measured in this study relate to the safety and tolerability of the peptide composition as well as its immunogenicity. Cellular immune responses to the peptide composition are an index of the intrinsic activity of this the peptide composition, and can therefore be viewed as a measure of biological efficacy. The following summarize the clinical and laboratory data that relate to safety and efficacy endpoints.
Safety: The incidence of adverse events is monitored in the placebo and drug treatment group and assessed in terms of degree and reversibility.
Evaluation of Vaccine Efficacy: For evaluation of vaccine efficacy, subjects are bled before and after injection. Peripheral blood mononuclear cells are isolated from fresh heparinized blood by Ficoll-Hypaque density gradient centrifugation, aliquoted in freezing media and stored frozen. Samples are assayed for CTL and HTL activity.
The vaccine is found to be both safe and efficacious.
A prophylactic field trial can also be conducted to evaluate a vaccine composition of the invention. In such a trial, issues of patient compliance are also considered in the determination of vaccine efficacy.
Example 20
Administration of Vaccine Compositions Using Dendritic Cells
Vaccines comprising peptide epitopes of the invention may be administered using dendritic cells. In this example, the immunogenic peptide epitopes are used to elicit a CTL and/or HTL response ex vivo.
Ex vivo CTL or HTL responses to a particular antigen (infectious or tumor-associated antigen) are induced by incubating in tissue culture the patient's, or genetically compatible, CTL or HTL precursor cells together with a source of antigen-presenting cells (APC), such as dendritic cells, and the appropriate immunogenic peptides. After an appropriate incubation time (typically about 14 weeks), in which the precursor cells are activated and expanded into effector cells, the cells are infused back into the patient, where they will destroy (CTL) or facilitate destruction (HTL) of their specific target cells, i.e., PF-infected cells.
Example 21
Alternative Method of Identifying Motif-Bearing Peptides
Another way of identifying motif-bearing peptides is to elute them from cells bearing defined MHC molecules. For example, EBV transformed B cell lines used for tissue typing, have been extensively characterized to determine which HLA molecules they express. In certain cases these cells express only a single type of HLA molecule. These cells can then be infected with a pathogenic organism, e.g., PF, HIV, etc. or transfected with nucleic acids that express the antigen of interest. Thereafter, peptides produced by endogenous antigen processing of peptides produced consequent to infection (or as a result of transfection) will bind to HLA molecules within the cell and be transported and displayed on the cell surface.
The peptides are then eluted from the HLA molecules by exposure to mild acid conditions and their amino acid sequence determined, e.g., by mass spectral analysis (e.g., Kubo et al., J. Immunol. 152:3913, 1994). Because, as disclosed herein, the majority of peptides that bind a particular HLA molecule are motif-bearing, this is an alternative modality for obtaining the motif-bearing peptides correlated with the particular HLA molecule expressed on the cell.
Alternatively, cell lines that do not express any endogenous HLA molecules can be transfected with an expression construct encoding a single HLA allele. These cells may then be used as described, i.e., they may be infected with a pathogenic organism or transfected with nucleic acid encoding an antigen of interest to isolate peptides corresponding to the pathogen or antigen of interest that have been presented on the cell surface. Peptides obtained from such an analysis will bear motif(s) that correspond to binding to the single HLA allele that is expressed in the cell.
As appreciated by one in the art, one can perform a similar analysis on a cell bearing more than one HLA allele and subsequently determine peptides specific for each HLA allele expressed. Moreover, one of skill would also recognize that means other than infection or transfection, such as loading with a protein antigen, can be used to provide a source of antigen to the cell.
The above examples are provided to illustrate the invention but not to limit its scope. For example, the human terminology for the Major Histocompatibility Complex, namely HLA, is used throughout this document. It is to be appreciated that these principles can be extended to other species as well. Thus, other variants of the invention will be readily apparent to one of ordinary skill in the art and are encompassed by the appended claims. All publications, patents, and patent application cited herein are hereby incorporated by reference for all purposes.










TABLE I








POSITION



POSITION 2
POSITION 3
C Terminus 



(Primary Anchor)
(Primary Anchor)
(Primary Anchor)







SUPER-





MOTIFS





A1
TILVMS

FWY


A2
LIVMATQ

IVMATL


A3
VSMATLI

RK


A24
YFWIVLMT

FIYWLM


B7
P

VILFMWYA


B27
RHK

FYLWMIVA


B44
ED

FWYLIMVA


B58
ATS

FWYLIVMA


B62
QLIVMP

FWYMIVLA


MOTIFS





A1
TSM

Y


A1

DEAS
Y


A2.1
LMVQIAT

VLIMAT


A3
LMVISATFCGD

KYRHFA


A11
VTMLISAGNCDF

KRYH


A24
YFWM

FLIW


A*3101
MVTALIS

RK


A*3301
MVALFIST

RK


A*6801
AVTMSLI

RK


B*0702
P

LMFWYAIV


B*3501
P

LMFWYIVA


B51
P

LIVFWYAM


B*5301
P

IMFWYALV


B*5401
P

ATIVLMFWY





Bolded residues are preferred, italicized residues are less preferred: A peptide is considered motif-bearing if it has primary anchors at each primary anchor position for a motif or superrnotif as specified in the above table.
















TABLE Ia








POSITION



POSITION 2
POSITION 3 
C Terminus 



(Primary Anchor)
(Primary Anchor)
(Primary Anchor)







SUPER-





MOTIFS





A1
TILVMS

FWY


A2
VQAT

VLIMAT


A3
VSMATLI

RK


A24
YFWIVLMT

FIYWLM


B7
P

VILFMWYA


B27
RHK

FYLWMIVA


B58
ATS

FWYLIVMA


B62
QLIVMP

FWYMIVLA


MOTIFS





A1
TSM

Y


A1

DEAS
Y


A2.1
VQAT*

VLIMAT


A3.2
LMVISATFCGD

KYRHFA


A11
VTMLISAGNCDF

KRHY


A24
YFW

FLIW





*If 2 is V, or Q, the C-term is not L


Bolded residues are preferred, italicized residues are less preferred: A peptide is considered motif-bearingif it has primary anchors at each primary anchor position for a motif or supermotifas specified in the above table.















TABLE II









POSITION



















1
2
3
4
5
6
7
8
C-terminus



















SUPERMOTIFS


























A1


1° Anchor






1° Anchor





TILVMS






FWY


A2


1° Anchor






1° Anchor





LIVM






LIVMAT





ATQ









A3
preferred

1° Anchor
YFW (4/5)


YFW (3/5)
YFW (4/5)
P (4/5)
1° Anchor





VSMA






RK





TLI










deleterious
DE (3/5); 

DE (4/5)










P (5/5)










A24


1° Anchor






1° Anchor





YFWIV






FIYWLM





LMT









B7
preferred
FWY (5/5)
1° Anchor
FWY (4/5)




FWY (3/5)
1° Anchor




LIVM (3/5)
P






VILFMWYA



deleterious
DE (3/5); 




/5)
QN (4/5)
DE (4/5)





P (5/5);












G (4/5); 












A (3/5);












QN (3/5)










B27


1° Anchor






1° Anchor





RHK






FYLWMIVA


B44


1° Anchor






1° Anchor





ED






FWYLIMVA


B58


1° Anchor






1° Anchor





ATS






FWYLIVMA


B62


1° Anchor






1° Anchor





QLIVMP






FWYMIVLA
















MOTIFS


























A1
preferred
GFYW
1° Anchor
DEA
YFW

P
DEQN
YFW
1° Anchor


9-mer


STM






Y



deleterious
DE

RHKLIV
A
G
A









MP








A1
preferred
GRHK
ASTCLIV
1° Anchor
GSTC

ASTC
LIVM
DE
1° Anchor


9-mer


M
DEAS





Y



deleterious
A
RHKDEP

DE
PQN
RHK
PG
GP






YFW














POSITION




























9













or C-
C-




1
2
3
4
5
6
7
8
terminus
terminus





A1
preferred
YFW
1° Anchor
DEAQN
A
YFWQN

PASTC
GDE
P
1° Anchor


10-mer


STM







Y



deleterious
GP

RHKGLIV
DE
RHK
QNA
RHKYFW
RHK
A







M









A1
preferred
YEW
STCLIVM
1° Anchor
A
YFW

PG
G
YFW
1° Anchor


10-mer



DEAS






Y



deleterious
RHK
RHKDEP


P
G

PRHK
QN






YFW










A2.1
preferred
YFW
1° Anchor
YFW
STC
YFW

A
P
1° Anchor



9-mer


LMIVQ






VLIMAT






AT











deleterious
DEP

DERKH


RKH
DERKH





A2.1
preferred
AYFW
1° Anchor
LVIM
G

G

FYWL

1° Anchor


10-mer


LMIVQ





VIM

VLIMAT





AT











deleterious
DEP

DE
RKHA
P

RKH
DERK
RKH












H




A3
preferred
RHK
1° Anchor
YFW
PRHKY
A
YFW

P
1° Anchor






LMVISA

FW




KYRHFA






TFCGD











deleterious
DEP

DE









A11
preferred
A
1° Anchor
YFW
YFW
A
YFW
YFW
P
1° Anchor






VTLMIS






KRYH






AGNCDF











deleterious
DEP





A
G




A24
preferred
YFWR
1° Anchor

STC


YFW
YFW
l° Anchor



9-mer

HK
YFWM






FLIW




deleterious
DEG

DE
G
QNP
DERHK
G
AQN




A24
preferred

1° Anchor

P
YFWP

P


1° Anchor


10-mer


YFWM







FLIW



deleterious


GDE
QN
RHK
DE
A
QN
DEA



A3101
preferred
RHK
1° Anchor
YFW
P

YFW
YFW
AP
1° Anchor






MVTAL






RK






IS











deleterious
DEP

DE

ADE
DE
DE
DE




A3301
preferred

1° Anchor
YFW



AYFW

1° Anchor






MVALF






RK






IST











deleterious
GP

DE









A6801
preferred
YFWSTC
1° Anchor


YFWLI

YFW
P
1° Anchor






AVTMS


VM



RK






LI











deleterious
GP

DEG

RHK


A




B0702
preferred
RHKFWY
1° Anchor
RHK

RHK
RHK
RHK
PA
1° Anchor






P






LMFWY




deleterious
DEQNP

DEP
DE
DE
GDE
QN
DE
AIV



B3501
preferred
FWYLIVM
1° Anchor
FWY



FWY

1° Anchor






P






LMFWY




deleterious
AGP



G
G


IVA



B51
preferred
LIVMFWY
1° Anchor
FWY
STC
FWY

G
FWY
1° Anchor






P






LIVFW




deleterious
AGPDER



DE
G
DEQN
GDE
YAM





HKSTC











B5301
preferred
LIVMF
1° Anchor
FWY
STC
FWY

LIVMFWY
FWY
1° Anchor





WY
P






IMFWY




deleterious
AGPQN




G
RHKQN
DE
ALV



B5401
preferred
FWY
1° Anchor
FWYLI

LIVM

ALIVM
FWYAP
1° Anchor






P
VM





ATIVLM













FWY




deleterious
GPQNDE

GDESTC

RHKDE
DE
QNDGE
DE





Italicized residues indicate less preferred or “tolerated” residues.


The information in Table II is specific for 9-mers unless otherwise specified.















TABLE III









POSITION

















SEQ ID

1°










NO:
MOTIFS
anchor 1
2
3
4
5
1° anchor 6
7
8
9






















DR4
preferred
FMYLIVW
M
T

I
VSTCPALIM
MH

MH




deleterious



W


R

WDE



DR1
preferred
MFLIVWY


PAMQ

VMATSPLIC
M

AVM




deleterious

C
CH
FD
CWD

GDE
D



3841
DR7
preferred
MFLIVWY
M
W
A

IVMSACTPL
M

IV


3842

deleterious

C

G


GRD
N
G



DR
Supermotif
MFLIVWY




VMSTACPLI



















DR3 MOTIFS
1° anchor 1
2
3
1° anchor 4
5
1° anchor 6







motif a










preferred
LIVMFY


D






motif b










preferred
LIVMFAY


DNQEST

KRH





Italicized residues indicate less preferred or “tolerated” residues.













TABLE IV







HLA Class I Standard Peptide Binding Affinity.














SEQ
STANDARD



STANDARD

ID
BINDING


ALLELE
PEPTIDE
SEQUENCE
NO:
AFFINITY (nM)














A*0101
944.02
YLEPAIAKY
3575
25


A*0201
941.01
FLPSDYFPSV
3576 
5.0


A*0202 
941.01
FLPSDYFPSV
3577 
4.3


A*0203
941.01
FLPSDYFPSV
3578 
10


A*0205
941.01
FLPSDYFPSV
3579 
4.3


A*0206
941.01
FLPSDYFPSV
3580 
3.7


A*0207
941.01
FLPSDYFPSV
3581 
23


A*6802
1072.34
YVIKVSARV
3582 
8.0


A*0301
941.12
KVFPYALINK
3583 
11


A*1101
940.06
AVDLYHFLK
3584 
6.0


A*3101
941.12
KVFPYALINK
3585 
18


A*3301
1083.02
STLPETYVVRR
3586 
29


A*6801
941.12
KVFPYALINK
3587 
8.0


A*2402
979.02
AYIDNYNKF
3588 
12


B*0702
1075.23
APRTLVYLL
3589 
5.5


B*3501
1021.05
FPFKYAAAF
3590 
7.2


B51
1021.05
FPFKYAAAF
3591 
5.5


B*5301
1021.05
FPFKYAAAF
3592
9.3


B*5401
1021.05
FPFKYAAAF
3593 
10
















TABLE V







HLA Class II Standard Peptide Binding Affinity.

















Binding




Standard


Affinity


Allele
Nomenclature 
Peptide
SEQ ID
Sequence
(nM)















DRB1*0101
DR1
515.01
3594
PKYVKQNTLKLAT
5.0


DRB1*0301
DR3
829.02
3595
YKTIAFDEEARR
300


DRB1*0401
DR4w4
515.01
3596
PKYVKQNTLKLAT
45


DRB1*0404
DR4w14
717.01
3597
YARFQSQTTLKQKT
50


DRB1*0405
DR4w15
717.01
3598
YARFQSQTTLKQKT
38


DRB1*0701
DR7
553.01
3599
QYIKANSKFIGITE
25


DRB1*0802
DR8w2
553.01
3600
QYIKANSKFIGITE
49


DRB1*0803
DR8w3
553.01
3601
QYIKANSKFIGITE
1600


DRB1*0901
DR9
553.01
3602
QYIKANSKFIGITE
75


DRB1*1101
DR5w11
553.01
3603
QYIKANSKFIGITE
20


DRB1*1201
DR5w12
1200.05
3604
EALIHQLKINPYVLS
298


DRB1*1302
DR6w19
650.22
3605
QYIKANAKFIGITE
3.5


DRB1*1501
DR2w2β1
507.02
3606
GRTQDENPVVHFFK
9.1






NIVTPRTPPP



DRB3*0101
DR52a
511
3607
NGQIGNDPNRDIL
470


DRB4*0101
DRw53
717.01
3608
YARFQSQTTLKQKT
58


DRB5*0101
DR2w2β2
553.01
3609
QYIKANSKFIGITE
20





The “Nomenclature” column lists the allelic designations used in Tables XIX and XX.













TABLE VI







Allelle-specific HLA-supertype members









HLA-




supertype
Verifieda
Predictedb





A1
A*0101, A*2501, A*2601, A*2602, A*3201
A*0102, A*2604, A*3601, A*4301, A*8001


A2
A*0201, A*0202, A*0203, A*0204, A*0205, 
A*0208, A*0210, A*0211, A*0212, A*0213



A*0206, A*0207, A*0209, A*0214, A*6802, 




A*6901



A3
A*0301, A*1101, A*3101, A*3301, A*6801
A*0302, A*1102, A*2603, A*3302, A*3303,




A*3401, A*3402, A*6601, A*6602, A*7401


A24
A*2301, A*2402, A*3001
A*2403, A*2404, A*3002, A*3003


B7
B*0702, B*0703, B*0704, B*0705, B*1508, 
B*1511, B*4201, B*5901



B*3501, B*3502, B*3503, B*3503, B*3504, 




B*3505, B*3506, B*3507, B*3508, B*5101, 




B*5102, B*5103, B*5104, B*5105, B*5301, 




B*5401, B*5501, B*5502, B*5601, B*5602, 




B*6701, B*7801



B27
B*1401, B*1402, B*1509, B*2702, B*2703, 
B*2701, B*2707, B*2708, B*3802, B*3903, 



B*2704, B*2705, B*2706, B*3801, B*3901, 
B*3904, B*3905, B*4801, 8*4802, B*1510, 



B*3902, B*7301
B*1518, B*1503


B44
B*1801, B*1802, B*3701, B*4402, B*4403, 
B*4101, B*4501, B*4701, B*4901, B*5001



B*4404, B*4001, B*4002, B*4006



B58
B*5701, B*5702, B*5801, B*5802, B*1516, 




B*1517



B62
B*1501, B*1502, B*1513, B*5201
B*1301, B*1302, B*1504, B*1505, B*1506, 




B*1507, B*1515, B*1520, B*1521, B*1512, 




B*1514, B*1510





aVerified alleles include alleles whose specificity has been determined by pool sequencing analysis, peptide binding assays, or by analysis of the sequences of CTL epitopes.


bPredicted alleles are alleles whose specificity is predicted on the basis of B and F pocket structure to overlap with the supertype specificity.













TABLE VII







Malaria A01 Super Motif Peptides With Binding Data

















No. of
Sequence
Conservancy




Protein
Sequence
Position
Amino Acids
Frequency
(%)
A*0101
Seq. Id.

















CSP
AILSVSSF
6
8
19
100

1


CSP
AILSVSSFLF
6
10
19
100

2


CSP
ALFQEYQCY
18
9
19
100

3


CSP
EMNYYGKQENW
52
11
19
100

4


CSP
FLFVEALF
13
8
19
100

5


CSP
FLFVEALFQEY
13
11
19
100

6


CSP
FVFALFQEY
15
9
19
100
3.4000
7


CSP
GLIMVLSF
421
8
19
100

8


CSP
GLIMVLSFLF
421
10
19
100

9


CSP
ILSVSSFLF
7
9
19
100

10


CSP
IMVLSFLF
423
8
19
100

11


CSP
KIQNSLSTEW
357
10
15
 79

12


CSP
KLAILSVSSF
4
10
19
100

13


CSP
KMEKCSSVF
405
9
19
100

14


CSP
LIMVLSFLF
422
9
19
100

15


CSP
LSVSSFLF
8
8
19
100

16


CSP
NLYNELEMNY
46
10
19
100

17


CSP
NLYNELEMNYY
46
11
19
100

18


CSP
NIRVLNELNY
31
10
19
100
0.0096
19


CSP
PSDKHIEQY
346
9
15
 79

20


CSP
RVLNELNY
33
8
19
100

21


CSP
SIGLIMVLSF
419
10
19
100

22


CSP
SSFLFVEALF
11
10
19
100

23


CSP
SSIGLIMVLSF
418
11
19
100

24


CSP
VSSFLFVEALF
10
11
19
100

25


EXP
EVNKRKSKY
66
9
1
100

26


EXP
FLALFFIIF
8
9
1
100

27


EXP
ILSVFFLALF
3
10
1
100

28


EXP
ILSVFFLALFF
3
11
1
100

29


EXP
KILSVFFLALF
2
11
1
100

30


EXP
LLGGVGLVLY
92
10
1
100

31


EXP
LSVFFLALF
4
9
1
100

32


EXP
LSVFFLALFF
4
10
1
100

33


EXP
LVEVNKRKSKY
64
11
1
100

34


EXP
NTEKGRHPF
102
9
1
100

35


EXP
SVFFLALF
5
8
1
100

36


EXP
SYFFLALFF
5
9
1
100

37


EXP
VLLGGVGLVLY
91
11
1
100

38


LSA
DLDEFKPIVQY
1781
11
1
100

39


LSA
DVLAEDLY
1646
8
1
100

40


LSA
DVNDFQISKY
1751
10
1
100

41


LSA
ELPSENERGY
1662
10
1
100

42


LSA
ELPSENERGYY
1662
10
1
100

43


LSA
EISEDITKY
1897
9
1
100

44


LSA
ELSEDITKYF
1897
10
1
100

45


LSA
ETVNISDVNDF
1745
11
1
100

46


LSA
FIKSLFHIF
1877
9
1
100

47


LSA
FILVNLLIF
11
9
1
100

48


LSA
HILYISFY
3
8
1
100

49


LSA
HILYISFYF
3
9
1
100

50


LSA
HVLSHNSY
59
8
1
100

51


LSA
IINDDDDKKKY
127
11
1
100

52


LSA
ILVNLLIF
12
8
1
100

53


LSA
ILYISFYF
4
8
1
100

54


LSA
KIKKGKKY
1834
8
1
100

55


LSA
KSLYDEHIKKY
1854
11
1
100

56


LSA
KTKNNENNKF
68
10
1
100

57


LSA
KTKNNENNKFF
68
11
1
100

58


LSA
LSEDITKY
1898
8
1
100

59


LSA
LSEDITKYF
1898
9
1
100

60


LSA
NISDVNDF
1748
8
1
100

61


LSA
NLGVSENIF
103
9
1
100

62


LSA
NVKNVSQTNF
88
10
1
100

63


LSA
PIVQYDNF
1787
8
1
100

64


LSA
PSENERGY
1664
8
1
100

65


LSA
PSENERGYY
1664
9
1
100
0.0790
66


LSA
QVNKEKEKF
1869
9
1
100

67


LSA
SLYDEHIKKY
1855
10
1
100

68


LSA
TVNISDVNDF
1746
10
1
100

69


SSP2
ALLACAGLAY
509
10
10
100

70


SSP2
ASCGVWDEW
242
9
10
100

71


SSP2
ATPYAGEPAPF
526
11
8
 80

72


SSP2
CSGSIRRHNW
55
10
10
100

73


SSP2
DLDEPEQF
546
8
10
100

74


SSP2
EVCNDEVDLY
41
10
8
 80

75


SSP2
EVEKTASCGVW
237
11
10
100

76


SSP2
FLIFFDLF
14
8
10
100

77


SSP2
FVVPGAATPY
520
10
8
 80

78


SSP2
GIGQGINVAF
189
10
10
100

79


SSP2
GINVAFNRF
193
9
10
100

80


SSP2
GSIRRHNW
57
8
10
100

81


SSP2
IVFLIFFDLF
12
10
10
100

82


SSP2
KTASCGVW
240
8
10
100

83


SSP2
KTASCGVWDEW
240
11
10
100

84


SSP2
LLACAGLAY
510
9
10
100

85


SSP2
LLACAGLAYKF
510
11
10
100

86


SSP2
LLSTNLPY
121
8
9
 90

87


SSP2
LVIVFLIF
10
8
10
100

88


SSP2
LVIVFLIFF
10
9
10
100

89


SSP2
NIVDEIKY
31
8
10
100

90


SSP2
NLYADSAW
213
8
10
100

91


SSP2
NVKNVIGPF
222
9
10
100

92


SSP2
NVKYLVIVF
6
9
10
100

93


SSP2
PSDGKCNLY
207
9
10
100
0.5400
94


SSP2
RLPEENEW
554
8
10
100

95


SSP2
SLLSTNLPY
120
9
9
 90

96


SSP2
VIVFLIFF
11
8
10
100

97


SSP2
VI VFLIFFDLF
11
11
10
100

98


SSP2
VVPGAATPY
521
9
8
 80

99


SSP2
YLVIVFLIF
9
9
10
100

100


SSP2
YLVIVFLIFF
9
10
10
100

101
















TABLE VIII







Malaria A02 Super Motif Peptides With Binding Information





















No. of
Sequence
Conservancy








Protein
Sequence
Position
Amino Acids
Frequency
(%)
A*0201
A*0202
A*0203
A*0206
A*6802
Seq. Id





















CSP
HIEQYLKKI
350
9
15
79





102


CSP
KIQNSLST
361
8
15
79





103


CSP
YLKKIQNSL
358
9
15
79





104


CSP
YLKKIQNSLST
358
11
15
79





105


CSP
NANANNAV
335
8
16
84





106


CSP
NVDENANANNA
331
11
16
84





107


CSP
ELNYDNAGI
37
9
18
95





108


CSP
ELNYDNAGINL
37
11
18
95





109


CSP
GINLYNEL
44
8
18
95





110


CSP
GINLYNELEM
44
10
18
95





111


CSP
NAGINLYNEL
42
10
18
95





112


CSP
SLSTEWSPCSV
365
11
18
95





113


CSP
AILSVSSFL
6
9
19
100
0.0220




114


CSP
AILSVSSFLFV
6
11
19
100





115


CSP
DIEKKICKM
402
9
19
100





116


CSP
GIQVRIKPGSA
380
11
19
100





117


CSP
GLIMVLSFL
425
9
19
100
0.0630




118


CSP
GLIMVLSFLFL
425
11
19
100





119


CSP
ILSVSSFL
7
8
19
100





120


CSP
ILSVSSFLFV
7
10
19
100
0.0300




121


CSP
IMVLSFLFL
427
9
19
100
0.0007




122


CSP
IQVRIKPGSA
381
10
19
100





123


CSP
KICKMEKCSSV
406
11
19
100





124


CSP
KLAILSVSSFL
4
11
19
100





125


CSP
KLRKPKHKKL
104
10
19
100
0.0001




126


CSP
KMEKCSSV
409
8
19
100





127


CSP
KMEKCSSVFNV
409
11
19
100





128


CSP
KQENWYSL
58
8
19
100





129


CSP
LAILSVSSFL
5
10
19
100





130


CSP
LIMVLSFL
426
8
19
100





131


CSP
LIMVLSFLFL
426
10
19
100
0.0019




132


CSP
MMRKLAIL
1
8
19
100





133


CSP
MMRKLAILSV
1
10
19
100
0.0012




134


CSP
MVLSFLFL
428
8
19
100





135


CSP
NANPNANPNA
300
10
19
100





136


CSP
NANPNVDPNA
196
10
19
100





137


CSP
NLYNELEM
46
8
19
100





138


CSP
NMPNDPNRNV
323
10
19
100
0.0007




139


CSP
NQGNGQGHNM
315
10
19
100





140


CSP
NTRVLNEL
31
8
19
100





141


CSP
NVDENANA
331
8
19
100





142


CSP
NVDPNANPNA
200
10
19
100





143


CSP
NVDPNANPNV
128
10
19
100





144


CSP
NVVNSSIGL
418
9
19
100





145


CSP
NVVNSSIGLI
418
10
19
100





146


CSP
NVVNSSIGLIM
418
11
19
100





147


CSP
QVRIKPGSA
382
9
19
100





148


CSP
RVLNELNYDNA
33
11
19
100





149


CSP
SIGLIMVL
423
8
19
100





150


CSP
SIGLIMVLSFL
423
11
19
100





151


CSP
SLKKNSRSL
64
9
19
100
0.0001




152


CSP
STEWSPCSV
367
9
19
100





153


CSP
STEWSPCSVT
367
10
19
100





154


CSP
SVFNVVNSSI
415
10
19
100
0.0005




155


CSP
SVSSFLFV
9
8
19
100





156


CSP
SVSSFLFVEA
9
10
19
100





157


CSP
SVSSFLFVEAL
9
11
19
100





158


CSP
SVTCGNGI
374
8
19
100





159


CSP
SVTCGNGIQV
374
10
19
100





160


CSP
VLNELNYDNA
34
10
19
100





161


CSP
VTCGNGIQV
375
9
19
100
0.0011




162


CSP
VTCGNGIQVRI
375
11
19
100





163


CSP
VVNSSIGL
419
8
19
100





164


CSP
VVNSSIGLI
419
9
19
100





165


CSP
VVNSSIGLIM
419
10
19
100





166


CSP
VVNSSIGLIMV
419
11
19
100





167


CSP
YQCYGSSSNT
23
10
19
100





168


EXP
ATSVLAGL
77
8
1
100





169


EXP
ATSVLAGLL
77
9
1
100





170


EXP
DMIKKEEEL
56
9
1
100





171


EXP
DMIKKEEELV
56
10
1
100





172


EXP
DVHDLISDM
49
9
1
100





173


EXP
DVHDLISDMI
49
10
1
100





174


EXP
EQPQGDDNNL
147
10
1
100





175


EXP
EQPQGDDNNLV
147
11
1
100





176


EXP
EVNKRKSKYKL
66
11
1
100





177


EXP
FIIFNKESL
13
9
1
100





178


EXP
FIIFNKESLA
13
10
1
100





179


EXP
FLALFFII
8
8
1
100





180


EXP
GLLGNVST
83
8
1
100





181


EXP
GLLGNVSTV
83
9
1
100
0.0160




182


EXP
GLLGNVSTVL
83
10
1
100
0.0380




183


EXP
GLLGNVSTVLL
83
11
1
100





184


EXP
GVGLVLYNT
95
9
1
100





185


EXP
IIFNKESL
14
8
1
100





186


EXP
IIFNKESLA
14
9
1
100





187


EXP
ILSVFFLA
3
8
1
100





188


EXP
ILSVFFLAL
3
9
1
100
0.0058




189


EXP
KIGSSDPA
111
8
1
100





190


EXP
KIGSSDPADNA
111
11
1
100





191


EXP
KILSVFFL
2
8
1
100





192


EXP
KILSVFFLA
2
9
1
100
0.8500




193


EXP
KILSVFFLAL
2
10
1
100





194


EXP
KLATSVLA
75
8
1
100





195


EXP
KLATSVLAGL
75
10
1
100
0.0047




196


EXP
KLATSVLAGLL
75
11
1
100





197


EXP
KTNKGTGSGV
24
10
1
100





198


EXP
LAEKTNKGT
21
9
1
100





199


EXP
LAGLLGNV
81
8
1
100





200


EXP
LAGLLGNVST
81
10
1
100





201


EXP
LAGLLGNVSTV
81
11
1
100





202


EXP
LATSVLAGL
76
9
1
100





203


EXP
LATSVLAGLL
76
10
1
100





204


EXP
LIDVHDLI
47
8
1
100





205


EXP
LIDVHDLISDM
47
11
1
100





206


EXP
LLGGVGLV
92
8
1
100





207


EXP
LLGGVGLVL
92
9
1
100
0.0038




208


EXP
LLGNVSTV
84
8
1
100





209


EXP
LLGNVSTVL
84
9
1
100
0.0350




210


EXP
LLGNVSTVLL
84
10
1
100
0.0059




211


EXP
MIKKEEEL
57
8
1
100





212


EXP
MIKKEEELV
57
9
1
100





213


EXP
MIKKEEELVEV
57
11
1
100





214


EXP
NADPQVTA
134
8
1
100





215


EXP
NADPQVTAQDV
134
11
1
100





216


EXP
NTEKGRHPFKI
102
11
1
100





217


EXP
NVSTVLLGGV
87
10
1
100





218


EXP
PADNANPDA
117
9
1
100





219


EXP
PLIDVHDL
46
8
1
100





220


EXP
PLIDVHDLI
46
9
1
100





221


EXP
PQGDDNNL
149
8
1
100





222


EXP
PQGDDNNLV
149
9
1
100





223


EXP
PQVTAQDV
137
8
1
100





224


EXP
PQVTAQDVT
137
9
1
100





225


EXP
QVTAQDVT
138
8
1
100





226


EXP
SLAEKTNKGT
20
10
1
100





227


EXP
STVLLGGV
89
8
1
100





228


EXP
STVLLGGVGL
89
10
1
100





229


EXP
STVLLGGVGLV
89
11
1
100





230


EXP
SVFFLALFFI
5
10
1
100
0.0017




231


EXP
SVFFLALFFII
5
11
1
100





232


EXP
SVLAGLLGNV
79
10
1
100
0.0022




233


EXP
TVLLGGVGL
90
9
1
100





234


EXP
TVLLGGVGLV
90
10
1
100





235


EXP
TVLLGGVGLVL
90
11
1
100





236


EXP
VLAGLLGNV
80
9
1
100
0.0210




237


EXP
VLAGLLGNVST
80
11
1
100





238


EXP
VLLGGVGL
91
8
1
100





239


EXP
VLLGGVGLV
91
9
1
100
0.0290




240


EXP
VLLGGVGLVL
91
10
1
100
0.0290




241


LSA
DIQNHTLET
1738
9
1
100





242


LSA
DIQNHTLETV
1738
10
1
100





243


LSA
DITKYFMKL
1901
9
1
100





244


LSA
DLDEFKPI
1781
8
1
100





245


LSA
DLDEFKPIV
1781
9
1
100
0.0001




246


LSA
DLEEKAAKET
148
10
1
100





247


LSA
DLEEKAAKETL
148
11
1
100





248


LSA
DLEQDRLA
1388
8
1
100





249


LSA
DLEQERLA
1609
8
1
100





250


LSA
DLEQERRA
1575
8
1
100





251


LSA
DLEQRKADT
1626
9
1
100





252


LSA
DLERTKASKET
1184
11
1
100





253


LSA
DLIEKNENL
1808
9
1
100





254


LSA
DLYGRLEI
1651
8
1
100





255


LSA
DLYGRLEIPA
1651
10
1
100





256


LSA
DLYGRLEIPAI
1651
11
1
100





257


LSA
DVLAEDLYGRL
1646
11
1
100





258


LSA
EILQIVDEL
1890
9
1
100





259


LSA
EISAEYDDSL
1763
10
1
100





260


LSA
EISAEYDDSLI
1763
11
1
100





261


LSA
EISIIEKT
1692
8
1
100





262


LSA
ELSEDITKYFM
1897
11
1
100





263


LSA
ELTMSNVKNV
83
10
1
100





264


LSA
EQDRLAKEKL
1390
10
1
100





265


LSA
EQERLAKEKL
1611
10
1
100





266


LSA
EQERLANEKL
1526
10
1
100





267


LSA
EQERRAKEKL
1577
10
1
100





268


LSA
EQKEDKSA
1730
8
1
100





269


LSA
EQKEDKSADI
1730
10
1
100





270


LSA
EQQRDLEQERL
1605
11
1
100





271


LSA
EQQRDLEQRKA
1622
11
1
100





272


LSA
EQQSDLEQDRL
1384
11
1
100





273


LSA
EQQSDLEQERL
1588
11
1
100





274


LSA
EQQSDLERT
1180
9
1
100





275


LSA
EQQSDLERTKA
1180
11
1
100





276


LSA
EQQSDSEQERL
517
11
1
100





277


LSA
EQRKADTKKNL
1628
11
1
100





278


LSA
ETLQEQQSDL
1193
10
1
100





279


LSA
ETLQGQQSDL
156
10
1
100





280


LSA
ETVNISDV
1745
8
1
100





281


LSA
FIKSLFHI
1877
8
1
100





282


LSA
FILVNLLI
11
8
1
100





283


LSA
FILVNLLIFHI
11
11
1
100





284


LSA
FQDEENIGI
1794
9
1
100





285


LSA
FQISKYEDEI
1755
10
1
100





286


LSA
GIEKSSEEL
1822
9
1
100





287


LSA
GIYKELEDL
1801
9
1
100





288


LSA
GIYKELEDLI
1801
10
1
100





289


LSA
GQDENRQEDL
140
10
1
100





290


LSA
GQQSDLEQERL
1129
11
1
100





291


LSA
GVSENTFL
105
8
1
100





292


LSA
HIFDGDNEI
1883
9
1
100





293


LSA
HIFDIGENEIL
1883
10
1
100





294


LSA
HIKKYKNDKQV
1860
11
1
100





295


LSA
HILYISFYFI
3
10
1
100
0.0033




296


LSA
HILYISFYFIL
3
11
1
100





297


LSA
HLEEKDGSI
1718
10
1
100





298


LSA
HTLETVNI
1742
8
1
100





299


LSA
HTLETVNISDV
1742
11
1
100





300


LSA
HVLSHNSYEKT
59
11
1
100





301


LSA
IIEKTNRESI
1695
10
1
100





302


LSA
IIEKTNRESIT
1695
11
1
100





303


LSA
IIKNSEKDEI
25
10
1
100





304


LSA
IIKNSEKDEII
25
11
1
100





305


LSA
ILQIVDEL
1891
8
1
100





306


LSA
ILVNLLIFHI
12
10
1
100
0.0076




307


LSA
ILYISFYFI
4
9
1
100
0.0023




308


LSA
ILYISFYFIL
4
10
1
100
0.0035




309


LSA
ILYISFYFILV
4
11
1
100





310


LSA
IQNHTLET
1739
8
1
100





311


LSA
IQNHTLETV
1739
9
1
100





312


LSA
IQNHTLETVNI
1739
11
1
100





313


LSA
ITKYFMKL
1902
8
1
100





314


LSA
ITTNVEGRRDI
1704
11
1
100





315


LSA
IVDELSEDI
1894
9
1
100





316


LSA
IVDELSEDIT
1894
10
1
100





317


LSA
KADTKKNL
1631
8
1
100





318


LSA
KIIKNSEKDEI
24
11
1
100





319


LSA
KIKKGKKYEKT
1834
11
1
100





320


LSA
KLNKEGKL
116
8
1
100





321


LSA
KLNKEGKLI
116
9
1
100





322


LSA
KLQEQQRDL
1619
9
1
100





323


LSA
KLQEQQSDL
1585
9
1
100
0.0019




324


LSA
KLQGQQSDL
1126
9
1
100





325


LSA
KQVNKEKEKFI
1868
11
1
100





326


LSA
KTNRESIT
1698
8
1
100





327


LSA
KTNRESITT
1698
9
1
100





328


LSA
KTNRESITTNV
1698
11
1
100





329


LSA
LAEDLYGRL
1648
9
1
100





330


LSA
LAEDLYGRLEI
1648
11
1
100





331


LSA
LIDEEEDDEDL
1772
11
1
100





332


LSA
LIEKNENL
1809
8
1
100





333


LSA
LIEKNENLDDL
1809
11
1
100





334


LSA
LIFHINGKI
17
9
1
100





335


LSA
LIFHINGKII
17
10
1
100
0.0002




336


LSA
LLIFHINGKI
16
10
1
100





337


LSA
LLIFHINGKII
16
11
1
100





338


LSA
LLRNLGVSENI
100
11
1
100





339


LSA
LQEQQRDL
1620
8
1
100





340


LSA
LQEQQSDL
1586
8
1
100





341


LSA
LQEQQSDLERT
1178
11
1
100





342


LSA
LQGQQSDL
1127
8
1
100





343


LSA
LQIVDELSEDI
1892
11
1
100





344


LSA
LTMSNVKNV
84
9
1
100
0.0010




345


LSA
LVNLLIFHI
13
9
1
100
0.0006




346


LSA
NIFLKENKL
109
9
1
100





347


LSA
NIGIYKEL
1799
8
1
100





348


LSA
NIGIYKELEDL
1799
11
1
100





349


LSA
NISDVNDFQI
1748
10
1
100





350


LSA
NLDDLDEGI
1815
9
1
100





351


LSA
NLERKKENGDV
1637
11
1
100





352


LSA
NLGVSENI
103
8
1
100





353


LSA
NLGVSENIFL
103
10
1
100





354


LSA
NLLIFHINGKI
15
11
1
100





355


LSA
NVEGRRDI
1707
8
1
100





356


LSA
NVKNVSQT
88
8
1
100





357


LSA
NVSQTNFKSL
91
10
1
100





358


LSA
NVSQTNFKSLL
91
11
1
100





359


LSA
QISKYEDEI
1756
9
1
100





360


LSA
QISKYEDEISA
1756
11
1
100





361


LSA
QIVDELSEDI
1893
10
1
100





362


LSA
QIVDELSEDIT
1893
11
1
100





363


LSA
QQRDLEQERL
1606
10
1
100





364


LSA
QQRDLEQERLA
1606
11
1
100





365


LSA
QQRDLEQERRA
1538
11
1
100





366


LSA
QQRDLEQRKA
1623
10
1
100





367


LSA
QQSDLEQDRL
1385
10
1
100





368


LSA
QQSDLEQDRLA
1385
11
1
100





369


LSA
QQSDLEQERL
1589
10
1
100





370


LSA
QQSDLEQERLA
1589
11
1
100





371


LSA
QQSDLEQERRA
1572
11
1
100





372


LSA
QQSDLERT
1181
8
1
100





373


LSA
QQSDLERTKA
1181
10
1
100





374


LSA
QQSDSEQERL
518
10
1
100





375


LSA
QQSDLEQERLA
518
11
1
100





376


LSA
QTNFKSLL
94
8
1
100





377


LSA
QTNFKSLLRNL
94
11
1
100





378


LSA
QVNKEKEKFI
1869
10
1
100





379


LSA
RLEIPAIEL
1655
9
1
100





380


LSA
RQEDLEEKA
145
9
1
100





381


LSA
RQEDLEEKAA
145
10
1
100





382


LSA
RTKASKET
1187
8
1
100





383


LSA
RTKASKETL
1187
9
1
100





384


LSA
SADIQNHT
1736
8
1
100





385


LSA
SADIQNHTL
1736
9
1
100





386


LSA
SADIQNHTLET
1736
11
1
100





387


LSA
SAEYDDSL
1765
8
1
100





388


LSA
SAEYDDSLI
1765
9
1
100





389


LSA
SIIEKTNRESI
1694
11
1
100





390


LSA
SLLRNLGV
99
8
1
100





391


LSA
SQTNFKSL
93
8
1
100





392


LSA
SQTNFKSLL
93
9
1
100





393


LSA
TLETVNISDV
1743
10
1
100





394


LSA
TLQEQQSDL
1194
9
1
100





395


LSA
TLQGQQSDL
157
9
1
100





396


LSA
TMSNVKNV
85
8
1
100





397


LSA
TMSNVKNVSQT
85
11
1
100





398


LSA
TTNVEGRRDI
1705
10
1
100





399


LSA
VLAEDLYGRL
1647
10
1
100





400


LSA
VLSHNSYEKT
60
10
1
100





401


LSA
YIPHQSSL
1672
8
1
100





402


LSA
YISFYFIL
6
8
1
100





403


LSA
YISFYFILV
6
9
1
100
0.0016




404


LSA
YISFYFILVNL
6
11
1
100





405


SSP2
AATPYAGEPA
525
10
8
80





406


SSP2
ATPYAGEPA
526
9
8
80





407


SSP2
EILHEGCTSEL
267
11
8
80





408


SSP2
EVCNDEVDL
41
9
8
80





409


SSP2
EVCNDEVDLYL
41
11
8
80





410


SSP2
EVDLYLLM
46
8
8
80





411


SSP2
FVVPGAATPYA
520
11
8
80





412


SSP2
GAATPYAGEPA
524
11
8
80





413


SSP2
ILHEGCTSEL
268
10
8
80





414


SSP2
LLSTNLPYGRT
121
11
8
80





415


SSP2
NLPYGRTNL
125
9
8
80





416


SSP2
SIRRHNWVNHA
58
11
8
80





417


SSP2
STNLPYGRT
123
9
8
80





418


SSP2
STNLPYGRTNL
123
11
8
80





419


SSP2
VVPGAATPYA
521
10
8
80





420


SSP2
WVNHAVPL
64
8
8
80





421


SSP2
WVNHAVPLA
64
9
8
80
0.0008




422


SSP2
WVNHAVPLAM
64
10
8
80





423


SSP2
YAGEPAPFDET
529
11
8
80





424


SSP2
ALLQVRKHL
136
9
9
90
0.0010




425


SSP2
DALLQVRKHL
135
10
9
90





426


SSP2
DASKNKEKALI
106
11
9
90





427


SSP2
DQPRPRGDNFA
302
11
9
90





428


SSP2
EIKYREEV
35
8
9
90





429


SSP2
IQDSLKESRKL
168
11
9
90





430


SSP2
IVDSKYREEV
32
11
9
90





431


SSP2
LLQVRKHL
137
8
9
90





432


SSP2
LQVRKHLNDRI
138
11
9
90





433


SSP2
QVRKHLNDRI
139
10
9
90
0.0001




434


SSP2
SLKESRKL
171
8
9
90





435


SSP2
ALLACAGL
509
8
10
100





436


SSP2
ALLACAGLA
509
9
10
100
0.0006




437


SSP2
AMKLIQQL
72
8
10
100





438


SSP2
AMKLIQQLNL
72
10
10
100
0.0006




439


SSP2
AVCVEVEKT
233
9
10
100





440


SSP2
AVCVEVEKTA
233
10
10
100





441


SSP2
AVFGIGQGI
186
9
10
100
0.0001




442


SSP2
AVFGIGQGINV
186
11
10
100





443


SSP2
AVPLAMKL
68
8
10
100





444


SSP2
AVPLAMKLI
68
9
10
100
0.0001




445


SSP2
CAGLAYKFV
513
9
10
100





446


SSP2
CAGLAYKFVV
513
10
10
100
0.0015




447


SSP2
CVEVEKTA
235
8
10
100





448


SSP2
DASKNKEKA
106
9
10
100





449


SSP2
DASKNKEKAL
106
10
10
100





450


SSP2
DLDEPEQFRL
546
10
10
100
0.0001




451


SSP2
DLFLVNGRDV
19
10
10
100





452


SSP2
DVQNNIVDEI
27
10
10
100





453


SSP2
EIIRLHSDA
99
9
10
100





454


SSP2
EILHEGCT
267
8
10
100





455


SSP2
ETLGEEDKDL
538
10
10
100





456


SSP2
EVEKTASCGV
237
10
10
100





457


SSP2
FLIFFDLFL
14
9
10
100
1.2000




458


SSP2
FLIFFDLFLV
14
10
10
100
0.8000




459


SSP2
FLVNGRDV
21
8
10
100





460


SSP2
FMKAVCVEV
230
9
10
100
0.0290




461


SSP2
FVVPGAAT
520
8
10
100





462


SSP2
GIAGGLAL
503
8
10
100





463


SSP2
GIAGGLALL
503
9
10
100
0.0022




464


SSP2
GIAGGLALLA
503
10
10
100





465


SSP2
GIGQGINV
189
8
10
100





466


SSP2
GIGQGINVA
189
9
10
100





467


SSP2
GINVAFNRFL
193
10
10
100





468


SSP2
GINVAFNRFLV
193
11
10
100





469


SSP2
GIPDSIQDSL
163
10
10
100





470


SSP2
GLALLACA
507
8
10
100





471


SSP2
GLALLACAGL
507
10
10
100
0.0170




472


SSP2
GLALLACAGLA
507
11
10
100





473


SSP2
GLAYKFVV
515
8
10
100





474


SSP2
GLAYKFVVPGA
515
11
10
100





475


SSP2
GTRSRKREI
260
9
10
100





476


SSP2
GTRSRKREIL
260
10
10
100





477


SSP2
GVKIAVFGI
182
9
10
100





478


SSP2
GVWDEWSPCSV
245
11
10
100





479


SSP2
HAVPLAMKL
67
9
10
100





480


SSP2
HAVPLAMKLI
67
10
10
100





481


SSP2
HLGNVKYL
3
8
10
100





482


SSP2
HLGNVKYLV
3
9
10
100
0.0017




483


SSP2
HLGNVKYLVI
3
10
10
100





484


SSP2
HLGNVKYLVIV
3
11
10
100





485


SSP2
HLNDRINRENA
143
11
10
100





486


SSP2
HVPNSEDRET
445
10
10
100





487


SSP2
IAGGIAGGL
500
9
10
100





488


SSP2
IAGGIAGGLA
500
10
10
100





489


SSP2
IAGGIAGGLAL
500
11
10
100





490


SSP2
IAGGLALL
504
8
10
100





491


SSP2
IAGGLALLA
504
9
10
100
0.0001




492


SSP2
IAGGLALLACA
504
11
10
100





493


SSP2
IAVFGIGQGI
185
10
10
100





494


SSP2
IIRLHSDA
100
8
10
100





495


SSP2
ILTDGIPDSI
159
10
10
100





496


SSP2
IVFLIFFDL
12
9
10
100
0.0024




497


SSP2
I VFLIFFDLFL 
12
11
10
100





498


SSP2
KAVCVEVEKT
232
10
10
100





499


SSP2
KAVCVEVEKTA
232
11
10
100





500


SSP2
KIAGGIAGGL
499
10
10
100





501


SSP2
KIAGGIAGGLA
499
11
10
100





502


SSP2
KIAVFGIGQGI
184
11
10
100





503


SSP2
KLIQQLNL
74
8
10
100





504


SSP2
LACAGLAYKFV
511
11
10
100





505


SSP2
LALLACAGL
508
9
10
100





506


SSP2
LALLACAGLA
508
10
10
100





507


SSP2
LAMKLIQQL
71
9
10
100





508


SSP2
LAMKLIQQLNL
71
11
10
100





509


SSP2
LAYKFVVPGA
516
10
10
100





510


SSP2
LAYKFVVPGAA
516
11
10
100





511


SSP2
LIFFDLFL
15
8
10
100





512


SSP2
LIFFDLFLV
15
9
10
100
0.0890




513


SSP2
LLACAGLA
510
8
10
100





514


SSP2
LLMDCSGSI
51
9
10
100
0.0460




515


SSP2
LMDCSGSI
52
8
10
100





516


SSP2
LIDGIPDSI
160
9
10
100





517


SSP2
LVIVFLIFFDL
10
11
10
100





518


SSP2
LVNGRDVQNNI
22
11
10
100





519


SSP2
LVVILTDGI
156
9
10
100





520


SSP2
NANQLVVI
152
8
10
100





521


SSP2
NANQLVVIL
152
9
10
100





522


SSP2
NANQLVVILT
152
10
10
100





523


SSP2
NIPEDSEKEV
366
10
10
100





524


SSP2
NLYADSAWENV
213
11
10
100





525


SSP2
NQLVVILT
154
8
10
100





526


SSP2
NQLVVILTDGI
154
11
10
100





527


SSP2
NVAFNRFL
195
8
10
100





528


SSP2
NVAFNRFLV
195
9
10
100
0.0001




529


SSP2
NVIGPFMKA
225
9
10
100
0.0002




530


SSP2
NVIGPFMKAV
225
10
10
100
0.0008




531


SSP2
NVKNVIGPFM
222
10
10
100





532


SSP2
NVKYLVIV
6
8
10
100





533


SSP2
NVKYLVIVFL
6
10
10
100





534


SSP2
NVKYLVIVFLI
6
11
10
100





535


SSP2
PAPFDETL
533
8
10
100





536


SSP2
PLAMKLIQQL
70
10
10
100





537


SSP2
QLVVILTDGI
155
10
10
100
0.0002




538


SSP2
RINRENANQL
147
10
10
100





539


SSP2
RINRENANQLV
147
11
10
100





540


SSP2
SAWENVKNV
218
9
10
100
0.0019




541


SSP2
SAWENVKNVI
218
10
10
100





542


SSP2
SIRRHNWV
58
8
10
100





543


SSP2
SQDNNGNRHV
437
10
10
100





544


SSP2
SVTCGKGT
254
8
10
100





545


SSP2
TLGEEDKDL
539
9
10
100
0.0001




546


SSP2
VAFNRFLV
196
8
10
100





547


SSP2
VIGPFMKA
226
8
10
100





548


SSP2
VIGPFMKAV
226
9
10
100
0.0004




549


SSP2
VIGPFMKAVCV
226
11
10
100





550


SSP2
VILTDGIPDSI
158
11
10
100





551


SSP2
VIVFLIFFDL
11
10
10
100
0.0038




552


SSP2
VQNNIVDEI
28
9
10
100





553


SSP2
VVILTDGI
157
8
10
100





554


SSP2
YADSAWENV
215
9
10
100





555


SSP2
YLLMDCSGSI
50
10
10
100
0.1700




556


SSP2
YLVIVFLI
9
8
10
100





557
















TABLE IX







Malaria A03 Super Motif Peptides With Binding Data





















No. of
Sequence
Conservancy








Protein
Sequence
Position
Amino Acids
Frequency
(%)
A*0301
A*1101
A*3101
A*3301
A*6801
Seq. Id.





















CSP
DIEKKICK
402
8
19
100





558


CSP
DIEKKICKMEK
402
11
19
100





559


CSP
ELEMNYYGK
50
9
19
100
0.0001
0.0003



560


CSP
KLRKPKHK
104
8
19
100





561


CSP
KLRKPKHKK
104
9
19
100
0.1300
0.0037



562


CSP
KLRKPKHKKLK
104
11
19
100





563


CSP
NANANNAVK
335
9
16
84
0.0001
0.0002
0.0006
0.0096
0.0210
564


CSP
NANPNANPNK
304
10
19
100
0.0005
0.0021
0.0009
0.0009
0.0054
565


CSP
NMPNDPNR
323
8
19
100





566


CSP
SVTCGNGIQVR
374
11
19
100





567


CSP
VTCGNGIQVR
375
10
19
100
0.0005
0.0340



568


CSP
YSLKKNSR
63
8
19
100





569


EXP
ALFFIIFNK
10
9
1
100
1.1000
1.2000



570


EXP
DLISDMIK
52
8
1
100





571


EXP
DLISDMIKK
52
9
1
100
0.0001
0.0003



572


EXP
DVHDLISDMIK
49
11
1
100





573


EXP
ELVEVNKR
63
8
1
100





574


EXP
ELVEVNKRK
63
9
1
100
0.0001
0.0002



575


EXP
ELVEVNKRKSK
63
11
1
100





576


EXP
ESLAEKTNK
19
9
1
100
0.0001
0.0002
0.0004
0.0110
0.0260
577


EXP
EVNKRKSK
66
8
1
100





578


EXP
EVNKRKSKYK
66
10
1
100
0.0005
0.0002



579


EXP
FLALFFIIFNK
8
11
1
100





580


EXP
GLVLYNTEK
97
9
1
100
0.0069
0.0055



581


EXP
GLVLYNTEKGR
97
11
1
100





582


EXP
GSGVSSKK
30
8
1
100





583


EXP
GSGVSSKKK
30
9
1
100
0.0003
0.0065
0.0004
0.0010
0.0002
584


EXP
GSGVSSKKKNK
30
11
1
100





585


EXP
GTGSGVSSK
28
9
1
100
0.0039
0.0180



586


EXP
GTGSGVSSKK
28
10
1
100
0.0071
0.0340



587


EXP
GTGSGVSSKKK
28
11
1
100





588


EXP
GVGLVLYNTEK
95
11
1
100





589


EXP
GVSSKKKNK
32
9
1
100
0.0001
0.0002



590


EXP
GVSSKKKNKK
32
10
1
100
0.0011
0.0002



591


EXP
IIFNKESLAEK
14
11
1
100





592


EXP
LALFFIIFNK
9
10
1
100
0.0140
0.0530
0.0072
0.0076
0.0039
593


EXP
LISDMIKK
53
8
1
100





594


EXP
LVEVNKRK
64
8
1
100





595


EXP
LVEVNKRKSK
64
10
1
100
0.0005
0.0002



596


EXP
LVLYNTEK
98
8
1
100





597


EXP
LVLYNTEKGR
98
10
1
100
0.0005
0.0002



598


EXP
NTEKGRHPFK
102
10
1
100
0.0047
0.0080



599


EXP
SLAEKTNK
20
8
1
100





600


EXP
SSKKKNKK
34
8
1
100





601


EXP
VLYNTEKGR
99
9
1
100
0.0110
0.0007
0.0039
0.0055
0.0022
602


EXP
VSSKKKNK
33
8
1
100





603


EXP
VSSKKKNKK
33
9
1
100
0.0001
0.0002
0.0004
0.0010
0.0002
604


LSA
AIELPSENER
1660
10
1
100
0.0001
0.0002
0.0009
0.0008
0.0029
605


LSA
DIHKGHLEEK
1713
10
1
100
0.0004
0.0002
0.0009
0.0055
0.0046
606


LSA
DIHKGHLEEKK
1713
11
1
100





607


LSA
DITKYFMK
1901
8
1
100





608


LSA
DLDEGIEK
1818
8
1
100





609


LSA
DLEEKAAK
148
8
1
100





610


LSA
DLEQDRLAK
1388
9
1
100
0.0001
0.0002



611


LSA
DLEQDRLAKEK
1388
11
1
100





612


LSA
DLEQERLAK
1609
9
1
100
0.0001
0.0002



613


LSA
DLEQERLAKEK
1609
11
1
100





614


LSA
DLEQERLANEK
1524
11
1
100





615


LSA
DLEQERRAK
1575
9
1
100
0.0001
0.0002



616


LSA
DLEQERRAKEK
1575
11
1
100





617


LSA
DLEQRKADTK
1626
10
1
100
0.0001
0.0002



618


LSA
DLEQRKADTKK
1626
11
1
100





619


LSA
DLERTKASK
1184
9
1
100
0.0001
0.0002



620


LSA
DSEQERLAK
521
9
1
100
0.0001
0.0002
0.0004
0.0010
0.0002
621


LSA
DSEQERLAKEK
521
11
1
100





622


LSA
DSKEISIIEK
1689
10
1
100
0.0001
0.0002



623


LSA
DTKKNLER
1633
8
1
100





624


LSA
DTKKNLERK
1633
9
1
100
0.0001
0.0002



625


LSA
DTKKNLERKK
1633
10
1
100
0.0001
0.0002



626


LSA
DVLAEDLYGR
1646
10
1
100
0.0001
0.0002



627


LSA
DVNDFQISK
1751
9
1
100
0.0001
0.0018



628


LSA
EIIKSNLR
33
8
1
100





629


LSA
EISIIEKTNR
1692
10
1
100
0.0001
0.0002



630


LSA
ELEDLIEK
1805
8
1
100





631


LSA
ELPSENER
1662
8
1
100





632


LSA
ELSEDITK
1897
8
1
100





633


LSA
ELSEEKIK
1829
8
1
100





634


LSA
ELSEEKIKK
1829
9
1
100
0.0002
0.0002



635


LSA
ELSEEKIKKGK
1829
11
1
100





636


LSA
ELTMSNVK
83
8
1
100





637


LSA
ESITTNVEGR
1702
10
1
100
0.0001
0.0002



638


LSA
ESITTNVEGRR
1702
11
1
100





639


LSA
FLKENKLNK
111
9
1
100
0.0260
0.0005



640


LSA
GSIKPEQK
1725
8
1
100





641


LSA
GSIKPEQKEDK
1725
11
1
100





642


LSA
GSSNSRNR
42
8
1
100





643


LSA
GVSENIFLK
105
9
1
100
0.2700
0.6600



644


LSA
HIINDDDDK
126
9
1
100
0.0002
0.0002



645


LSA
HIINDDDDKK
126
10
1
100
0.0001
0.0002
0.0009
0.0009
0.0003
646


LSA
HIINDDDDKKK
126
11
1
100





647


LSA
HIIKKYKNDK
1860
9
1
100
0.0002
0.0002



648


LSA
HINGKIIK
20
8
1
100





649


LSA
HLEEKKDGSIK
1718
11
1
100





650


LSA
HVLSHNSYEK
59
10
1
100
0.0170
0.0140



651


LSA
IINDDDDK
127
8
1
100





652


LSA
IINDDDDKK
127
9
1
100
0.0002
0.0002



653


LSA
IINDDDDKKK
127
10
1
100
0.0001
0.0002



654


LSA
ISDYNDFQISK
1749
11
1
100





655


LSA
ISIIEKTNR
1693
9
1
100
0.0001
0.0008
0.0320
0.0150
0.0054
656


LSA
ITTNVEGR
1704
8
1
100





657


LSA
ITTNVEGRR
1704
9
1
100
0.0002
0.0007
0.0025
0.0043
0.3200
658


LSA
IVDELSEDITK
1894
11
1
100





659


LSA
KADTKKNLER
1631
10
1
100
0.0001
0.0002
0.0086
0.0011
0.0003
660


LSA
KADTKKNLERK
1631
11
1
100





661


LSA
KIIKNSEK
24
8
1
100





662


LSA
KIKKGKKYEK
1834
10
1
100
0.0081
0.0007
0.0042
0.0009
0.0003
663


LSA
KLQEQQSDLER
1177
11
1
100





664


LSA
KSLYDEHIK
1854
9
1
100
0.0005
0.0340
0.0004
0.0010
0.0002
665


LSA
KSLYDEHIKK
1854
10
1
100
0.0094
0.0490



666


LSA
KSSEELSEEK
1825
10
1
100
0.0001
0.0009



667


LSA
KTKDNNFK
1843
8
1
100





668


LSA
KTKNNENNK
68
9
1
100
0.0028
0.0038



669


LSA
LAEDLYGR
1648
8
1
100





670


LSA
LAKEKLQEQQR
1615
11
1
100





671


LSA
LANEKLQEQQR
1530
11
1
100





672


LSA
LIFHINGK
17
8
1
100





673


LSA
LIFHINGKIIK
17
11
1
100





674


LSA
LLIFHINGK
16
9
1
100
0.0260
0.0100



675


LSA
LSEDMCYFMK
1898
11
1
100





676


LSA
LSEEKIKK
1830
8
1
100





677


LSA
LSEEKIKKGK
1830
10
1
100
0.0004
0.0002



678


LSA
LSEEKIKKGKK
1830
11
1
100





679


LSA
LSHNSYEK
61
8
1
100





680


LSA
LSHNSYEKTK
61
10
1
100
0.0004
0.0002



681


LSA
NIFLKENK
109
8
1
100.





682


LSA
NIFLKENKLNK
109
11
1
100





683


LSA
NLDDLDEGIEK
1815
11
1
100





684


LSA
NLGVSENIFLK
103
11
1
100





685


LSA
NLLIFHINGK
15
10
1
100
0.0049
0.0008



686


LSA
NLRSGSSNSR
38
10
1
100
0.0004
0.0002



687


LSA
NSEKDEIIK
28
9
1
100
0.0002
0.0002
0.0004
0.0010
0.0002
688


LSA
NSRNRINEEK
45
10
1
100
0.0004
0.0002



689


LSA
NVEGRRDIHK
1707
10
1
100
0.0004
0.0002



690


LSA
NVKNVSQTNFK
88
11
1
100





691


LSA
NVSQTNFK
91
8
1
100





692


LSA
PAIELPSENER
1659
11
1
100





693


LSA
QSDLEQDR
1386
8
1
100





694


LSA
QSDLEQDRLAK
1386
11
1
100





695


LSA
QSDLEQER
1590
8
1
100





696


LSA
QSDSEQERLAK
1590
11
1
100





697


LSA
QSDLEQERR
1573
9
1
100
0.0002
0.0002
0.0006
0.0005
0.0005
698


LSA
QSDLEQERRAK
1573
11
1
100





699


LSA
QSDLERTK
1182
8
1
100





700


LSA
QSDLERTKASK
1182
11
1
100





701


LSA
QSDSEQER
519
8
1
100





702


LSA
QSDSEQERLAK
519
11
1
100





703


LSA
QSSLPQDNR
1676
9
1
100
0.0002
0.0013
0.0150
0.0140
0.0480
704


LSA
QTNFKSLLR
94
9
1
100
0.0320
0.0440
0.0820
0.0180
0.1300
705


LSA
QVNKEKEK
1869
8
1
100





706


LSA
QVNKEKEKFIK
1869
11
1
100





707


LSA
RINEEKHEK
49
9
1
100
0.0033
0.0370



708


LSA
RINEEKHEKK
49
10
1
100
0.0024
0.0018
0.0009
0.0009
0.0003
709


LSA
RSGSSNSR
40
8
1
100





710


LSA
RSGSSNSRNR
40
10
1
100
0.0011
0.0002



711


LSA
SIIEKTNR
1694
8
1
100





712


LSA
SIKPEQKEDK
1726
10
1
100
0.0002
0.0002
0.0009
0.0009
0.0003
713


LSA
SITTNVEGR
1703
9
1
100
0.0002
0.0027



714


LSA
SITTNVEGRR
1703
10
1
100
0.0002
0.0002



715


LSA
SLPQDNRGNSR
1678
11
1
100





716


LSA
SLYDEHIK
1855
8
1
100





717


LSA
SLYDEHIKK
1855
9
1
100
0.0460
0.4100



718


LSA
SLYDEHIKKYK
1855
11
1
100





719


LSA
SSEELSEEK
1826
9
1
100
0.0002
0.0017
0.0004
0.0010
0.0002
720


LSA
SSEELSEEKIK
1826
11
1
100





721


LSA
SSLPQDNR
1677
8
1
100





722


LSA
TTNVEGRR
1705
8
1
100.





723


LSA
VLAEDLYGR
1647
9
1
100
0.0013
0.0004
0.0083
0.0220
0.0032
724


LSA
VLSHNSYEK
60
9
1
100
0.0280
0.0280



725


LSA
VLSHNSYEKTK
60
11
1
100





726


LSA
VSENIFLK
106
8
1
100





727


LSA
VSENIFLKENK
106
11
1
100





728


LSA
VSQTNFKSLLR
92
11
1
100





729


LSA
YIKGQDENR
137
9
1
100
0.0025
0.0002



730


SSP2
ALLACAGLAYK
509
11
10
100





731


SSP2
AVCVEVEK
233
8
10
100





732


SSP2
CSVTCGKGTR
253
10
10
100
0.0002
0.0002



733


SSP2
DALLQVRK
135
8
9
90





734


SSP2
DASKNKEK
106
8
10
100





735


SSP2
DIPKKPENK
392
9
10
100
0.0004
0.0002



736


SSP2
DLDEPEQFR
546
9
10
100
0.0002
0.0002
0.0004
0.0170
0.0002
737


SSP2
DLFLVNGR
19
8
10
100





738


SSP2
DSAWENVK
217
8
10
100





739


SSP2
DSIQDSLK
166
8
10
100





740


SSP2
DSIQDSLKESR
166
11
10
100





741


SSP2
DSLKESRK
170
8
9
90





742


SSP2
DVPKNPEDDR
378
10
10
100
0.0002
0.0002



743


SSP2
DVQNNIVDEIK
27
11
10
100





744


SSP2
EIIRLHSDASK
99
11
10
100





745


SSP2
ELQEQCEEER
276
10
8
80
0.0002
0.0002



746


SSP2
ETLGEEDK
538
8
10
100





747


SSP2
EVPSDVPK
374
8
10
100





748


SSP2
FLVGCHPSDGK
201
11
10
100





749


SSP2
FMKAVCVEVEK
230
11
10
100





750


SSP2
GINVAFNR
193
8
10
100





751


SSP2
GIPDSIQDSLK
163
11
10
100





752


SSP2
HAVPLAMK
67
8
10
100





753


SSP2
HLNDRINR
143
8
10
100





754


SSP2
HSDASKNK
104
8
10
100





755


SSP2
HSDASKNKEK
104
10
10
100
0.0004
0.0002



756


SSP2
HVPNSEDR
445
8
10
100





757


SSP2
HVPNSEDRETR
445
11
9
90





758


SSP2
IIRLHSDASK
100
10
10
100
0.0230
0.0002
0.0009
0.0009
0.0013
759


SSP2
IVDEIKYR
32
8
9
90





760


SSP2
KAVCVEVEK
232
9
10
100
0.0004
0.0076
0.0009
0.0005
0.0029
761


SSP2
KVLDNERK
421
8
8
80





762


SSP2
LACAGLAYK
511
9
10
100
0.0240
0.0290
0.0150
0.3200
0.1100
763


SSP2
LLACAGLAYK
510
10
10
100
0.9500
0.0870



764


SSP2
LLMDCSGSIR
51
10
10
100
0.0004
0.0005



765


SSP2
LLMDCSGSIRR
51
11
10
100





766


SSP2
LLQVRKHLNDR
137
11
9
90





767


SSP2
LLSTNLPYGR
121
10
8
80
0.0017
0.0025



768


SSP2
LMDCSGSIR
52
9
10
100
0.0004
0.0002
0.0370
0.0430
0.0010
769


SSP2
LMDCSGSIRR
52
10
10
100
0.0015
0.0002



770


SSP2
LSTNLPYGR
122
9
8
80
0.0004
0.0100
0.2900
0.0760
0.2700
771


SSP2
LVGCHPSDGK
202
10
10
100
0.0004
0.0002



772


SSP2
NIPEDSEK
366
8
10
100





773


SSP2
NIVDEIKYR
31
9
9
90
0.0005
0.0002



774


SSP2
NLPNDKSDR
406
9
10
100
0.0005
0.0002



775


SSP2
NSEDRETR
448
8
9
90





776


SSP2
NVIGPFMK
225
8
10
100





777


SSP2
NVKNVIGPFMK
222
11
10
100





778


SSP2
PSPNPEEGK
328
9
10
100
0.0005
0.0002
0.0004
0.0010
0.0002
779


SSP2
QSQDNNGNR
436
9
10
100
0.0005
0.0002
0.0020
0.0093
0.0018
780


SSP2
QVRKHLNDR
139
9
9
90
0.0005
0.0002
0.0041
0.0570
0.0002
781


SSP2
RLHSDASK
102
8
10
100





782


SSP2
RLHSDASKNK
102
10
10
100
0.0240
0.0002



783


SSP2
SIQDSLKESR
167
10
10
100
0.0004
0.0009



784


SSP2
SIQDSLKFSRK
167
11
9
90





785


SSP2
SLLSTNLPYGR
120
11
8
80





786


SSP2
STNLPYGR
123
8
8
80





787


SSP2
SVTCGKGTR
254
9
10
100
0.0005
0.0009
0.0031
0.0039
0.0310
788


SSP2
SVTCGKGTRSR
254
11
10
100





789


SSP2
VTCGKGTR
255
8
10
100





790


SSP2
VTCGKGTRSR
255
10
10
100
0.0004
0.0017



791


SSP2
VTCGKGTRSRK
255
11
10
100





792


SSP2
WSPCSVTCGK
250
10
10
100
0.0004
0.0002



793


SSP2
WVNHAVPLAMK
64
11
8
80





794


SSP2
YADSAWENVK
215
10
10
100
0.0004
0.0002
0.0009
0.0009
0.0077
795


SSP2
YLLMDCSGSIR
50
11
10
100





796
















TABLE X







Malaria A24 Super Motif Peptides With Binding Information

















No. of
Sequence
Conservancy




Protein
Sequence
Position
Amino Acids
Frequency
(%)
A*2401
Seq. Id.

















CSP
AILSVSSF
6
8
18
95

797


CSP
AILSVSSFL
6
9
19
100

798


CSP
AILSVSSFLF
6
10
19
100

799


CSP
ALFQEYQCY
18
9
19
100

800


CSP
CYGSSSNTRVL
25
11
19
100

801


CSP
DIEKKKKM
402
9
19
100

802


CSP
DYENDIEKKI
398
10
18
95

803


CSP
ELNYDNAGI
37
9
18
95

804


CSP
ELNYDNAGINL
37
11
18
95

805


CSP
EMNYYGKQENW
52
11
19
100

806


CSP
FLFVEALF
13
8
19
100

807


CSP
FLFVEALFQEY
13
11
19
100

808


CSP
FVEALFQEY
15
9
19
100

809


CSP
GINLYNEL
44
8
18
95

810


CSP
GINLYNELEM
44
10
18
95

811


CSP
GLIMVLSF
425
8
19
100

812


CSP
GLIMVLSFL
425
9
19
100

813


CSP
GLIMVLSFLF
425
10
19
100

814


CSP
GLIMVLSFLFL
425
11
19
100

815


CSP
HIBQYLKKI
350
9
15
79

816


CSP
ILSVSSFL
7
8
19
100

817


CSP
ILSVSSFLF
7
9
19
100

818


CSP
IMVLSFLF
427
8
19
100

819


CSP
IMVLSFLFL
427
9
19
100
0.0008
820


CSP
KIQNSLSTEW
361
10
15
79

821


CSP
KLAILSVSSF
4
10
19
100

822


CSP
KLAILSVSSFL
4
11
19
100

823


CSP
KLRKPKHKKL
104
10
19
100

824


CSP
KMEKCSSVF
409
9
19
100

825


CSP
LFQEYQCY
19
8
19
100

826


CSP
LFVEALFQEY
14
10
19
100

827


CSP
LIMVLSFL
426
8
19
100

828


CSP
LIMVLSFLF
426
9
19
100

829


CSP
LIMVLSFLFL
426
10
19
100

830


CSP
LYNELEMNY
47
9
19
100

831


CSP
LYNELEMNYY
47
10
19
100

832


CSP
MMRKLAIL
1
8
19
100

833


CSP
MVLSFLFL
428
8
19
100

834


CSP
NLYNELEM
46
8
19
100

835


CSP
NLYNELEMNY
46
10
19
100

836


CSP
NLYNELEMNYY
46
11
19
100

837


CSP
NTRVLNEL
31
8
19
100

838


CSP
NTRVLNELNY
31
10
19
100

839


CSP
NVVNSSIGL
418
9
19
100

840


CSP
NVVNSSIGLI
418
10
19
100

841


CSP
NVVNSSIGLIM
418
11
19
100

842


CSP
NYDNAGINL
39
9
18
95
0.0004
843


CSP
NYDNAGINLY
39
10
18
95

844


CSP
NYYGKQENW
54
9
19
100

845


CSP
NYYGKQENWY
54
10
19
100

846


CSP
RVLNELNY
33
8
19
100

847


CSP
SFLFVEAL
12
8
19
100

848


CSP
SFLFVEALF
12
9
19
100

849


CSP
SIGLIMVL
423
8
19
100

850


CSP
SIGLIMVLSF
423
10
19
100

851


CSP
SIGLIMVLSFL
423
11
19
100

852


CSP
SLKKNSRSL
64
9
19
100

853


CSP
SVFNVVNSSI
415
10
19
100

854


CSP
SVSSFLFVEAL
9
11
19
100

855


CSP
SVTCGNGI
374
8
19
100

856


CSP
VFNVVNSSI
416
9
19
100

857


CSP
VFNVVNSSIGL
416
11
19
100

858


CSP
VTCGNGIQVRI
375
11
19
100

859


CSP
VVNSSIGL
419
8
19
100

860


CSP
VVNSSIGLI
419
9
19
100

861


CSP
VVNSSIGLIM
419
10
19
100

862


CSP
WYSLKKNSRSL
62
11
19
100

863


CSP
YLKKIQNSL
358
9
15
79

864


CSP
YYGKQENW
55
8
19
100

865


CSP
YYGKQENWY
55
9
19
100

866


CSP
YYGKQENWYSL
55
11
19
100

867


EXP
ATSVLAGL
77
8
1
100

868


EXP
ATSVLAGLL
77
9
1
100

869


EXP
DMIKKEEEL
56
9
1
100

870


EXP
DVHDLISDM
49
9
1
100

871


EXP
DVHDLISDMI
49
10
1
100

872


EXP
EVNKRKSKY
66
9
1
100

873


EXP
EVNKRKSKYKL
66
11
1
100

874


EXP
FFIIFNKESL
12
10
1
100

875


EXP
FFLALFFI
7 
8
1
100

876


EXP
FFLALFFII
7
9
1
100

877


EXP
FFLALFFIIF
7
10
1
100

878


EXP
FIIFNKESL
13
9
1
100

879


EXP
FLALFFII
8
8
1
100

880


EXP
FLALFFIIF
8
9
1
100

881


EXP
GLLGNVSTVL
83
10
1
100

882


EXP
GLLGNVSTVLL
83
11
1
100

883


EXP
IIFNKESL
14
8
1
100

884


EXP
ILSVFFLAL
3
9
1
100

885


EXP
ILSVFFLALF
3
10
1
100

886


EXP
ILSVFFLALFF
3
11
1
100

887


EXP
KILSVFFL
2
8
1
100

888


EXP
KILSVFFLAL
2
10
1
100

889


EXP
KILSVFFLALF
2
11
1
100

890


EXP
KLATSVLAGL
75
10
1
100

891


EXP
KLATSVLAGLL
75
11
1
100

892


EXP
KYKLATSVL
73
9
1
100
0.0960
893


EXP
LFFIIFNKESL
11
11
1
100

894


EXP
LIDVHDLI
47
8
1
100

895


EXP
LIDVHDLISDM
47
11
1
100

896


EXP
LLGGVGLVL
92
9
1
100

897


EXP
LLGGVGLVLY
92
10
1
100

898


EXP
LLGNVSTVL
84
9
1
100

899


EXP
LLGNVSTVLL
84
10
1
100

900


EXP
LVEVNKRKSKY
64
11
1
100

901


EXP
LYNTEKGRHPF
100
11
1
100

902


EXP
MIKKEEEL
57
8
1
100

903


EXP
NTEKGRHPF
102
9
1
100

904


EXP
NTEKGRHPFKI
102
11
1
100

905


EXP
PLIDVHDL
46
8
1
100

906


EXP
PLIDVHDLI
46
9
1
100

907


EXP
STVLLGGVGL
89
10
1
100

908


EXP
SVFFLALF
5
8
1
100

909


EXP
SVFFLALFF
5
9
1
100

910


EXP
SVFFLALFFI
5
10
1
100

911


EXP
SVFFLALFFII
5
11
1
100

912


EXP
TVLLGGVGL
90
9
1
100

913


EXP
TVLLGGVGLVL
90
11
1
100

914


EXP
VFFLALFF
6
8
1
100

915


EXP
VFFLALFFI
6
9
1
100

916


EKP
VFFLALFFII
6
10
1
100

917


EXP
VFFLALFFIIF
6
11
1
100

918


EKP
VLLGGVGL
91
8
1
100

919


EXP
VLLGGVGLVL
91
10
1
100

920


EXP
VLLGGVGLVLY
91
11
1
100

921


LSA
DFQISKYEDEI
1754
11
1
100

922


LSA
DITKYFMKL
1901
9
1
100

923


LSA
DLDEFKPI
1781
8
1
100

924


LSA
DLDEFKPIVQY
1781
11
1
100

925


LSA
DLEEKAAKETL
148
11
1
100

926


LSA
DLIEKNENL
1808
9
1
100

927


LSA
DLYGRLEI
1651
8
1
100

928


LSA
DLYGRLEIPAI
1651
11
1
100

929


LSA
DVLAEDLY
1646
8
1
100

930


LSA
DVLAEDLYGRL
1646
11
1
100

931


LSA
DVNDFQISKY
1751
10
1
100

932


LSA
EFKPIVQY
1784
8
1
100

933


LSA
EFKPIVQYDNF
1784
11
1
100

934


LSA
EILQIVDEL
1890
9
1
100

935


LSA
EISAEYDDSL
1763
10
1
100

936


LSA
EISAEYDDSLI
1763
11
1
100

937


LSA
ELPSENERGY
1662
10
1
100

938


LSA
ELPSENERGYY
1662
11
1
100

939


LSA
ELSEDITKY
1897
9
1
100

940


LSA
ELSEDITKYF
1897
10
1
100

941


LSA
ELSEDITKYFM
1897
11
1
100

942


LSA
ETLQEQQSDL
1193
10
1
100

943


LSA
ETLQGQQSDL
156
10
1
100

944


LSA
ETVNISDVNDF
1745
11
1
100

945


LSA
FFDKDKEL
77
8
1
100

946


LSA
FFDKDKELTM
77
10
1
100

947


LSA
FIKSLFHI
1877
8
1
100

948


LSA
FIKSLFHIF
1877
9
1
100

949


LSA
FILVNLLI
11
8
1
100

950


LSA
FILVNLLIF
11
9
1
100

951


LSA
FILVNLLIFHI
11
11
1
100

952


LSA
FYFILVNL
9
8
1
100

953


LSA
FYFILVNLL
9
9
1
100
7.5000
954


LSA
FYFILVNLLI
9
10
1
100

955


LSA
FYFILVNLLIF
9
11
1
100

956


LSA
GIEKSSEEL
1822
9
1
100

957


LSA
GIYKELEDL
1801
9
1
100

958


LSA
GIYKELEDLI
1801
10
1
100

959


LSA
GVSENIFL
105
8
1
100

960


LSA
GYYIPHQSSL
1670
10
1
100
0.0074
961


LSA
HIFDGDNEI
1883
9
1
100

962


LSA
HIFDGDNEIL
1883
10
1
100

963


LSA
HILYISFY
3
8
1
100

964


LSA
HILYISFYF
3
9
1
100

965


LSA
HILYISFYFI
3
10
1
100

966


LSA
HILYISFYFIL
3
11
1
100

967


LSA
HLEEKKDGSI
1718
10
1
100

968


LSA
HTLETVNI
1742
8
1
100

969


LSA
HVLSHNSY
59
8
1
100

970


LSA
IFDGDNEI
1884
8
1
100

971


LSA
IFDGDNEIL
1884
9
1
100

972 


LSA
IFDGDNEILQI
1884
11
1
100

973


LSA
IFHINGKI
18
8
1
100

974


LSA
IFHINGKII
18
9
1
100

975


LSA
IFLKENKL
110
8
1
100

976


LSA
IIEKTNRESI
1695
10
1
100

977


LSA
IIKNSEKDEI
25
10
1
100

978


LSA
IIKNSEKDEII
25
11
1
100

979


LSA
IINDDDDKKKY
127
11
1
100

980


LSA
ILQIVDEL
1891
8
1
100

981


LSA
ILVNLLIF
12
8
1
100

982


LSA
ILVNLLIFHI
12
10
1
100

983


LSA
ILYISFYF
4
8
1
100

984


LSA
ILYISFYFI
4
9
1
100

985


LSA
ILYISFYFIL
4
10
1
100

986


LSA
ITKYFMKL
1902
8
1
100

987


LSA
ITTNVEGRRDI
1704
11
1
100

988


LSA
IVDELSEDI
1894
9
1
100

989


LSA
IYKELEDL
1802
8
1
100

990


LSA
IYKELEDLI
1802
9
1
100

991


LSA
KFFDKDKEL
76
9
1
100

992


LSA
KFFDKDKELTM
76
11
1
100

993


LSA
KFIKSLFHI 
1876
9
1
100

994


LSA
KFIKSLFHIF
1876
10
1
100

995


LSA
KIIKNSEKDEI
24
11
1
100

996


LSA
KIKKGKKY
1834
8
1
100

997


LSA
KLNKEGKL
116
8
1
100

998


LSA
KLNKEGKLI
116
9
1
100

999


LSA
KLQEQQRDL
1619
9
1
100

1000


LSA
KLQEQQSDL
1585
9
1
100

1001


LSA
KLQGQQSDL
1126
9
1
100

1002


LSA
KTKNNENNKF
68
10
1
100

1003


LSA
KTKNNENNKFF
68
11
1
100

1004


LSA
KYEDEISAEY
1759
10
1
100

1005


LSA
KYEKTKDNNF
1840
10
1
100
0.0004
1006


LSA
LFHIFDGDNEI
1881
11
1
100

1007


LSA
LIDEEEDDEDL
1772
11
1
100

1008


LSA
LIEKNENL
1809
8
1
100

1009


LSA
LIEKNENLDDL
1809
11
1
100

1010


LSA
LIFHINGKI
17
9
1
100

1011


LSA
LIFHINGKII
17
10
1
100

1012


LSA
LLIFHINGKI
16
10
1
100

1013


LSA
LLIFHINGKII
16
11
1
100

1014


LSA
LLRNLGVSENI
100
11
1
100

1015


1SA
LVNLLIFHI
13
9
1
100

1016


LSA
LYDEHIKKY
1856
9
1
100

1017


LSA
LYGRLEIPAI
1652
10
1
100

1018


LSA
LYISFYFI
5
8
1
100

1019


LSA
LYISFYFIL
5
9
1
100
0.0088
1020


LSA
NFKPNDKSL
1848
9
1
100

1021


LSA
NFKPNDKSLY
1848
10
1
100

1022


LSA
NFKSLLRNL
96
9
1
100

1023


LSA
NFQDEENI
1793
8
1
100

1024


LSA
NFQDEENIGI
1793
10
1
100

1025


LSA
NFQDEENIGIY
1793
11
1
100

1026


LSA
NIFLKENKL
109
9
1
100

1027


LSA
NIGIYKEL
1799
8
1
100

1028


LSA
NIGIYKELEDL
1799
11
1
100

1029


LSA
NISDVNDF
1748
8
1
100

1030


LSA
NISDVNDFQI
1748
10
1
100

1031


LSA
NLDDLDEGI
1815
9
1
100

1032


LSA
NLGVSENI
103
8
1
100

1033


LSA
NLGVSENIF
103
9
1
100

1034


LSA
NLGVSENIFL
103
10
1
100

1035


LSA
NLLIFHINGKI
15
11
1
100

1036


LSA
NVEGRRDI
1707
8
1
100

1037


LSA
NVKNVSQTNF
88
10
1
100

1038


LSA
NVSQTNFKSL
91
10
1
100

1039


LSA
NVSQTNFKSLL
91
11
1
100

1040


LSA
PIVQYDNF
1787
8
1
100

1041


LSA
QISKYEDEI
1756
9
1
100

1042


LSA
QIVDELSEDI
1893
10
1
100

1043


LSA
QTNFKSLL
94
8
1
100

1044


LSA
QTNFKSLLRNL
94
11
1
100

1045


LSA
QVNKEKEKF
1869 
9
1
100

1046


LSA
QVNKEKEKFI
1869
10
1
100

1047


LSA
QYDNFQDEENI
1790
11
1
100

1048


LSA
RLEIPAIEL
1655
9
1
100

1049


LSA
RTKASKETL
1187
9
1
100

1050


LSA
SFYFILVNL
8
9
1
100

1051


LSA
SFYFILVNLL
8
10
1
100

1052


LSA
SFYFILVNLLI
8
11
1
100

1053


LSA
SIIEKTNRESI
1694
11
1
100

1054


LSA
SLYDEHIKKY
1855
10
1
100

1055


LSA
TLQEQQSDL
1194
9
1
100

1056


LSA
TLQGQQSDL
157
9
1
100

1057


LSA
TINVEGRRDI
1705
10
1
100

1058


LSA
TVNISDVNDF
1746
10
1
100

1059


LSA
VLAEDLYGRL
1647
10
1
100

1060


LSA
YFILVNLL
10
8
1
100

1061


LSA
YFILVNLLI
10
9
1
100

1062


LSA
YFILVNLLIF
10
10
1
100

1063


LSA
YIPHQSSL
1672
8
1
100

1064


LSA
YISFYFIL
6
8
1
100

1065


LSA
YISFYFILVNL
6
11
1
100

1066


LSA
YYIPHQSSL
1671
9
1
100
4.3000
1067


SSP2
ALLACAGL
509
8
10
100

1068


SSP2
ALIACAGLAY
509
10
10
100

1069


SSP2
ALLQVRKHL
136
9
9
90

1070


SSP2
AMKLIQQL
72
8
8
100

1071


SSP2
AMKLIQQLNL
72
10
10
100
0.0006
1072


SSP2
ATPYAGEPAPF
526
11
8
80

1073


SSP2
AVFGIGQGI
186
9
10
100

1074


SSP2
AVPLAMKL
68
8
10
100

1075


SSP2
AVPLAMKLI
68
9
10
100

1076


SSP2
AWENVKNVI
219
9
10
100

1077


SSP2
DLDEPEQF
546
8
10
100

1078


SSP2
DLDEPEQFRL
546
10
10
100

1079


SSP2
DVQNNIVDEI
27
10
10
100

1080


SSP2
EILHEGCTSEL
267
11
8
80

1081


SSP2
ETLGEEDKDL
538
10
10
100

1082


SSP2
EVCNDEVDL
41
9
8
80

1083


SSP2
EVCNDEVDLY
41
10
8
80

1084


SSP2
EVCNDEVDLYL
41
11
8
80

1085


SSP2
EVDLYLLM
46
8
8
80

1086


SSP2
EVEKTASCGVW
237
11
10
100

1087


SSP2
FLIFFDLF
14
8
10
100

1088


SSP2
FLIFFDLFL
14
9
10
100

1089


SSP2
FVVPGAATPY
520
10
8
80

1090


SSP2
GIAGGLAL
503
8
10
100

1091


SSP2
GIAGGLALL
503
9
10
100

1092


SSP2
GIGQGINVAF
189
10
10
100

1093


SSP2
GINVAFNRF
193
9
10
100

1094


SSP2
GINVAFNRFL
193
10
10
100

1095


SSP2
GIPDSIQDSL
163
10
10
100

1096


SSP2
GLALLACAGL
507
10
10
100

1097


SSP2
GTRSRKREI
260
9
10
100

1098


SSP2
GTRSRKREIL
260
10
10
100

1099


SSP2
GVKIAVFGI
182
9
10
100

1100


SSP2
HLGNVKYL
3
8
10
100

1101


SSP2
HLGNVKYLVI
3
10
10
100

1102


SSP2
ILHEGCTSEL
268
10
8
80

1103


SSP2
ILTDGIPDS1
159
10
10
100

1104


SSP2
IVFLIFFDL
12
9
10
100

1105


SSP2
IVFLIFFDLF
12
10
10
100

1106


SSP2
IVFLIFFDLFL
12
11
10
100

1107


SSP2
KFVVPGAATPY
519
11
8
80

1108


SSP2
KIAGGIAGGL
499
10
10
100

1109


SSP2
KIAVFGIGQGI
184
11
10
100

1110


SSP2
KLIQQLNL
74
8
10
100

1111


SSP2
KTASCGVW
240
8
10
100

1112


SSP2
KTASCGVWDEW
240
11
10
100

1113


SSP2
KYKIAGGI
497
8
9
90

1114


SSP2
KYLVIVFL
8
8
10
100

1115


SSP2
KYLVIVFLI
8
9
10
100
4.6000
1116


SSP2
KYLVIVFLIF
8
10
10
100
0.0003
1117


SSP2
KYLVIVFLIFF
8
11
10
100

1118


SSP2
LIFFDLFL
15
8
10
100

1119


SSP2
LLACAGLAY
510
9
10
100

1120


SSP2
LLACAGLAYKF
510
11
10
100

1121


SSP2
LLMDCSGSI
51
9
10
100

1122


SSP2
LLQVRKHL
137
8
9
90

1123


SSP2
LLSTNLPY
121
8
9
90

1124


SSP2
LMDCSGSI
52
8
10
100

1125


SSP2
LTDGIPDSI
160
9
10
100

1126


SSP2
LVIVFLIF
10
8
10
100

1127


SSP2
LVIVFLIFF
10
9
10
100

1128


SSP2
LVIVFLIFFDL
10
11
10
100

1129


SSP2
LVNGRDVQNNI
22
11
10
100

1130


SSP2
LVVILTDGI
156
9
10
100

1131


SSP2
LYLLMDCSGSI
49
11
9
90

1132


SSP2
NIVDEIKY
31
8
10
100

1133


SSP2
NLPYGRTNL
125
9
8
80

1134


SSP2
NLYADSAW
213
8
10
100

1135


SSP2
NVAFNRFL
195
8
10
100

1136


SSP2
NVKNVIGPF
222
9
10
100

1137


SSP2
NVKNVIGPFM
222
10
10
100

1138


SSP2
NVKYLVIVF
6
9
10
100

1139


SSP2
NVKYLVIVFL
6
10
10
100

1140


SSP2
NVKYLVIVFLI
6
11
10
100

1141


SSP2
NWVNHAVPL
63
9
8
80

1142


SSP2
NWVNHAVPLAM
63
11
8
80

1143


SSP2
PLAMKLIQQL
70
10
10
100

1144


SSP2
PYAGEPAPF
528
9
8
80
0.0370
1145


SSP2
QFRLPEENEW
552
10
10
100

1146


SSP2
QLVVILTDGI
155
10
10
100

1147


SSP2
QVRKHLNDRI
139
10
9
90

1148


SSP2
RINRENANQL
147
10
10
100

1149


SSP2
RLPEENEW
554
8
10
100

1150


SSP2
SLKESRKL
171
8
9
90

1151


SSP2
SLLSTNLPY
120
9
9
90

1152


SSP2
STNLPYGRTNL
123
11
8
80

1153


SSP2
TLGEEDKDL
539
9
10
100

1154


SSP2
VFGIGQGI 
187
8
10
100

1155


SSP2
VFLIFFDL
13
8
10
100

1156


SSP2
VFLIFFDLF
13
9
10
100

1157


SSP2
VFLIFFDLFL
13
10
10
100

1158


SSP2
VILTDGIPDSI
158
11
10
100

1159


SSP2
VIVFLIFF
11
8
10
100

1160


SSP2
VIVFLIFFDL
11
10
10
100

1161


SSP2
VIVFLIFFDLF
11
11
10
100

1162


SSP2
VVILTDGI
157
8
10
100

1163


SSP2
VVPGAATPY
521
9
8
80

1164


SSP2
WVNHAVPL
64
8
8
80

1165


SSP2
WVNHAVPLAM
64
10
8
80

1166


SSP2
YLLMDCSGSI
50
10
10
100

1167


SSP2
YLVIVFLI
9
8
10
100

1168


SSP2
YLVIVFLIF
9
9
10
100

1169


SSP2
YLVIVFLIFF
9
10
10
100

1170
















TABLE XI







Malaria B07 Super Motif Peptides With Binding Information

















No of
Sequence
Conservancy




Protein
Sequence
Position
Amino Acids
Frequency
(%)
B*0702
Seq. Id.

















CSP
EPSDKHIEQY
345
10
15
79

1171


CSP
EPSDKHIEQYL
345
11
15
79

1172


CSP
DPNANPNA
202
8
19
100

1171


CSP
DPNANPNV
130
8
19
100

1174


CSP
DPNRNVDENA
327
10
19
100
0.0002
1175


CSP
MPNDPNRNV
324
9
19
100
0.0001
1176


CSP
NPDPNANPNV
120
10
19
100
0.0001
1177


CSP
NPNANPNA
302
8
19
100
0.0001
1178


CSP
NPNVDPNA
198
8
19
100
0.0001
1179


CSP
QPGDGNPDPNA
115
11
19
100

1180


CSP
SPCSVTCGNGI
371
11
19
100

1181


EXP
DPADNANPDA
116
10
1
100
0.0002
1182


EXP
DPQVTAQDV
136
9
1
100
0.0001
1183


EXP
EPLIDVHDL
45
9
1
100
0.0001
1184


EXP
EPLIDVHDLI
45
10
1
100
0.0002
1185


EXP
EPNADPQV
132
8
1
100
0.0001
1186


EXP
EPNADPQVTA
132
10
1
100
0.0002
1187


EXP
HPFKIGSSDPA
108
11
1
100

1188


EXP
QPQGDDNNL
148
9
1
100
0.0001
1189


EXP
QPQGDDNNLV
148
10
1
100
0.0002
1190


LSA
KPEQKEDKSA
1728
10
1
100
0.0002
1191


LSA
KPIVQYDNF
1786
9
1
100
0.0001
1192


LSA
KPNDKSLY
1850
8
1
100
0.0004
1193


LSA
LPSENERGY
1663
9
1
100
0.0001
1194


LSA
LPSENERGYY
1663
10
1
100
0.0001
1195


LSA
LPSENERGYYI
1663
11
1
100

1196


SSP2
EPAPFDETL
532
9
10
100
0.0001
1197


SSP2
GPFMKAVCV
228
9
10
100
0.0023
1198


SSP2
GPFMKAVCVEV
228
11
10
100

1199


SSP2
HPSDGKCNL
206
9
10
100
0.0220
1200


SSP2
HPSDGKCNLY
206
10
10
100
0.0001
1201


SSP2
HPSDGKCNLYA
206
11
10
100

1202


SSP2
IPDSIQDSL
164
9
10
100
0.0022
1203


SSP2
IPEDSEKEV
367
9
10
100
0.0001
1204


SSP2
LPYGRTNL
126
8
8
80
0.1100
1205


SSP2
NPEDDREENF
382
10
10
100
0.0001
1206


SSP2
QPRPRGDNF
303
9
9
90
0.0160
1207


SSP2
QPRPRGDNFA
303
10
9
90
0.0009
1208


SSP2
QPRPRGDNFAV
303
11
9
90

1209


SSP2
RPRGDNFA
305
8
9
90
0.0110
1210


SSP2
RPRGDNFAV
305
9
9
90
0.4800
1211


SSP2
TPYAGEPA
527
8
8
80

1212


SSP2
TPYAGEPAPF
527
0
8
80
0.0990
1213


SSP2
VPGAATPY
522
8
8
80

1214


SSP2
VFGAATPYA
522
9
8
80
0.0001
1215


SSP2
VPLAMKLI
69
8
10
100
0.0001
1216


SSP2
VPLAMKLIQQL
69
11
10
100

1217
















TABLE XII







Malaria B27 Super Motif Peptides
















No. of
Sequence
Conservancy



Protein
Sequence
Position
Amino Acids
Frequency
(%)
Seq. Id
















CSP
CKMEKCSSVF
408
10
19
100
1218


CSP
DKHIEQYL 
348
8
15
79
1219


CSP
DKHIEQYLKKI
348
11
15
79
1220


CSP
EKLRKFKHKKL
103
11
19
100
1221


CSP
GKQENWYSL
57
9
19
100
1222


CSP
KHIEQYLKKI
349
10
15
79
1223


CSP
KKIQNSLSTEW
360
11
15
79
1224


CSP
LKKIQNSL
359
8
15
79
1225


CSP
LKKNSRSL
65
8
19
100
1226


CSP
LRKPKHKKL
105
9
19
100
1227


CSP
RKLAILSVSSF
3
11
19
100
1228


CSP
RKPKHKKL
106
8
19
100
1229


CSP
TRVLNELNY
32
9
19
100
1230


EXP
EKGRHPFKI
104
9
1
100
1231


EXP
KKGSGEPL
40
8
1
100
1232


EXP
KKGSGEPLI
40
9
1
100
1233


EXP
KKNKKGSGEPL
37
11
1
100
1234


EXP
KRKSKYKL
69
8
1
100
1235


EXP
MKILSVFF
1
8
1
100
1236


EXP
MKILSVFFL
1
9
1
100
1237


EXP
MKILSVFFLAL
1
11
1
100
1238


EXP
NKKGSGEPL
39
9
1
100
1239


EXP
NIUCGSGEPLI
39
10
1
100
1240


EXP
NKRKSKYKL
68
9
1
100
1241


EXP
SKYKLATSVL
72
10
1
100
1242


EXP
VHDLISDM
50
8
1
100
1243


EXP
VHDLISDMI
50
9
1
100
1244


EXP
YKLATSVL
74
8
1
100
1245


EXP
YKLATSVLAGL
74
11
1
100
1246


LSA
DKDKELTM
79
8
1
100
1247


LSA
DKQVNKEKEKF
1867
11
1
100
1248


LSA
DKSADIQNHTL
1734
11
1
100
1249


LSA
DKSLYDEHI
1853
9
1
100
1250


LSA
DRLAKEKL
1392
8
1
100
1251


LSA
EHGDVLAEDL
1643
10
1
100
1252


LSA
EHGDVLAEDLY
1643
11
1
100
1253


LSA
EKAAKETL
151
8
1
100
1254


LSA
EKDEIIKSNL
30
10
1
100
1255


ISA
EKEKFIKSL
1873
9
1
100
1256


LSA
EKEKFIKSLF
1873
10
1
100
1257


LSA
EKFIKSLF
1875
8
1
100
1258


LSA
EKFIKSLFHI
1875
10
1
100
1259


LSA
EKFIKSLFHIF
1875
11
1
100
1260


LSA
EKHEKKHVL
53
9
1
100
1261


LSA
EKIKKGKKY
1833
9
1
100
1262


LSA
EKKHVLSHNSY
56
11
1
100
1263


LSA
EKLQEQQRDL
1618
10
1
100
1264


LSA
EKLQEQQSDL
1584
10
1
100
1265


LSA
SCLQGQQSDL
1125
10
1
100
1266


LSA
EKNENLDDL
1811
9
1
100
1267


LSA
EKTKDNNF
1842
8
1
100
1268


LSA
EKTKNNENNKF
67
11
1
100
1269


LSA
EKTNRESI
1697
8
1
100
1270


LSA
ERKKEHGDVL
1639
10
1
100
1271


LSA
ERLAKEKL
1613
8
1
100
1272


LSA
ERLANEKL
1528
8
1
100
1273


LSA
ERRAKEKL
1579
8
1
100
1274


LSA
ERIXASKETL
1186
10
1
100
1275


LSA
FHIFDGDNEI
1882
10
1
100
1276


LSA
FHIFDGDNEIL
1882
11
1
100
1277


LSA
FHINGKII
19
8
1
100
1278


LSA
FKPIVQYDNF
1785
10
1
100
1279


LSA
FKPNDKSL
1849
8
1
100
1280


LSA
FKPNDKSLY
1849
9
1
100
1281


LSA
FKSLLRNL
97
8
1
100
1282


LSA
GHLEEKKDOSI
1717
11
1
100
1283


LSA
GKLIHIII
121
8
1
100
1284


LSA
GRLEIPAI
1654
8
1
100
1285


LSA
GRLEIPAIEL
1654
10
1
100
1286


LSA
GRRDIHKGHL
1710
10
1
100
1287


LSA
IKNSEKDEI
26
9
1
100
1288


LSA
IKNSEKDEll
26
10
1
100
1289


LSA
IKSLFHIF
1878
8
1
100
1290


LSA
KHEKKHVL
54
8
1
100
1291


LSA
KHILYISF
2
8
1
100
1292


LSA
KHILYISFY
2
9
1
100
1293


LSA
KHILYISFYF
2
10
1
100
1294


LSA
KHILYISFYFI
2
11
1
100
1295


LSA
KHVLSHNSY
58
9
1
100
1296


LSA
KKEHGDVL
1641
8
1
100
1297


LSA
KKHVLSHNSY
57
10
1
100
1298


LSA
KKYEKTKDNNF
1839
11
1
100
1299


LSA
LRNLGVSENI
101
10
1
100
1300


LSA
LRNLGVSENIF
101
11
1
100
1301


LSA
MKHILYISF
1
9
1
100
1302


LSA
MKHILYISFY
1
10
1
100
1303


LSA
MKHILYISFYF
1
11
1
100
1304


LSA
NHTLETVNI
1741
9
1
100
1305


LSA
NKEGKLIEHI
118
10
1
100
1306


LSA
NKEGKLIEHII
118
11
1
100
1307


LSA
NKEKEKFI
1871
8
1
100
1308


LSA
NKEKEKFIKSL
1871
11
1
100
1309


LSA
NKFFDKDKEL
75
10
1
100
1310


LSA
NKLNKI3GKL
115
9
1
100
1311


LSA
NKLNKEGKLI
115
10
1
100
1312


LSA
NRGNSRDSKEI
1683
11
1
100
1313


LSA
QKEDILSADI
1731
9
1
100
1314


LSA
QRDLEQERL
1607
9
1
100
1315


LSA
QRKADTKKNL
1629
10
1
100
1316


LSA
FUCADIKKNL
1630
9
1
100
1317


LSA
RKKEHODVL
1640
9
1
100
1318


LSA
RRDTHKGHL
1711
9
1
100
1319


LSA
SKYEDEISAEY
1758
11
1
100
1320


LSA
SRDSKEISI
1687
9
1
100
1321


LSA
SRDSKEISII
1687
10
1
100
1322


LSA
TKASKED
1188
8
1
100
1323


LSA
TKNNENNKF
69
9
1
100
1324


LSA
TKNNENNKFF
69
10
1
100
1325


LSA
VKNVSQTNF
89
9
1
100
1326


LSA
YKELEDLI
1803
8
1
100
1327


SSP2
CHPSDGKCNL
205
10
10
100
1328


SSP2
CHPSDGKCNLY
205
11
10
100
1329


SSP2
DIOLDEPEQF
544
10
10
100
1330


SSP2
DREENFDI
386
8
10
100
1331


SSP2
DROVKIAVF
180
9
9
90
1332


SSP2
DRGVKIAVFGI
180
11
9
90
1333


SSP2
DRINRENANQL
146
11
10
100
1334


SSP2
EKTASCGVW
239
9
10
100
1335


SSP2
FRLPEENEW
553
9
10
100
1336


SSP2
GKCNLYADSAW
210
11
10
100
1337


SSP2
GKGIRSRKREI
258
11
10
100
1338


SSP2
GRDVQNNI
25
8
10
100
1339


SSP2
GRNNENRSY
458
9
10
100
1340


SSP2
KHDNQNNL
400
8
io
100
1341


SSP2
LHEGCTSEL
269
9
8
80
1342


SSP2
MKLIQQLNL
73
9
10
100
1343


SSP2
NHAVPLAM
66
8
8
80
1344


SSP2
NHAVPLAMKL
66
10
8
80
1345


SSP2
NHAVPLAMKLI
66
11
8
80
1346


SSP2
NHIXINVKY
2
8
10
100
1347


SSP2
NHLGNVKYL
2
9
10
100
1348


SSP2
NHLGNVKYLVI
2
11
10
100
1349


SSP2
NKEKALII
110
8
9
90
1350


SSP2
NKEKALIII
110
9
9
90
1351


SSP2
NKHDNQNNL
399
9
10
100
1352


SSP2
NKYKIAGGI
496
9
9
90
1353


SSP2
NRENANQL
149
8
10
100
1354


SSP2
NRENANQLVVI
149
11
10
100
1355


SSP2
PHGRNNENRSY
456
11
10
100
1356


SSP2
PRPRGDNF
304
8
9
90
1357


SSP2
RHNWVNHAVPL
61
11
8
80
1358


SSP2
RKHLNDRI
141
8
10
100
1359


SSP2
SKNKEKAL
108
8
10
100
1360


SSP2
SKNKSKALI
108
9
9
90
1361


SSP2
SKNKEKALII
108
10
9
90
1362


SSP2
SKNKEKALIII
108
11
9
90
1363


SSP2
TRSRKREI
261
8
10
100
1364


SSP2
TRSRKREIL
261
9
10
100
1365


SSP2
VKIAVFGI
183
8
10
100
1366


SSP2
VKNVIGPF
223
8
10
100
1367


SSP2
VKNVIGPFM
223
9
10
100
1368


SSP2
VKYLVIVF
7
8
10
100
1369


SSP2
VKYLVIVFL
7
9
10
100
1370


SSP2
VKYLVIVFLI
7
10
10
100
1371


SSP2
VKYLVIVFLIF
7
11
10
100
1372


SSP2
VRKHLNDRI
140
9
10
100
1373


SSP2
YKIAGGIAGGL
498
11
10
100
1374
















TABLE XIII







Malaria B58 Super Motif Peptides
















No. of
Sequence
Conservancy



Protein
Sequence
Position
Amino Acids
Frequency
(%)
Seq. Id
















CSP
CSSVFNVV
413
8
19
100
1375


CSP
CSYTCONGI
373
9
19
100
1376


CSP
CSVTCONGIQV
373
11
19
100
1377


CSP
EALFQEYQCY
17
10
19
100
1378


CSP
GSSSNTRV
27
8
19
100
1379


CSP
GSSSNTRVL
27
9
19
100
1380


CSP
LAILSVSSF
5
9
19
100
1381


CSP
LAILSVSSFL
5
10
19
100
1382


CSP
LAILSVSSFLF
5
11
19
100
1383


CSP
LSTEWSPCSV
366
10
18
95
1384


CSP
LSVSSFLF
8
8
19
100
1385


CSP
LSVSSFLFV
8
9
19
100
1386


CSP
NAGINLYNB
42
10
18
95
1387


CSP
NANANNAV
335
8
16
84
1388


CSP
NSSIGLIM
421
8
19
100
1389


CSP
NSSIGLIMV
421
9
19
100
1390


CSP
NSSIGLIMVL
421
10
19
100
1391


CSP
NTRVLNEL
31
8
19
100
1392


CSP
NTRVLNELNY
31
10
i9
100
1393


CSP
PSDKHIEQY
346
9
15
79
1394


CSP
PSDKHIEQYL
346
10
15
79
1395


CSP
SSFLFVEAL
11
9
19
100
1396


CSP
SSFLFVEALF
11
10
19
100
1397


CSP
SSIGLIMV
422
8
19
100
1398


CSP
SSIGLIMVL
422
9
19
100
1399


CSP
SSIGLIMVLSF
422
11
19
100
1400


CSP
SSKIRVLNEL
29
10
19
100
1401


CSP
SSSNTRVL
28
8
19
100
1402


CSP
SSSNTRVLNEL
28
11
19
100
1403


CSP
SSVFNVVNSSI
414
11
19
100
1404


CSP
STEWSPCSV
367
9
19
100
1405


CSP
VSSFLFVEAL
10
10
19
100
1406


CSP
VSSFLFVEALF
10
11
19
100
1407


CSP
VKONGIQV
375
9
19
100
1408


CSP
VTCGNGIQVRI
375
11
19
100
1409


CSP
YSLKKNSRSL
63
10
19
100
1410


EXP
ATSVLAGL
77
8
1
100
1411


EXP
ATSVLAGLL
77
9
1
100
1412


EXP
GSGEPLIDV
42
9
1
100
1413


EXP
ISDMIKKEEEL
S4
11
1
100
1414


EXP
KSKYKLATSV
71
10
1
100
1415


EXP
KSKYKLATSVL
71
11
1
100
1416


EXP
KTNKOTOSOV
24
10
1
100
1417


EXP
LAGLLGNV
81
8
1
100
1418


EXP
LAGLLGNVSTV
81
11
1
100
1419


EXP
LALFFIW
9
8
1
100
1420


EXP
LATSVLAGL
76
9
1
100
1421


EXP
LATSVLAGLL
76
10
1
100
1422


EXP
LSVFFLAL
4
8
1
100
1423


EXP
LSVFFLALF
4
9
1
100
1424


EXP
LSVFFLALFF
4
10
1
100
1425


EXP
LSVFFLALFFI
4
11
1
100
1426


EXP
NADPQVTAQDV
134
11
1
100
1427


EXP
NTEKGRHPF
102
9
1
100
1428


EXP
NTEKGRHPFKL
102
11
1
100
1429


EXP
STVLLGGV
89
8
1
100
1430


EXP
STVLLGGVGL
89
10
1
100
1431


EXP
STVLLOOVGLV
89
11
1
100
1432


EXP
TSVLAGLL
78
8
1
100
1433


EXP
TSVLAGLLGNV
78
11
1
100
1434


EXP
VSTVLLGGV
88
9
1
100
1435


EXP
VSTVLLGGVGL
88
11
1
100
1436


LSA
DSKEISII
1689
8
1
100
1437


LSA
ETLQEQQSDL
1193
10
1
100
1438


LSA
ETLQGQQSDL
156
10
1
100
1439


LSA
ETVNISDV
1745
8
1
100
1440


LSA
EIVNISDVNDF
1745
11
1
100
1441


LSA
GSSNSRNRI
42
9
1
100
1442


LSA
HTLETVNI
1742
8
1
100
1443


LSA
HTLETVNISDV
1742
11
1
100
1444


LSA
ISAEYDDSL
1764
9
1
100
1445


LSA
ISAEYDDSLI
1764
10
1
100
1446


LSA
ISDVNDFQI
1749
9
1
100
1447


LSA
ISFYFILV
7
8
1
100
1448


LSA
ISFYFILVNL
7
10
1
100
1449


LSA
ISFYFILVNLL
7
11
1
100
1450


LSA
ISKYEDEI
1757
8
1
100
1451


LSA
ITKYFMKL
1902
8
1
100
1452


LSA
ITTNVEGRRDI
1704
11
1
100
1453


LSA
KADTKKNL
1631
8
1
100
1454


LSA
KSADIQNHTL
1735
10
1
100
1455


LSA
KSLLRNLGV
98
9
1
100
1456


LSA
KSLYDEHI
1854
8
1
100
1457


LSA
KSLYDEHIKKY
1854
11
1
100
1458


LSA
KSSEELSEEKI
1825
11
1
100
1459


LSA
KTKNNENNKF
68
10
1
100
1460


LSA
KTKNNENNKFF
68
11
1
100
1461


LSA
KTNRESITTNV
1698
11
1
100
1462


LSA
LAEDLYGRL
1648
9
1
100
1463


LSA
LAEDLYGRLEI
1648
11
1
100
1464


LSA
LSEDTIKY
1898
8
1
100
1465


LSA
LSED1TKYF
1898
9
1
100
1466


LSA
LSEDITKYFM
1898
10
1
100
1467


LSA
LTNISNVKNV
84
9
1
100
1468


LSA
NSEKDEII
28
8
1
100
1469


LSA
NSRDSKEI
1686
8
1
100
1470


LSA
NSRDSKEISI
1686
10
1
100
1471


LSA
NSRDSKEISII
1686
11
1
100
1472


LSA
PSENERGY
1664
8
1
100
1473


LSA
PSENERGYY
1664
9
1
100
1474


LSA
PSENERGYYI
1664
10
1
100
1475


LSA
QSDLEQDRL
1386
9
1
100
1476


LSA
QSDLEQERL
1590
9
1
100
1477


LSA
QSDSEQERL
519
9
1
100
1478


LSA
QTNFKSLL
94
8
1
100
1479


LSA
QTNFKSLLRNL
94
11
1
100
1480


LSA
RSGSSNSRNRI
40
11
1
100
1481


LSA
RTKASKETL
1187
9
1
100
1482


LSA
SADIQNHTL
1736
9
1
100
1483


LSA
SAEYDDSL
1765
8
1
100
1484


LSA
SAEYDDSLI
1765
9
1
100
1485


LSA
SSEELSEEKI
1826
10
1
100
1486


LSA
SSNSRNRI
43
8
1
100
1487


LSA
TINVEGRRDI
1705
10
1
100
1488


LSA
VSQTNFKSL
92
9
1
100
1489


LSA
VSQINFKSLL
92
10
1
100
1490


SSP2
ASCGVWDEW
242
9
10
100
1491


SSP2
ASKNKEKAL
107
9
10
100
1492


SSP2
ASKNKEKALI
107
10
9
90
1493


SSP2
ASKNKEKALII
107
11
9
90
1494


SSP2
ATPYAGEPAPF
526
11
8
80
1495


SSP2
CAGLAYKF
513
8
10
100
1496


SSP2
CAGLAYKFV
513
9
10
100
1497


SSP2
CAGLAYKFVV
513
10
10
100
1498


SSP2
CSGSIRRHNW
55
10
10
100
1499


SSP2
CSGSIRRHNWV
55
11
10
100
1500


SSP2
DALLQVRKHL
135
10
9
90
1501


SSP2
DASKNKEKAL
106
10
10
100
1502


SSP2
DASKNKEKALI
106
11
9
90
1503


SSP2
DSAWENVKNV
217
10
10
100
1504


SSP2
DSAWENVKNVI
217
11
10
100
1505


SSP2
DSEKEVPSDV
370
10
10
100
1506


SSP2
DSLKESRKL
170
9
9
90
1507


SSP2
ETLGEEDKDL
538
10
10
100
1508


SSP2
GSIRRHNW
57
8
10
100
1509


SSP2
GSIRRHNWV
57
9
10
100
1510


SSP2
GTRSRKREI
260
9
10
100
1511


SSP2
GTRSRKRE3L
260
10
10
100
1512


SSP2
HAVPLAMKL
67
9
10
100
1513


SSP2
HAVPLAMKLI
67
10
10
100
1514


SSP2
IAGGIAGGL
500
9
10
100
1515


SSP2
IAGGIAGGLAL
500
11
10
100
1516


SSP2
IAGGLALL
504
8
10
100
1517


SSP2
IAVFGIGQGI
185
10
10
100
1518


SSP2
KTASCGVW
240
8
10
100
1519


SSP2
KTASCGVWDEW
240
11
10
100
1520


SSP2
LACAGLAY
511
8
10
100
1521


SSP2
LACAGLAYKF
511
10
10
100
1522


SSP2
LACAGLAYKFV
511
11
10
100
1523


SSP2
LALLACAGL
508
9
10
100
1524


SSP2
LALLACAGLAY
508
11
10
100
1525


SSP2
LAMKLIQQL
71
9
10
100
1526


SSP2
LAMKLIQQLNL
71
11
10
100
1527


SSP2
LTDGIPDSI
160
9
10
100
1528


SSP2
NANQLVVI
152
8
10
100
1529


SSP2
NANQLVVIL
152
9
10
100
1530


SSP2
PAPFDETL
533
8
10
100
1531


SSP2
PSCOKCNL
207
8
10
100
1532


SSP2
PSDGKCNLY
207
9
10
100
1533


SSP2
QSQDNNGNRHV
436
11
10
100
1534


SSP2
RSRKREIL
262
8
10
100
1535


SSP2
SAWENVKNV
218
9
10
100
1536


SSP2
SAWENVKNVI
218
10
10
100
1537


SSP2
STNLPYGRTNL
123
11
8
80
1538


SSP2
TASCGVWDEW
241
10
10
100
1539


SSP2
VAFNRFLV
196
8
10
100
1540


SSP2
YADSAWENV
215
9
10
100
1541


SSP2
YAGEPAPF
529
8
8
80
1542
















TABLE XIV







Malaria B62 Super Motif Peptides
















No. of
Sequence
Conservancy 



Protein
Sequence
Position
Amino Acids
Frequency
(%)
Seq. Id.
















CSP
AILSVSSF
6
8
9
100
1543


CSP
AILSVSSFLF
6
10
9
100
1544


CSP
AILSVSSFLFV
6
11
9
100
1545


CSP
ALFQEYQCY
18
9
9
100
1546


CSP
DIEKKKKM
402
9
9
100
1547


CSP
DPNANPNV
130
8
9
100
1548


CSP
ELNYDNAGI
37
9
8
95
1549


CSP
ENINYYGKQENW
52
11
9
100
1550


CSP
EPSDKHIEQY
345
10
5
79
1551


CSP
FLFVEALF
13
8
9
100
1552


CSP
FLFVEALFQEY
13
11
9
100
1553


CSP
FVEALFQEY
IS
9
9
100
1554


CSP
GINLYNELEM
44
10
8
95
1555


CSP
GLIMVLSF
425
8
9
100
1556


CSP
GLIMVLSFLF
425
10
9
100
1557


CSP
HIEQYLKKI
350
9
5
79
1558


CSP
ILSVSSFLF
7
9
9
100
1559


CSP
ILSVSSFLFV
7
10
9
100
1560


CSP
IMVLSFLF
427
8
9
100
1561


CSP
IQNSLSTEW
362
9
5
79
1562


CSP
KKKMEKCSSV
406
11
9
100
1563


CSP
KIQNSLSTEW
361
10
5
79
1564


CSP
KLAILSVSSF
4
10
9
100
1565


CSP
KMEKCSSV
409
8
9
100
1566


CSP
KMEXCSSVF
409
9
9
100
1567


CSP
KMEKCSSVFNV
409
11
9
100
1568


CSP
LIMVLSFLF
426
9
9
100
1569


CSP
MMRKLAILSV
1
10
9
100
1570


CSP
MPNDPNRNV
324
9
9
100
1571


CSP
NLYNELEM
46
8
9
100
1572


CSP
NLYNELEMNY
46
10
9
100
1573


CSP
NLYNELEMNYY
46
11
9
100
1574


CSP
NMPNDPNRNV
323
10
9
100
1575


CSP
NPDPNANPNV
120
10
9
100
1576


CSP
NQGNGQGHNM
315
10
9
100
1577


CSP
NVDPNANPNV
128
10
9
100
1578


CSP
NVVNSSIGLI
418
10
9
100
1579


CSP
NVVNSSIGLIM
418
11
9
100
1580


CSP
RVLNELNY
33
8
9
100
1581


CSP
SIGLIMVLSF
423
10
9
100
1582


CSP
SLSTEWSPCSV
365
11
8
95
1583


CSP
SPCSVTCGNGI
371
11
9
100
1584


CSP
SVFNVVNSSI
415
10
9
100
1585


CSP
SVSSFLFV
9
8
9
100
1586


CSP
SVTCGNGI
374
8
9
100
1587


CSP
SVTCGNGIQV
374
10
9
100
1588


CSP
VVNSSIGLI
419
9
9
100
1589


CSP
VVNSSIGLIM
419
10
9
100
1590


CSP
VVNSSIGLIMV
419
11
9
100
1591


EXP
DMIKKEEELV
56
10
1
100
1592


EXP
DPQVTAQDV
136
9
1
100
1593


EXP
DVHDLISDM
49
9
1
100
1594


EXP
DVHDLISDMI
49
10
1
100
1595


EXP
EPLIDVHDLI
45
10
1
100
1596


EXP
EPNADPQV
132
8
1
100
1597


EXP
EQPQGDDNNLV
147
11
1
100
1598


EXP
EVNKRKSKY
66
9
1
100
1599


EXP
FLALFFII
8
8
1
100
1600


EXP
FLALFFIIF
8
9
1
100
1601


EXP
GLLGNVSTV
83
9
1
100
1602


EXP
ILSVFFLALF
3
10
1
100
1603


EXP
ILSVFFLALFF
3
11
1
100
1604


EXP
KILSVFFLALF
2
11
1
100
1605


EXP
LIDVHDLI
47
8
1
100
1606


EXP
LIDVHDLISDM
47
11
1
100
1607


EXP
LLGGVGLV
92
8
1
100
1608


EXP
LLGGVGLVLY
92
10
1
100
1609


EXP
LLGNVSTV
84
8
1
100
1610


EXP
LVEVNKRKSKY
64
11
1
100
1611


EXP
MIKKEEELV
57
9
1
100
1612


EXP
MIKKEEELVEV
57
11
1
100
1613


EXP
NVSTVLLGGV
87
10
1
100
1614


EXP
PLIDVHDLI
46
9
1
100
1615


EXP
PQGDDNNLV
149
9
1
100
1616


EXP
PQVTAQDV
137
8
1
100
1617


EXP
QPQGDDNNLV
148
10
1
100
1618


EXP
SVFFLALF
5
8
1
100
1619


EXP
SVFFLALFF
5
9
1
100
1620


EXP
SVFFLALFFI
5
10
1
100
1621


EXP
SVFFLALFFII
5
11
1
100
1622


EXP
SVLAGLLGNV
79
10
1
100
1623


EXP
TVLLGOVCILV
90
10
1
100
1624


EXP
VLAGLLGNV
80
9
1
100
1625


EXP
VLLGGVGLV
91
9
1
100
1626


EXP
VLLGGVGLVLY
91
11
1
100
1627


LSA
DIQNHTLETV
1738
10
1
100
1628


LSA
DLDEFKPI
1781
8
1
100
1629


LSA
DLDEFKPIV
1781
9
1
100
1630


LSA
DLDEFKPIVQY
1781
11
1
100
1631


LSA
DLYGRLEI
1651
8
1
100
1632


LSA
DLYGRLEIPAI
1651
11
1
100
1633


LSA
DVLAEDLY
1646
8
1
100
1634


LSA
DVNDFQISKY
1751
10
1
100
1635


LSA
EISAEYDDSLI
1763
11
1
100
1636


LSA
ELPSENERGY
1662
10
1
100
1637


LSA
ELPSENERGYY
1662
11
1
100
1638


LSA
ELSEDITKY
1897
9
1
100
1639


LSA
ELSEDITKYF
1897
10
1
100
1640


LSA
ELSEDITKYFM
1897
11
1
100
1641


LSA
ELTMSNVKNV
83
10
1
100
1642


LSA
EQKEDKSADI
1730
10
1
100
1643


LSA
FIKSLFHI
1877
8
1
100
1644


LSA
FIKSLFHIF
1877
9
1
100
1645


LSA
FILVNLLI
11
8
1
100
1646


LSA
FILVNLLIF
11
9
1
100
1647


LSA
FILVNLLIFHI
11
11
1
100
1648


LSA
FQDEENIGI
1794
9
1
100
1649


LSA
FQDEENIGIY
1794
10
1
100
1650


LSA
FQISKYEDEI
1755
10
1
100
1651


LSA
GIYKELEDLI
1801
10
1
100
1652


LSA
HIFDODNEI
1883
9
1
100
1653


LSA
HIKKYKNDKQV
1860
11
1
100
1654


LSA
HILYISFY
3
8
1
100
1655


LSA
HILYISFYF
3
9
1
100
1656


LSA
HILYISFYFI
3
10
1
100
1657


LSA
HLEEKKDOSI
1718
10
1
100
1658


LSA
HVLSHNSY
59
8
1
100
1659


LSA
IIEKTNRESI
1695
10
1
100
1660


LSA
IIKNSEKDEI
25
10
1
100
1661


LSA
IIKNSEKDEII
25
11
1
100
1662


LSA
IINDDDDKKKY
127
11
1
100
1663


LSA
ILVNLLIF
12
8
1
100
1664


LSA
ILVNLLIFHI
12
10
1
100
1665


LSA
ILYISFYF
4
8
1
100
1666


LSA
ILYISFYFI
4
9
1
100
1667


LSA
ILYISFYFILV
4
11
1
100
1668


LSA
IQNHTLETV
1739
9
1
100
1669


LSA
IQNHTLETVNI
1739
11
1
100
1670


LSA
IVDELSEDI
1894
9
1
100
1671


LSA
KLIKNSEKDEI
24
11
1
100
1672


LSA
KIKKGKKY
1834
8
1
100
1673


LSA
KLNKEGKLI
116
9
1
100
1674


LSA
KPIVQYDNF
1786
9
1
100
1675


LSA
KPNDKSLY
1850
8
1
100
1676


LSA
KQVNKEKEKF
1868
10
1
100
1677


LSA
KQVNKEKEKFI
1868
11
1
100
1678


LSA
LIFHINGKI
17
9
1
100
1679


LSA
LIFHINGKII
17
10
1
100
1680


LSA
LLIFHINGKI
16
10
1
100
1681


LSA
LLIFHINGKII
16
11
1
100
1682


LSA
LLRNLGVSENI
100
11
1
100
1683


LSA
LPSENERGY
1663
9
1
100
1684


LSA
LPSENERGYY
1663
10
1
100
1685


LSA
LPSENERGYYI
1663
11
1
100
1686


LSA
LQIVDELSEDI
1892
11
1
100
1687


LSA
LVNLLIFHI
13
9
1
100
1688


LSA
NISDVNDF
1748
8
1
100
1689


LSA
NISDVNDFQI
1748
10
1
100
1690


LSA
NLDDLDEGI
1815
9
1
100
1691


LSA
NLERKKEHGDV
1637
11
1
100
1692


LSA
NLGVSENI
103
8
1
100
1693


LSA
NLGVSENIF
103
9
1
100
1694


LSA
NLLIFHINGKI
15
11
1
100
1695


LSA
NVEGRRDI
707
8
1
100
1696


LSA
NVKNVSQTNF
88
10
1
100
1697


LSA
PIVQYDNF
787
8
1
100
1698


LSA
QISKYEDEI
756
9
1
100
1699


LSA
QIVDELSEDI
893
10
1
100
1700


LSA
QVNKEKEKF
869
9
1
100
1701


LSA
QVNKEKEKFI
869
10
1
100
1702


LSA
SIIEKTNRESI
694
11
1
100
1703


LSA
SLLRNLGV
99
8
1
100
1704


LSA
SLYDEHIKKY
855
10
1
100
1705


LSA
TLETVMSDV
743
10
1
100
1706


LSA
TMSNVKNV
85
8
1
100
1707


LSA
TVNISDVNDF
746
10
1
100
1708


LSA
YISFYFILV
6
9
1
100
1709


SSP2
ALLACAGLAY
509
10
10
100
1710


SSP2
AVFGIGQGI
186
9
10
100
1711


SSP2
AVFGIGQGINV
186
11
10
100
1712


SSP2
AVPLAMKLI
68
9
10
100
1713


SSP2
DLDEPEQF
546
8
10
100
1714


SSP2
DLFLVNGRDV
19
10
10
100
1715


SSP2
DQPRPRGDNF
302
10
9
90
1716


SSP2
DVQNNIVDEI
27
10
10
100
1717


SSP2
EIKYREEV
35
8
9
90
1718


SSP2
EQFRLPEENEW
551
11
10
100
1719


SSP2
EVCNDEVDLY
41
10
8
80
1720


SSP2
EVDLYLLM
46
8
8
80
1721


SSP2
EVEKTASCGV
237
10
10
100
1722


SSP2
EVEKTASCGVW
237
11
10
100
1723


SSP2
FLIFFDLF
14
8
10
100
1724


SSP2
FLIFFDLFLV
I4
10
10
100
1725


SSP2
FLVNGRDV
21
8
10
100
1726


SSP2
FMKAVCVEV
230
9
10
100
1727


SSP2
FVVPGAATPY
520
10
8
80
1728


SSP2
G1GQGNV
189
8
10
100
1729


SSP2
GIGQGINVAF
189
10
10
100
1730


SSP2
GINVAFNRF
193
9
10
100
1731


SSP2
GINVAFNRFLV
193
11
10
100
1732


SSP2
GLAYKFVV
515
8
10
100
1733


SSP2
GPFMKAVCV
228
9
10
100
1734


SSP2
GPFMKAVCVEV
228
11
10
100
1735


SSP2
GQGINVAF
191
8
10
100
1736


SSP2
GQGINVAFNRF
191
11
10
100
1737


SSP2
GVKIAVFGI
182
9
10
100
1738


SSP2
GVWDEWSPCSV
245
11
10
100
1739


SSP2
HLGNVKYLV
3
9
10
100
1740


SSP2
HLGNVKYLVI
3
10
10
100
1741


SSP2
HLGNVKYLVIV
3
11
10
100
1742


SSP2
HPSDGKCNLY
206
10
10
100
1743


SSP2
ILTDGIPDS1
159
10
10
100
1744


SSP2
IPEDSEKEV
367
9
10
100
1745


SSP2
IVDEIKYREEV
32
11
9
90
1746


SSP2
IVFLIFFDLF
12
10
10
100
1747


SSP2
KIAVFGIGQGI
184
11
10
100
1748


SSP2
LEFFDLFLV
15
9
10
100
1749


SSP2
LLACAGLAY
510
9
10
100
1750


SSP2
LLACAGLAYKF
510
11
10
100
1751


SSP2
LLMDCSGSI
51
9
10
100
1752


SSP2
LLSTNLPY
121
8
9
90
1753


SSP2
LMDCSGS1
52
8
10
100
1754


SSP2
LQVRKHLNDRI
138
11
9
90
1755


SSP2
LVIVFLIF
10
8
to
100
1756


SSP2
LVIVFLIFF
10
9
10
100
1757


SSP2
LVNGRDVQNNI
22
11
10
100
1758


SSP2
LVVILTDGI
156
9
10
100
1759


SSP2
NIPEDSEKEV
366
10
10
100
1760


SSP2
NIVDEIKY
31
8
10
100
1761


SSP2
NLYADSAW
213
8
10
100
1762


SSP2
NLYADSAWENV
213
11
10
100
1763


SSP2
NPEDDRENF
382
10
10
100
1764


SSP2
NQLVVILTDGI
154
11
10
100
1765


SSP2
NVAFNRFLV
195
9
10
100
1766


SSP2
NVIGPFMKAV
225
10
10
100
1767


SSP2
NVKNVIGPF
222
9
10
100
1768


SSP2
NVKNVIGPFM
222
10
10
100
1769


SSP2
NVKYLVIV
6
8
10
100
1770


SSP2
NVKYLVIVF
6
9
10
100
1771


SSP2
NVKYLVIVFLI
6
11
10
100
1772


SSP2
QLVVILTDG1
155
10
10
100
1773


SSP2
QPRPRGDNF
303
9
9
90
1774


SSP2
QPRPRGDNFAV
303
11
9
90
1775


SSP2
QVRKHLNDRI
139
10
9
90
1776


SSP2
RINRENANQLV
147
11
10
100
1777


SSP2
RLPEENEW
554
8
10
100
1778


SSP2
RPRGDNFAV
305
9
9
90
1779


SSP2
SIRRHNWV
58
8
10
100
1780


SSP2
SLLSTNLPY
120
9
9
90
1781


SSP2
SQDNNGNRHV
437
10
10
100
1782


SSP2
TPYAGEPAPF
527
10
8
80
1783


SSP2
VIGPFMKAV
226
9
10
100
1784


SSP2
VIGPFMKAVCV
226
11
10
100
1785


SSP2
VILTDGIPDSI
158
11
10
100
1786


SSP2
VIVFLIFF
11
8
10
100
1787


SSP2
VIVFLIFFDLF
11
11
10
100
1788


SSP2
VPGAATPY
522
8
8
80
1789


SSP2
VPLAMKLI
69
8
10
100
1790


SSP2
VQNNIVDEI
28
9
10
100
1791


SSP2
VQNNIVDEIKY
28
11
10
100
1792


SSP2
VVILTDGI
157
8
10
100
1793


SSP2
VVPGAATPY
521
9
8
80
1794


SSP2
WVNHAVPLAM
64
10
8
80
1795


SSP2
YLLMDCSGSI
50
10
10
100
1796


SSP2
YLVIVFLI
9
8
10
100
1797


SSP2
YLVIVFLIF
9
9
10
100
1798


SSP2
YLVIVFLFF
9
10
10
100
1799
















TABLE XV







Malaria A01 Motif Peptides With Binding Information

















No. of
Sequence 
Conservancy




Protein
Sequence
Position
Amino Acids
Freq.
(%)
A*0101
Seq. Id.

















CSP
DNAGINLY
41
8
19
100

1800


CSP
EPSDKHIEQY
345
10
15
79

1801


CSP
FVEALFQEY
15
9
19
100
3.4000
1802


CSP
NTRYLNELNY
31
10
19
100
0.0096
1803


CSP
NYDNAGINLY
39
10
18
95
0.0012
1804


CSP
PSDKHIEQY
346
9
15
79

1805


CSP
VEALFQEY
16
8
19
100

1806


CSP
VEALFQEYQCY
16
11
19
100

1807


CSP
YNELEMNY
48
8
19
100

1808


CSP
YNELEMNYY
48
9
19
100

1809


EXP
LVEVNKRKSKY
64
11
1
100

1810


LSA
DDDDKKKY
130
8
1
100

1811


LSA
DEENIGIY
1796
8
1
100

1812


LSA
DLDEFKPIVQY
1781
11
1
100

1813


LSA
EDEISAEY
1761
8
1
100

1814


LSA
ELSEDITKY
1897
9
1
100

1815


LSA
FQDEENIGIY
1794
10
1
100
1.1000
1816


LSA
HGDVLAEDLY
1644
10
1
100
0.0012
1817


LSA
INDDDDKKKY
128
10
1
100

1818


LSA
KSLYDEHIKKY
1854
11
1
100

1819


LSA
KYEDEISAEY 
1759
10
1
100
0.0011
1820


LSA
LDEFKPIVQY
1782
10
1
100

1821


LSA
LPSENERGY
1663
9
1
100
0.6700
1822


LSA
LPSENERGYY
1663
10
1
100
0.0011
1823


LSA
LSEDITKY
1898
8
1
100

1824


LSA
LYDEHIKKY
1856
9
1
100
0.0011
1825


LSA
NDDDDKKKY
129
9
1
100

1826


LSA
PSENERGY
1664
8
1
100

1827


LSA
PSENERGYY
1664
9
1
100
0.0790
1828


LSA
QDEENIGIY
1795
9
1
100

1829


LSA
SEEKIKKGKKY
1831
11
1
100

1830


LSA
VDELSEDITKY
1895
11
1
100

1831


LSA
VNDFQISKY
1752
9
1
100

1832


LSA
YDEHIKKY
1857
8
1
100

1833


LSA
YEDEISAEY
1760
9
1
100
0.0012
1834


SSP2
CNDEVDLY
43
8
8
80

1835


SSP2
HPSDGKCNLY
206
10
10
100
0.0260
1836


SSP2
LLACAGLAY
510
9
10
100

1837


SSP2
LLSTNLPY
121
8
9
90

1838


SSP2
PSDGKCNLY
207
9
10
100
0.5400
1839
















TABLE XVI







Malaria A3 Motif Peptides With Binding Information

















No. of
Sequence
Conservancy




Protein
Sequence
Position
Amino Acids
Frequency
(%)
A*0301
Seq. Id

















CSP
AILSVSSF
6
8
19
100

1840


CSP
AILSVSSFLF
6
10
19
100

1841


CS!
ALFQEYQCY
I8
9
19
100
0.0027
1842


CSP
CGNGIQVR
377
8
19
100

1843


CSP
CONGIQVRIK
377
10
19
100
0.0005
1844


CSP
DONNEDNEK
96
9
19
100
0.0001
1845


CSP
DGNNEDNEKLR
96
11
19
100

1846


CSP
DGNNNNGDNGR
77
11
17
89

1847


CSP
DGNPDPNA
118
8
19
100

1848


CSP
D1EKKKK
402
8
19
100

1849


CSP
D1EKKKKMEK
402
11
19
100

1850


CSP
EALFQEYQCY
17
10
19
100
0.0005
1851


CSP
EDNEKLRK
100
8
19
100

1852


CSP
EDNEKLRKPK
100
10
19
100
0.0005
1853


CSP
EDNEKLRKPKH
100
11
19
100

1854


CSP
EGKDEDKR
88
8
19
100

1855


CSP
ELBANYYOK
50
9
19
100
0.0001
1856


CSP
FLFVEALF
13
8
19
100

1857


CSP
FLFVEALFQEY
13
11
19
100

1858


CSP
FVEALFQEY
15
9
19
100
0.0001
1859


CSP
GDGNPDPNA
117
9
19
100

1860


CSP
GDNGREOK
83
8
19
100

1861


CSP
GIQVRIKPGSA
380
11
19
100

1862


CSP
GLIMVLSF
425
8
19
100

1863


CSP
GLIMVLSFLF
425
10
19
100

1864


CSP
HIEQYLKK
350
8
15
79

1865


CSP
KKMEKCSSVF
407
11
19
100

1866


CSP
IGLIMVLSF
424
9
19
100

1867


CSP
IGLIMVLSFLF
424
11
19
100

1868


CSP
ILSVSSFLF
7
9
19
100

1869


CSP
IMVLSFLF
427
8
19
100

1870


CSP
KLAILSVSSF
4
10
19
100

1871


CSP
KLRKPKHK
104
8
19
100

1872


CSP
KLAKANKK
104
9
19
100
0.1300
1873


CSP
KLRKPKEIKKLK
104
11
19
100

1874


CSP
KMEKCSSVF
409
9
19
100

1875


CSP
LAILSVSSF
5
9
19
100

1876


CSP
LAILSVSSFLF
5
11
19
100

1877


CSP
LDYENDIEK
397
9
18
95
0.0002
1878


CSP
LDYENDIEKK
397
10
18
95
0.0005
1879


CSP
LFQEYQCY
19
8
19
100

1880


CSP
LFVEALFQEY
14
10
19
100

1881


CSP
LIMVLSFLF
426
9
19
100

1882


CSP
LSVSSFLF
8
8
19
100

1883


CSP
LSVSSFLFVEA
8
11
19
100

1884


CSP
NANANNAVK
335
9
16
84
0.0001
1885


CSP
NANPNANPNA
300
10
19
100

1886


CSP
NANPNANPNK
304
10
19
100
0.0005
1887


CSP
NANPNVDPNA
196
10
19
100

1888


CSP
NDIEKKICK
401
9
19
100
0.0001
1889


CSP
NDPNRNVDENA
326
11
19
100

1890


CSP
NGDNGREGK
82
9
19
100
0.0001
1891


CSP
NGIQVRIK
379
8
19
100

1892


CSP
NGREGKDEDK
85
10
19
100
0.0005
1893


CSP
NGREGKDEDKR
85
11
19
100

1894


CSP
NLYNELEMNY
46
10
19
100
0.0005
1895


CSP
NLYNELEMNYY
46
11
19
100

1896


CSP
NMPNDPNR
323
8
19
100

1897


CSP
NTRVLNELNY
31
10
19
100
0.0005
1898


CSP
NVDENANA
331
8
19
100

1899


CSP
NVDENANANNA
331
11
16
84

1900


CSP
NVDPNANPNA
200
10
19
100

1901


CSP
PGDGNPDPNA
116
10
19
100

1902


CSP
PSDKHIEQY
346
9
15
79

1903


CSP
PSDKHIEQYLK
346
11
15
79

1904


CSP
QCYGSSSNTR
24
10
19
100

1905


CSP
QGHNMPNDPNR
320
11
19
100

1906


CSP
QVRIKPGSA
382
9
19
100

1907


CSP
RDONNEDNEK
95
10
19
100
0.0005
1908


CSP
RVLNEI-NY
33
8
19
100

1909


CSP
RVLNELNYDNA
33
11
19
100

1910


CSP
SDKHIEQY
347
8
15
79

1911


CSP
SDKHIEQYLK
347
10
15
79

1912


CSP
SDKHIEQYLKK
347
11
15
79

1913


CSP
SFLFVEALF
12
9
19
100

1914


CSP
StGLIMVLSF
423
10
19
100

1915


CSP
SSFLFVEA
11
8
19
100

1916


CSP
SSFLFVEALF
11
10
19
100

1917


CSP
SSIGLIMVLSF
422
11
19
100

1918


CSP
SVSSFLFVEA
9
10
19
100

1919


CSP
SYPCGNGIQVR
374
11
19
100

1920


CSP
TCGNGIQVR
376
9
19
100

1921


CSP
TCGNGIQVRIK
376
11
19
100

1922


CSP
VDENANANNA
332
10
16
84

1923


CSP
VDPNANPNA
201
9
19
100

1924


CSP
VLNELNYDNA
34
10
19
100

1925


CSP
VSSFLFVEA
10
9
19
100

1926


CSP
VSSFLFVEALF
10
11
19
100

1927


CSP
VTCGNGIQVR
375
10
19
100
0.0005
1928


CSP
YDNAGINLY
40
9
18
95

1929


CSP
YGKQENWY
56
8
19
100

1930


CSP
YGKQENWYSLK
56
11
19
100

1931


CSP
YGSSSNTR
26
8
19
100

1932


CSP
YSLKKNSR
63
8
19
100

1933


EXP
ADNANPDA
118
8
1
100

1934


EXP
ADSESNGEPNA
125
11
1
100

1935


EXP
ALFFIFNK
10
9
1
100
1.1000
1936


EXP
DDNNLVSGPEH
152
11
1
100

1937


EXP
DLISDMIK
52
8
1
100

1938


EXP
DLISDMIKK
52
9
1
100
0.0001
1939


EXP
DSESNGEPNA
126
10
1
100

1940


EXP
DVHDLISDMIK
49
11
1
100

1941


EXP
ELVEVNKR
63
8
1
100

1942


EXP
ELVEVNKRK
63
9
1
100
0.0001
1943


EXP
ELVEVNKRKSK
63
11
1
100

1944


EXP
ESLAEKTNK
19
9
1
100
0.0001
1945


EXP
ESNGEPNA
128
8
1
100

1946


EXP
EVNKRKSK
66
8
1
100

1947


EXP
EVNKRKSKY
66
9
1
100
0.0001
1948


EXP
EVNKRKSKYK
66
10
1
100
0.0005
1949


EXP
FFIIFNKESLA
12
11
1
100

1950


EXP
FFLALFFIIF
7
10
1
100

1951


EXP
FIIFNKESLA
13
10
1
100

1952


EXP
FLALFFIIF
8
9
1
100

1953


EXP
FLALFFIIFNK
8
11
1
100

1954


EXP
GGVGLVLY
94
8
1
100

1955


EXP
GLVLYNTEK
97
9
1
100
0.0069
1956


EXP
GLVLYNTEKGR
97
11
1
100

1957


EXP
GSGEPLIDVH
42
10
1
100
0.0005
1958


EXP
GSGVSSKK
30
8
1
100

1959


EXP
GSGVSSKKK
30
9
1
100
0.0003
1960


EXP
GSGVSSKKKNK
30
11
1
100

1961


EXP
GSSDPADNA
113
9
1
100

1962


EXP
GTGSGVSSK
28
9
1
100
0.0039
1963


EXP
GTGSGVSSKK
28
10
1
100
0.0071
1964


EXP
GTGSGVSSKKK
28
11
1
100

1965


EXP
GVGLVLYNTEK
95
11
1
100

1966


EXP
GVSSKKKNK
32
9
1
100
0.0001
1967


EXP
GVSSKKKNKK
32
10
1
100
0.0011
1968


EXP
HDLISDMIK
51
9
1
100
0.0001
1969


EXP
HDLISDMIKK
51
10
1
100
0.0009
1970


EXP
IFNKESLA
15
8
1
100

1971


EXP
IFNKESLAEK
15
10
1
100
0.0005
1972


EXP
IGSSDPADNA
112
10
1
100

1973


EXP
IIFNKESLA
14
9
1
100

1974


EXP
IIFNKESLAEK
14
11
1
100

1975


EXP
ILSVFFLA
3
8
1
100

1976


EXP
ILSVFFLALF
3
10
1
100.

1977


EXP
ILSVFFLALFF
3
11
1
100

1978


EXP
KGSGEPLIDVH
41
11
1
100

1979


EXP
KGTGSGVSSK
27
10
1
100
0.0005
1980


EXP
KGTGSGVSSKK
27
11
1
100

1981


EXP
KIGSSDPA
111
8
1
100

1982


EXP
KlGSSDPADNA
111
11
1
100

1983


EXP
K1LSVFFLA
2
9
1
100
0.1400
1984


EXP
KILSVFFLALF
2
11
1
100

1985


EXP
KLATSVLA
75
8
1
100

1986


EXP
LALFFIIF
9
8
1
100

1987


EXP
LALFFIIFNK
9
10
1
100
0.0140
1988


EXP
LFFIIFNK
11
8
1
100

1989


EXP
LGGVGLVLY
93
9
1
100
0.0001
1990


EXP
LISDMIKK
53
8
1
100

1991


EXP
LLGGVGLVLY
92
10
1
100
0.0034
1992


EXP
LSVFFLALF
4
9
1
100

1993


EXP
LSVFFLALFF
4
10
1
100

1994


EXP
LVEVNKRK
64
8
1
100

1995


EXP
LVEVNKRKSK
64
10
1
100
0.0005
1996


EXP
LVEVNKRKSKY
64
11
1
100

1997


EXP
LVLYNIEK
98
8
1
100

1998


EXP
LVLYNTEKGR
98
10
1
100
0.0005
1999


EXP
LVLYNTEKGRH
99
11
1
100

2000


EXP
NADPQVTA
134
8
1
100

2001


EXP
NLVSGPEH
155
8
1
100

2002


EXP
NTEKGRHPF
102
9
1
100

2003


EXP
NTEKGRHPFK
102
10
1
100
0.0047
2004


EXP
PADNANPDA
117
9
1
100

2005


EXP
PFKIGSSDPA
109
10
1
100

2006


EXP
SDPADNANPDA
115
11
1
100

2007


EXP
SGEPLIDVH
43
9
1
100
0.0001
2008


EXP
SGVSSKKK
31
8
1
100

2009


EXP
SGVSSKKKNK
31
10
1
100
0.0005
2010


EXP
SGVSSKKKNKK
31
11
1
100

2011


EXP
SLAEKITIK
20
8
1
100

2012


EXP
SSDPADNA
114
8
1
100

2013


EXP
SSKKKNKK
34
8
1
100

2014


EXP
SVFFLALF
5
8
1
100

2015


EXP
SVFFLALFF
5
9
1
100

2016


EXP
TGSGVSSK
29
8
1
100

2017


EXP
MSGVSSKK
29
9
1
100
0.0001
2018


EXP
TGSGVSSKKK
29
10
1
100
0.0005
2019


EXP
VFFLALFF
6
8
1
100

2020


EXP
VFFLALFFIIF
6
11
1
100

2021


EXP
VGLVLYNTEK
96
10
1
100
0.0005
2022


EXP
VLLGGVGLVLY
91
11
1
100

2023


EXP
VLYNTEKGR
99
9
1
100
0.0110
2024


EXP
VLYNTEKGRH
99
10
1
100
0.0029
2025


EXP
VSSKKKNK
33
8
1
100

2026


EXP
VSSKKKNKK
33
9
1
100
0.0001
2027


LSA
ADTKKNLER
1632
9
1
100

2028


LSA
ADTKKNLERK
1632
10
1
100
0.0001
2029


LSA
ADTKKNLERKK
1632
11
1
100

2030


LSA
AIELPSENER
1660
10
1
100
0.0001
2031


LSA
DDDDKKKY
130
8
1
100

2032


LSA
DDDDKKKY1K
130
10
1
100
0.0001
2033


LSA
DDDKKKYIK
131
9
1
100
0.0001
2034


LSA
DDEDLDEF
1778
8
1
100

2035


LSA
DDEDLDEFK
1778
9
1
100
0.0001
2036


LSA
DDKKKYIK
132
8
1
100

2037


LSA
DDLDEG1EK
1817
9
1
100
0.0001
2038


LSA
DGSIKPEQK
1724
9
1
100
0.0001
2039


LSA
DIHKGHLEEK
1713.
10
1
100
0.0004
2040


LSA
DIHKGHLEEKK
1713
11
1
100

2041


LSA
DITKYFMK
1901
8
1
100

2042


LSA
DLDEFKPIVQY
1781
11
1
100

2043


LSA
DLDEGIEK
1818
8
1
100

2044


LSA
DLEEKAAK
148
8
1
100

2045


LSA
DLEQERLA
1388
8
1
100

2046


LSA
DLEQDRLAK
1388
9
1
100
0.0001
2047


LSA
DLEQDRLAKEK
1388
11
1
100

2048


LSA
DLEQERLA
1609
8
1
100

2049


LSA
DLEQERLAK
1609
9
1
100
0.0001
2050


LSA
DLEQERLAKEK
1609
11
1
100

2051


LSA
DLEQERLANEK
1524
11
1
100

2052


LSA
DLEQERRA
1575
8
1
100

2053


LSA
DLEQERRAK
1575
9
1
100
0.0001
2054


LSA
DLEQERRAKEK
1575
11
1
100

2055


LSA
DLEQRKADTK
1626
10
1
100
0.0001
2056


LSA
DLEQRKADTKK
1626
11
1
100

2057


LSA
DLERTKASK
1184
9
1
100
0.0001
2058


ISA
DLYGRLEIPA
1651
10
1
100

2059


LSA
DSEQERLA
521
8
1
100

2060


LSA
DSEQERLAK
521
9
1
100
0.0001
2061


LSA
DSEQERLAKEK
521
11
1
100

2062


LSA
DSKEISIIEK
1689
10
1
100
0.0001
2063


LSA
DTKKNLER
1633
8
1
100

2064


LSA
DTKKNLERK
1633
9
1
100
0.0001
2065


LSA
DTKKNLERKK
1633
10
1
100
0.0001
2066


LSA
DVLAEDLY
1646
8
1
100

2067


LSA
DVLAEDLYGR
1646
10
1
100
0.0001
2068


LSA
DVNDFQISK
1751
9
1
100
0.0001
2069


LSA
DVNDFQISKY
1751
10
1
100
0.0003
2070


LSA
EDDEDLDEF
I777
9
1
100

2071


ISA
EDDEDLDEFK
1777
10
1
100
0.0001
2072


LSA
EDEISAEY
1761
8
1
100

2073


LSA
EDITKYFMK
1900
9
1
100
0.0001
2074


LSA
EDKSADIQNH
I733
10
1
100

2075


LSA
EDLEEKAA
147
8
1
100

2076


LSA
EDLEEKAAK
147
9
1
100
0.0002
2077


LSA
EDLYGRLEIPA
1650
11
1
100

2078


ISA
EFKPIVQY
1784
8
1
100

2079


LSA
EFKPIVQYDNF
1784
11
1
100

2080


LSA
EGRRDIHK
1709
8
1
100

2081


LSA
EGRRDIHKGH
1709
10
1
100
0.0001
2082


LSA
EIIKSNLR
33
8
1
100

2083


LSA
EISIIEKTNR
1692
10
1
100
0.0001
2084


LSA
ELEDLIEK
1805
8
1
100

2085


LSA
ELPSENER
1662
8
1
100

2086


LSA
ELPSENERGY
1662
10
1
100
0.0001
2087


LSA
ELPSENERGYY
1662
11
1
100

2088


LSA
ELSEDITK
1897
8
1
100

2089


LSA
ELSEDITKY
1897
9
1
100
0.0002
2090


LSA
ELSEDITKYF
1897
10
1
100

2091


LSA
ELSEEKIK
1829
8
1
100

2092


LSA
ELSEEKIKK
1929
9
1
100
0.0002
2093


LSA
ELSEEKIKKGK
1829
11
1
100

2094


LSA
ELTMSNVK
83
8
1
100

2095


LSA
ESITTNVEGR
1702
10
1
100
0.0001
2096


LSA
ESMNVEGRR
1702
11
1
100

2097


LSA
ETVNISDVNDF
1745
11
1
100

2098


LSA
FIKSLFHIF
1877
9
1
100

2099


LSA
FILVNLLIF
11
9
1
100

2100


LSA
FILVNLLIFH
11
10
1
100
0.0310
2101


LSA
FLKENKLNK
111
9
1
100
0.0260
2102


LSA
GDVLAEDLY
1645
9
1
100

2103


LSA
GDVLAEDLYGR
1645
11
1
100

2104


LSA
GSIKPEQK
1725
8
1
100

2105


LSA
GSIKPEQKEDK
1725
11
1
100

2106


LSA
GSSNSRNR
42
8
1
100

2107


LSA
GVSENIFLK
105
9
1
100
0.2700
2108


LSA
HGDVLAEDLY
1644
10
1
100
0.0001
2109


LSA
HIINDDDDK
126
9
1
100
0.0002
2110


LSA
H11NDDIDDKK
126
10
1
100
0.0001
2111


LSA
HITNDDDDKKK
126
11
1
100

2112


LSA
HIKKYKNDK
1860
9
1
100
0.0002
2113


LSA
HILYISFY
3
8
1
100

2114


LSA
HILYISFYF
3
9
1
100

2115


LSA
HINGKIIK
20
8
1
100

2116


LSA
HLEEKKDGSIK
1718
11
1
100

2117


LSA
HVLSHNSY
59
8
1
100

2118


LSA
HVLSHNSYEK
59
10
1
100
0.0170
2119


LSA
IFHINGKIIK
18
10
1
100
0.0001
2120


LSA
IFLKENKLINK
110
10
1
100
0.0001
2121


LSA
IINDDDDK
127
8
1
100

2122


LSA
IINDDDDKK
127
9
1
100
0.0002
2123


LSA
IINDDDDKKK
127
10
1
100
0.0001
2124


LSA
IINDDDDKKKY
127
11
1
100

2125


LSA
ILVNLLIF
12
8
1
100

2126


LSA
ILVNLLIFH
12
9
1
100
0.0150
2127


LSA
ILYISFYF
4
8
1
100

2128


LSA
ISDVNDFQISK
1749
11
1
100

2129


LSA
ISIIEKTNR
1693
9
1
100
0.0001
2130


LSA
ISKYEDEISA
1757
10
1
100

2131


LSA
ITTNVEGR
1704
8
1
100

2132


LSA
ITTNVEGRR
1704
9
1
100
0.0002
2133


LSA
IVDELSEDMC
1894
11
1
100

2134


LSA
KADTKKNLER
1631
10
1
100
0.0001
2135


LSA
KADTKKNLERK
631
11
1
100

2136


LSA
KDBIKSNLR
31
10
1
100

2137


LSA
KDGSIKPEQK
1723
10
1
100
0.0004
2138


LSA
KDKELTMSNVK
80
11
1
100

2139


LSA
KDNNFKPNDK
1845
10
1
100
0.0001
2140


LSA
KFIKSLFH
1876
8
1
100

2141


LSA
KFIKSLFHIF
1876
10
1
100

2142


LSA
KGHLEEKK
1716
8
1
100

2143


LSA
KGKKYEKTK
1837
9
1
100
0.0002
2144


LSA
KIWNSEK
24
8
1
100

2145


LSA
KIKKGKKY
1834
8
1
100

2146


LSA
KIKKGKKYEK
1834
10
1
100
0.0081
2147


LSA
KLNKEGKLIEH
116
11
1
100

2148


LSA
KLQEQQSDLER
1177
11
1
100

2149


LSA
KSADIQNH
1735
8
1
100

2150


LSA
KSLYDEHIK
1854
9
1
100
0.0005
2151


LSA
KSLYDEHIKK
1854
10
1
100
0.0094
2152


LSA
KSLYDEHIKKY
1854
11
1
100

2153


LSA
KSSEELSEEK
1825
10
1
100
0.0001
2154


LSA
KTKDNNFK
1843
8
1
100

2155


LSA
KIKNNENNK
68
9
1
100
0.0028
2156


LSA
KTKNNENNKF
68
10
1
100

2157


LSA
KTKNNENNKFF
68
11
1
100

2158


LSA
LAEDLYGR
1648
8
1
100

2159


LSA
LAKEKLQEQQR
1615
11
1
100

2160


LSA
LANEKLQEQQR
1530
11
1
100

2161


LSA
LDDLDEGIEK
1816
10
1
100
0.0001
2162


LSA
LDEFKPIVQY
1782
10
1
100

2163


LSA
LGVSENIF
104
8
1
100

2164


LSA
LGVSENIFLK
104
10
1
100
0.0001
2165


LSA
LIFHINGK
17
8
1
100

2166


LSA
LIFHINGKIIK
17
11
1
100

2167


LSA
LLIFHINGK
16
9
1
100
0.0260
2168


LSA
LSEDMCY
1898
8
1
100

2169


LSA
LSEDITKYF
1898
9
1
100

2170


LSA
LSEDITKYFMK
1898
11
1
100

2171


LSA
LSEEKIKK
1830
8
1
100

2172


LSA
LSEEKIKKGK
1830
10
1
100
0.0004
2173


LSA
LSEEKIKKGKK
1830
11
1
100

2174


LSA
LSHNSYEK
61
8
1
100

2175


LSA
LSHNSYEKTK
61
10
1
100
0.0004
2176


LSA
LVNLLIFH
13
8
1
100

2177


LSA
NDDDOKKK
129
8
1
100

2178


LSA
NDDDDKKKY
129
9
1
100

2179


LSA
NDDDDKKKYIK
129
11
1
100

2180


LSA
NDFQISKY
1753
8
1
100

2181


LSA
NDKQVNKEK
1866
9
1
100
0.0002
2182


LSA
NDKQVNKEKEK
1866
11
1
100

2183


LSA
NDKSLYDER
1852
9
1
100

2184


LSA
NDKSLYDEHIK
1852
11
1
100

2185


LSA
NFKPNDKSLY
1848
10
1
100

2186


LSA
NFQDEENIGIY
1793
11
1
100

2187


LSA
NGKIIKNSEK
22
10
1
100
0.0004
2188


LSA
NIFLKENK
109
8
1
100

2189


LSA
NIFLKENKLNK
109
11
1
100

2190


LSA
NISDVNDF
1748
8
1
100

2191


LSA
NLDDLDEGIEK
1815
11
1
100

2192


LSA
NLERKKEH
1637
8
1
100

2193


LSA
NLGVSENIF
103
9
1
100

2194


LSA
NILVSENIFLK
103
11
1
100

2195


LSA
NLLIFHINGK
15
10
1
100
0.0049
2196


LSA
NLRSGSSNSR
38
10
1
100
0.0004
2197


LSA
NSEKDEIIK
28
9
1
100
0.0002
2198


LSA
NSRNRINEEK
45
10
1
100
0.0004
2199


LSA
NSRNRINEEKH
45
11
1
100

2200


LSA
NVEGRRDIH
1707
9
1
100
0.0002
2201


LSA
NVEGRRDIHK
1707
10
1
100
0.0004
2202


LSA
NVKNVSQTNF
88
10
1
100

2203


LSA
NVKNVSQTNFK
88
11
1
100

2204


LSA
NVSQTNFK
91
8
1
100

2205


LSA
PAIELPSENER
1659
11
1
100

2206


LSA
PIVQYDNF
1787
8
1
100

2207


LSA
PSENERGY
1664
8
1
100

2208


LSA
PSENERGYY
1664
9
1
100
0.0001
2209


LSA
QDEENIGIY
1795
9
1
100

2210


LSA
QDEENIGIYK
1795
10
1
100
0.0004
2211


LSA
QDNRGNSR
1681
8
1
100

2212


LSA
QDNRGNSRDSK
1681
11
1
100

2213


LSA
QDRLAKEK
1391
8
1
100

2214


LSA
QGQQQSDLEQER
1128
11
1
100

2215


LSA
QISKYEDEISA
756
11
1
100

2216


LSA
QSDLEQDR
386
8
1
100

2217


LSA
QSDLEQDRLA
386
10
1
100

2218


LSA
QSDLEQDRLAK
386
11
1
100

2219


LSA
QSDLEQDR
590
8
1
100

2220


LSA
QSDLEQERLA
590
10
1
100

2221


LSA
QSDLEQERLAK
590
11
1
100

2222


LSA
QSDLEQERR
573
9
1
100
0.0002
2223


LSA
QSDLEQERRA
573
10
1
100

2224


LSA
QSDLEQERRAK
573
11
1
100

2225


LSA
QSDLERTK
182
8
1
100

2226


LSA
QSDLERTKA
182
9
1
100

2227


LSA
QSDLERTKASK
182
11
1
100

2228


LSA
QSDSEQER
519
8
1
100

2229


LSA
QSDSEQERLA
519
10
1
100

2230


LSA
QSDSEQERLAK
519
11
1
100

2231


LSA
QSSLPQDNR
1676
9
1
100
0.0002
2232


LSA
QTNFKSLLR
94
9
1
100
0.0320
2233


LSA
QVNKEKEK
1869
8
1
100

2234


LSA
QVNKEKERF
1869
9
1
100

2235


LSA
QVNKEKEKFIK
1869
11
1
100

2236


LSA
RDIHKGHLEEK
1712
11
1
100

2237


LSA
RDLEQERLA
1608
9
1
100

2238


LSA
RDLEQERLAK
1608
10
1
100
0.0004
2239


LSA
RDLEQERR
1540
8
1
100

2240


LSA
RDLEQERRA
1540
9
1
100

2241


LSA
RDLEQERRAK
1540
10
1
100
0.0004
2242


LSA
RDLEQRKA
1625
8
1
100

2243


LSA
RDLEQRKADTK
1625
11
1
100

2244


LSA
RDSKEISIIEK
1688
11
1
100

2245


LSA
RGNSRDSK
1684
8
1
100

2246


LSA
RINEEKHEK
49
9
1
100
0.0033
2247


LSA
RINEEKHEKK
49
10
1
100
0.0024
2248


LSA
RINEEKHEKKH
49
11
1
100

2249


LSA
RSGSSNSR
40
8
1
100

2250


LSA
RSGSSNSRNR
40
10
1
100
0.0011
2251


LSA
SDLEQDRLA
1387
9
1
100

2252


LSA
SDLEQDRLAK
1387
10
1
100
0.0002
2253


LSA
SDLEQERLA
1591
9
1
100

2254


LSA
SDLEQERLAK
1591
10
1
100
0.0002
2255


LSA
SDLEQERR
1574
8
1
100

2256


LSA
SDLMERRA
1574
9
1
100

2257


LSA
SDLEQERRAK
1574
10
1
100
0.0002
2258


LSA
SDLERTKA
1183
8
1
100

2259


LSA
SDLERTKASK
1183
10
1
100
0.0002
2260


LSA
SDSEQERLA
520
9
1
100

2261


LSA
SDSEQERLAK
520
10
1
100
0.0002
2262


LSA
SDVNDFQISK
1750
10
1
100
0.0002
2263


LSA
SDVNDFQISKY
1750
11
1
100

2264


LSA
SGSSNSRNR
41
9
1
100
0.0002
2265


LSA
SIIEKTNR
1694
8
1
100

2266


LSA
SIKPEQKEDK
1726
10
1
100
0.0002
2267


LSA
SITTNVEGR
1703
9
1
100
0.0002
2268


LSA
SITTNVEGRR
1703
10
1
100
0.0002
2269


LSA
SLPQDNRGNSR
1678
11
1
100

2270


LSA
SLYDEHIK
1855
8
1
100

2271


LSA
SLYDEHIKK
1855
9
1
100
0.0460
2272


LSA
SLYDDIIKKY
1855
10
1
100
0.0015
2273


LSA
SLYDEHIKKYK
1855
11
1
100

2274


LSA
SSEELSEEK
1826
9
1
100
0.0002
2275


LSA
SSEELSEEK
1826
11
1
100

2276


LSA
SSLPQDNR
1677
8
1
100

2277


LSA
TTNVEGRR
1705
8
1
100

2278


LSA
TTNVEGRPDIH
1705
11
1
100

2279


LSA
TVNISDVNDF
1746
10
1
100

2280


LSA
VDELSEDITK
1895
10
1
100
0.0002
2281


LSA
VDELSEDTIKY
1895
11
1
100

2282


LSA
VLAEDLYGR
1647
9
1
100
0.0013
2283


LSA
VLSHNSYEK
60
9
1
100
0.0280
2284


LSA
VLSHNSYEKTK
60
11
1
100

2285


LSA
VSENIFLK
106
8
1
100

2286


LSA
VSENIFLKENK
106
11
1
100

2287


LSA
VSQTNFKSLLR
92
11
1
100

2288


LSA
YDEHIKKY
1857
8
1
100

2289


LSA
YDEHIKKYK
1857
9
1
100
0.0005
2290


LSA
YFILVNLLIF
10
10
1
100

2291


LSA
YFILVNLLFH
10
11
1
100

2292


LSA
VGRLEIPA
1653
8
1
100

2293


LSA
YIKGQDENR
137
9
1
100
0.0025
2294


SSP2
AATPYAGEPA
525
10
8
80

2295


SSP2
ACAGLAYK
512
8
10
100

2296


SSP2
ACAGLAYKF
512
9
10
100

2297


SSP2
ADSAWENVK
216
9
10
100
0.0002
2298


SSP2
AFNRFLVGCH
197
10
10
100

2299


SSP2
AGGLAGGLA
501
9
10
100

2300


SSP2
AGGLALLA
505
8
10
100

2301


SSP2
AGGLALLACA
505
10
10
100

2302


SSP2
ALLACAGLA
509
9
10
100
0.0002
2303


SSP2
ALLACAGLAY
509
10
10
100
0.0630
2304


SSP2
ALLACAGLAYK
509
11
10
100

2305


SSP2
ALLQVRKH
136
8
9
90

2306


SSP2
ASKNKEKA
107
8
10
100

2307


SSP2
ATPYAGEPA
526
9
8
80

2308


SSP2
ATPYAGEPAPF
526
11
8
80

2309


SSP2
AVCVEVEK
233
8
10
100

2310


SSP2
AVCVEVEKTA
233
10
10
100

2311


SSP2
CAGLAYKF
513
8
10
100

2312


SSP2
CGKGTRSR
257
8
10
100

2313


SSP2
CGKGTRSRK
257
9
10
100
0.0002
2314


SSP2
CGKCIRSRKR
257
10
10
100
0.0002
2315


SSP2
CSGSIRRH
55
8
10
100

2316


SSP2
CSVTCGKGTR
253
10
10
100
0.0002
2317


SSP2
CVEVEKTA
235
8
10
100

2318


SSP2
DALLQVRK
135
8
9
90

2319


SSP2
DALLQVRKH
135
9
9
90
0.0004
2320


SSP2
DASKNKEK
106
8
10
100

2321


SSP2
DASKNKEKA
106
9
10
100

2322


SSP2
DCKSIRR
54
8
10
100

2323


SSP2
DCSGSIRRH
54
9
10
100

2324


SSP2
DDQPRPRGDNF
301
11
9
90

2325


SSP2
DDREENFDIPK
385
11
10
100

2326


SSP2
DGKCNLYA
209
8
10
100

2327


SSP2
DGKCNLYADSA
209
11
10
100

2328


SSP2
DIPKKPENK
392
9
10
100
0.0004
2329


SSP2
DIPKKPENKE
392
10
10
100
0.0002
2330


SSP2
DLDEPEQF
546
8
10
100

2331


SSP2
DLDEPEQFR
546
9
10
100
0.0002
2332


SSP2
DLFLVNGR
19
8
10
100

2333


SSP2
DSAWENVK
217
8
10
100

2334


SSP2
DSIQDSLK
166
8
10
100

2335


SSP2
DSIQDSLKESR
166
11
10
100

2336


SSP2
DSLKESRK
170
8
9
90

2337


SSP2
DVPKNPEDDR
378
10
10
100
0.0002
2338


SSP2
DVQNNIVDEIK
27
11
10
100

2339


SSP2
EDDQPRPR
300
8
10
100

2340


SSP2
EDDREENF
384
8
10
100

2341


SSP2
EDKDLDEPEQF
543
11
10
100

2342


SSP2
EDRETRPH
450
8
9
90

2343


SSP2
EDRETRPHGR
450
10
9
90

2344


SSP2
EIIRLHSDA
99
9
10
100

2345


SSP2
EIIRLHSDASK
99
11
10
100

2346


SSP2
ELQEQCEEER
276
10
8
80
0.0002
2347


SSP2
ETLGEEDK
538
8
10
100

2348


SSP2
EVCNDEVDLY
41
10
8
80
0.0002
2349


SSP2
EVPSDVPK
374
8
10
100

2350


SSP2
FDETLGEEDK
536
10
10
100
0.0002
2351


SSP2
FDIPKKPENK
391
10
10
100
0.0002
2352


SSP2
FDIPKKPENKH
391
11
10
100

2353


SSP2
FDLFLVNGR
18
9
10
100

2354


SSP2
FFDLFLVNGR
17
10
10
100

2355


SSP2
FGIGQGINVA
188
10
10
100

2356


SSP2
FGIGQGINVAF
188
11
10
100

2357


SSP2
FLIFFDLF
14
8
10
100

2358


SSP2
FLVGCHPSDGK
201
11
10
100

2359


SSP2
FMKAVCVEVEK
230
11
10
100

2360


SSP2
FVVPGAATPY
520
10
8
80
0.0002
2361


SSP2
FVVPGAATPYA
520
11
8
80

2362


SSP2
GAATPYAGEPA
524
11
8
80

2363


SSP2
GCHPSDGK
204
8
10
100

2364


SSP2
GDNFAVEK
308
8
9
90

2365


SSP2
GGIAGGLA
502
8
10
100

2366


SSP2
GGIAGGLALLA
502
11
10
100

2367


SSP2
GGLALLACA
506
9
10
100

2368


SSP2
GIAGGLALLA
503
10
10
100

2369


SSP2
GIGQGINVA
189
9
10
100

2370


SSP2
GIGQGINVAF
189
10
10
100

2371


SSP2
GINVAFNR
193
8
10
100

2372


SSP2
GINVAFNRF
193
9
10
100

2373


SSP2
GIPDSIQDSLK
163
11
10
100

2374


SSP2
GLALLACA
507
8
10
100

2375


SSP2
GLALLACAGLA
507
11
10
100

2376


SSP2
GLAYKFVVPGA
515
11
10
100

2377


SSP2
GSIRRHNWVNH
57
11
8
80

2378


SSP2
GTRSRKIZEILH
260
11
10
100

2379


SSP2
HAVPLAMK
67
8
10
100

2380


SSP2
HDNQNNLPNDK
401
11
10
100

2381


SSP2
HGRNNENR
457
8
10
100

2382


SSP2
HGRNNENRSY
457
10
10
100
00004
2383


SSP2
HLNDRINR
143
8
10
100

2384


SSP2
HLNDRINRENA
143
11
10
100

2385


SSP2
HSDASKNK
104
8
10
100

2386


SSP2
HSDASKNKEK
104
10
to
100
0.0004
2387


SSP2
HSDASKNKEKA
104
11
10
100

2388


SSP2
HVPNSEDR
445
8
10
100

2389


SSP2
HVPNSEDRETR
445
11
9
90

2390


SSP2
IAGGIAGGLA
500
10
10
100

2391


SSP2
IAGGLALLA
504
9
10
100
0.0002
2392


SSP2
IAGGLALLACA
504
11
10
100

2393


SSP2
IFFDLFLVNGR
16
11
10
100

2394


SSP2
IGQGINVA
190
8
10
100

2395


SSP2
IGQGINVAF
190
9
10
100

2396


SSP2
IGQGINVAFNR
190
11
10
100

2397


SSP2
IIRLHSDA
100
8
10
100

2398


SSP2
IIRLHSDASK
100
10
10
100
0.0230
2399


SSP2
IVDEIKYR
32
8
9
90

2400


SSP2
IVFLIFFDLF
12
10
10
100

2401


SSP2
KAVCVEVEK
232
9
10
100
0.0004
2402


SSP2
KAVCVEVEKTA
232
11
10
100

2403


SSP2
KCNLYADSA
211
9
10
100

2404


SSP2
KDLDEPEQF
545
9
10
100

2405


SSP2
KDLDEPEQFR
545
10
10
100

2406


SSP2
KFVVPGAA
519
8
10
100

2407


SSP2
KFVVPGAATPY
519
11
8
80
.
2408


SSP2
KGIRSRKR
259
8
10
100

2409


SSP2
KIAGGIAGGLA
499
11
10
100

2410


SSP2
KVLDNERK
421
8
8
80

2411


SSP2
LACACLAY
511
8
10
100

2412


SSP2
LACAGLAYK
511
9
10
100
0.0240
2413


SSP2
LACAGLAYKF
511
10
10
100

2414


SSP2
LALLACAGLA
508
10
10
100

2415


SSP2
LALLACAGLAY
508
11
10
100

2416


SSP2
LAYKFVVPGA
516
10
10
100

2417


SSP2
LAYKFVVPGAA
516
11
10
100

2418


SSP2
LDEPEQFR
547
8
10
100

2419


SSP2
LGNVKYLVIVF
4
11
10
100

2420


SSP2
LLACAGLA
510
8
10
100

2421


SSP2
LLACAGLAY
510
9
10
100
0.0120
2422


SSP2
LLACAGLAYK
510
10
10
100
0.9500
2423


SSP2
LLACAGLAYKF
510
11
10
100

2424


SSP2
LLMDCSGSIR
5I
10
10
100
0.0004
2425


SSP2
LLMDCSGSIRR
5I
11
10
100

2426


SSP2
LLQVRKHLNDR
137
11
9
90

2427


SSP2
LLSTNLPY
121
8
9
90

2428


SSP2
LLSTNLPYGR
121
10
8
80
0.0017
2429


SSP2
LMDCSGSIR
52
9
10
100
0.0004
2430


SSP2
LMDCSGSIRR
52
10
10
100
0.0015
2431


SSP2
LMDCSGSIRRH
52
11
10
100

2432


SSP2
LSTNLPYGR
122
9
8
80
0.0004
2433


SSP2
LVGCHPSDGK
202
10
10
100
0.0004
2434


SSP2
LVIVFLIF
10
8
10
100

2435


SSP2
LVIVFLIFF
10
9
10
100

2436


SSP2
MDCSGSIR
53
8
10
100

2437


SSP2
MDCSGS1RR
53
9
10
100

2438


SSP2
MDCSGSIRRH
S3
10
10
100

2439


SSP2
NDRINRENA
145
9
10
100

2440


SSP2
NFDIPKKPENK
390
11
10
100

2441


SSP2
NIPEDSEK
366
8
10
100

2442


SSP2
NIVDEIKY
31
8
10
100

2443


SSP2
NIVDEIKYR
31
9
9
90
0.0005
2444


SSP2
NLPNDKSDR
406
9
10
100
0.0005
2445


SSP2
NSEDRETR
448
8
9
90

2446


SSP2
NSEDRETRPH
448
10
9
90
0.0004
2447


SSP2
NVIGPFMK
225
8
10
100

2448


SSP2
NVIGPFMKA
225
9
10
100
0.0002
2449


SSP2
NVKNVIGPF
222
9
10
100

2450


SSP2
NVKNVIGPFMK
222
11
10
100

2451


SSP2
NVKYLVIVF
6
9
10
100

2452


SSP2
PCSVTCGK
252
8
10
100

2453


SSP2
PCSVTCGKGTR
252
11
10
100

2454


SSP2
PDSIQDSLK
165
9
10
100
0.0005
2455


SSP2
PFDETLGEEDK
535
11
10
100

2456


SSP2
PGAATPYA
523
8
8
80

2457


SSP2
PSDGKCNLY
207
9
10
100
0.0002
2458


SSP2
PSDGKCNLYA
207
10
10
101

2459


SSP2
PSPNPEEGK
328
9
10
100
0.0005
2460


SSP2
QCEEERCPPK
280
10
8
80
0.0004
2461


SSP2
QDNNGNRH
438
8
10
100

2462


SSP2
QDSLKESR
169
8
10
100

2463


SSP2
QDSLKESRK
169
9
9
90
0.0005
2464


SSP2
QGINVAFNR
192
9
10
100
0.0009
2465


SSP2
QGINVAFNRF
192
10
10
100

2466


SSP2
QSQDNNGNR
436
9
10
100
0.0005
2467


SSP2
QSQDNNGNRH
436
10
10
100
0.0004
2468


SSP2
QVRKHLNDR
139
9
9
90
0.0005
2469


SSP2
RGDNFAVEK
307
9
9
90
0.0005
2470


SSP2
RGVKIAVF
181
8
9
90

2471


SSP2
RLHSDASK
102
8
10
100

2472


SSP2
RLHSDASKNK
102
10
10
100
0.0240
2473


SSP2
RSRKREILH
262
9
10
100
0.0110
2474


SSP2
SDASKNKEK
105
9
10
100
0.0005
2475


SSP2
SDASKNKEKA
105
10
10
100

2476


SSP2
SDGKCNLY
208
8
10
100

2477


SSP2
SDGKCNLYA
208
9
10
100

2478


SSP2
SDNKYKIA
494
8
9
90

2479


SSP2
SDVPKNPEDDR
377
11
10
100

2480


SSP2
SIQDSLKESR
167
10
10
100
0.0004
2481


SSP2
SIQDSLKESRK
167
11
9
90

2482


SSP2
SIRRHNWVNH
58
10
8
80
0.0011
2483


SSP2
SIRRHNWVNHA
58
11
8
80

2484


SSP2
SLLSTNLPY
120
9
9
90
0.0280
2485


SSP2
SLLSTNLPYGR
120
11
8
80

2486


SSP2
STNLPYGR
123
8
8
80

2487


SSP2
SVTCGKGTR
254
9
10
100
0.0005
2488


SSP2
SVTCGKGTRSR
254
11
10
100

2489


SSP2
TCGKGTRSR
256
9
10
100

2490


SSP2
TCGKGTRSRK
256
10
10
100
0.0004
2491


SSP2
TCGKGTRSRKR
256
11
10
100

2492


SSP2
VAFNRFLVGCH
196
11
10
100

2493


SSP2
VCNDEVDLY
42
9
8
80

2494


SSP2
VCVEVEKTA
234
9
10
100

2495


SSP2
VFGIGQGINVA
187
11
10
100

2496


SSP2
VFLIFFDLF
13
9
10
100

2497


SSP2
VGCHPSDGK
203
9
10
100
0.0005
2498


SSP2
VIGPFMKA
226
8
10
100

2499


SSP2
VIVFLIFF
11
8
10
100

2500


SSP2
VIVFLIFFDLF
11
11
10
100

2501


SSP2
VTCGKGTR
255
8
10
100

2502


SSP2
VTCGKGTRSR
255
10
10
100
0.0004
2503


SSP2
VTCGKGTRSRK
255
11
10
100

2504


SSP2
VVPGAATPY
521
9
8
80
0.0005
2505


SSP2
VVPGAATPYA
521
10
8
80

2506


SSP2
WSPCSVTCGK
250
10
10
100
0.0004
2507


SSP2
WVNHAVPLA
64
9
8
80
0.0002
2508


SSP2
WVNHAVPLAMK
64
11
8
80

2509


SSP2
YADSAWENVK
215
10
10
100
0.0004
2510


SSP2
YAGEPAPF
529
8
8
80

2511


SSP2
YLLMDCSGSIR
50
11
10
100

2512


SSP2
YLVIVFLIF
9
9
10
100

2513


SSP2
YLVIVFLIFF
9
10
10
100

2514
















TABLE XVII







Malaria A11 Motif Peptides With Binding Information

















No. of
Sequence
Conservancy




Protein
Sequence
Position
Amino Acids
Frequency
(%)
A*1101
Seq. Id.

















CSP
ALFQEYQCY
18
9
19
100
0.0021
2515


CSP
ANANNAVK
336
8
16
84

2516


CSP
ANPNANPNK
305
9
19
100

2517


CSP
CGNGIQVR
377
8
19
100

2518


CSP
CGNGIQVRIK
377
10
19
100
0.0002
2519


CSP
DGNNEDNEK
96
9
19
100
0.0002
2520


CSP
DGNNEDNEKLR
96
11
19
100

2521


CSP
DGNNNNGDNGR
77
11
17
89

2522


CSP
DIEKKICK
402
8
19
100

2523


CSP
DIEKKICKMEK
402
11
19
100

2524


CSP
DNAGINLY
41
8
18
95

2525


CSP
DNEKLRKPK
101
9
19
100

2526


CSP
DNEKLRKPKH
101
10
19
100

2527


CSP
DNEKLRKPKHK
101
11
19
100

2528


CSP
DNGREGKDEDK
84
11
19
100

2529


CSP
EALFQEYQCY
17
10
19
100
0.0002
2530


CSP
EDNEKLRK
100
8
19
100

2531


CSP
EDNEKLRKPK
100
10
19
100
0.0002
2532


CSP
EDNEKLRKPKH
100
11
19
100

2533


CSP
EGKDEDKR
88
8
19
100

2534


CSP
ELEMNYYGK
50
9
19
100
0.0003
2535


CSP
ENANANNAVK
334
10
16
84

2536


CSP
ENDIEKKICK
400
10
19
100

2537


CSP
ENWYSLKK
60
8
19
100

2538


CSP
ENWYSLKKNSR
60
11
19
100

2539


CSP
FLFVEALFQEY
13
11
19
100

2540


CSP
FVEALFQEY
15
9
19
100
0.0003
2541


CSP
GDNGREGK
83
8
19
100

2542


CSP
GNGIQVRIK
378
9
19
100

2543


CSP
GNNEDNEK
97
8
19
100

2544


CSP
GNNEDNEKLR
97
10
19
100

2545


CSP
GNNEDNEKLRK
97
11
19
100

2546


CSP
GNNNNGDNGR
78
10
19
100

2547


CSP
HIEQYLKK
350
8
15
79

2548


CSP
HNMPNDPNR
322
9
19
100

2549


CSP
INLYNELEMNY
45
11
18
95

2550


CSP
KLRKPKHK
104
8
19
100

2551


CSP
KLRKPKHKK
104
9
19
100
0.0037
2552


CSP
KLRKPKHKKLK
104
11
19
100

2553


CSP
KNNNNEEPSDK
343
11
19
100

2554


CSP
KNNQGNGQGH
313
10
19
100

2555


CSP
LDYENDIEK
397
9
18
95
0.0002
2556


CSP
LDYENDIEKK
397
10
18
95
0.0002
2557


CSP
LFQEYQCY
19
8
19
100

2558


CSP
LFVEALFQEY
14
10
19
100

2559


CSP
LNYDNAGINLY
38
11
18
95

2560


CSP
MNYYGKQENWY
53
11
19
100

2561


CSP
NANANNAVK
335
9
16
84
0.0002
2562


CSP
NANPNANPNK
304
10
19
100
0.0021
2563


CSP
NDIEKKIK
401
9
19
100
0.0002
2564


CSP
NGDNGREGK
82
9
19
100
0.0002
2565


CSP
NGIQVRIK
379
8
19
100

2566


CSP
NGREGKDEDK
85
10
19
100
0.0002
2567


CSP
NGREGKDEDKR
85
11
19
100

2568


CSP
NLYNELEMNY
46
10
19
100
0.0002
2569


CSP
NLYNELEMNYY
46
11
19
100

2570


CSP
NMPNDPNR
323
8
19
100

2571


CSP
NNEDNEKLR
98
9
19
100

2572


CSP
NNEDNEKLRK
98
10
19
100

2573


CSP
NNEEPSDK
346
8
19
100

2574


CSP
NNEEPSDKH
346
9
19
100

2575


CSP
NNGDNGREGK
81
10
19
100

2576


CSP
NNNEEPSDK
345
9
19
100

2577


CSP
NNNEEPSDKH
345
10
19
100

2578


CSP
NNNGDNGR
80
8
19
100

2579


CSP
NNNGDNGREGK
80
11
19
100

2580


CSP
NNNNEEPSDK
344
10
19
100

2581


CSP
NNNNEEPSDKH
344
11
19
100

2582


CSP
NNNNGDNGR
79
9
19
100

2583


CSP
NNQGNGQGH
314
9
19
100

2584


CSP
NTRVLNELNY
31
10
19
100
0.0002
2585


CSP
PNANPNANPNK
303
11
19
100

2586


CSP
PSDKHIEQY
346
9
15
79

2587


CSP
PSDKHIEQYLK
346
11
15
79

2588


CSP
QCYGSSSNTR
24
10
19
100

2589


CSP
QGHNMPNDPNR
320
11
19
100

2590


CSP
RDGNNEDNEK
95
10
19
100
0.0002
2591


CSP
RVLNELNY
33
8
19
100

2592


CSP
SDKHIEQY
347
8
15
79

2593


CSP
SDKHIEQYLK
347
10
15
79

2594


CSP
SDKHIEQYLKK
347
11
15
79

2595


CSP
SNTRVLNELNY
30
11
19
100

2596


CSP
SVTCGNGIQVR
374
11
19
100

2597


CSP
TCGNGIQVR
376
9
19
100

2598


CSP
TCGNGIQVRIK
376
11
19
100

2599


CSP
VTCGNGIQVR
375
10
19
100
0.0340
2600


CSP
YDNAGINLY
40
9
18
95

2601


CSP
YGKQENWY
56
8
19
100

2602


CSP
YGKQENWYSLK
56
11
19
100

2603


CSP
YGSSSNTR
26
8
19
100

2604


CSP
YNELEMNY
48
8
19
100

2605


CSP
YNELEMNYY
48
9
19
100

2606


CSP
YNELEMNYYGK
48
11
19
100

2607


CSP
YSLKKNSR
63
8
19
100

2608


EXP
ALFFIIFNK
10
9
1
100
1.2000
2609


EXP
DDNNLVSGPEH
152
11
1
100

2610


EXP
DLISDMIK
52
8
1
100

2611


EXP
DLISDMIKK
52
9
1
100
0.0003
2612


EXP
DNNLVSGPEH
153
10
1
100

2613


EXP
DVHDLISDMIK
49
11
1
100

2614


EXP
ELVEVNKR
63
8
1
100

2615


EXP
ELVEVNKRK
63
9
1
100
0.0002
2616


EXP
ELVEVNKRKSK
63
11
1
100

2617


EXP
ESLAEKTNK
19
9
1
100
0.0002
2618


EXP
EVNKRKSK
66
8
1
100

2619


EXP
EVNKRKSKY
66
9
1
100
0.0002
2620


EXP
EVNKRKSKYK
66
10
1
100
0.0002
2621


EXP
FLALFFIIFNK
8
11
1
100

2622


EXP
FNKESLAEK
16
9
1
100

2623


EXP
GGVGLVLY
94
8
1
100

2624


EXP
GLVLYNTEK
97
9
1
100
0.0055
2625


EXP
GLVLYNTEKGR
97
11
1
100

2626


EXP
GSGEPLIDVH
42
10
1
100
0.0002
2627


EXP
GSGVSSKK
30
8
1
100

2628


EXP
GSGVSSKKK
30
9
1
100
0.0065
2629


EXP
GSGVSSKKKNK
30
11
1
100

2630


EXP
GTGSGVSSK
28
9
1
100
0.0180
2631


EXP
GTGSGVSSKK
28
10
1
100
0.0340
2632


EXP
GTGSGVSSKKK
28
11
1
100

2633


EXP
GVGLVLYNTEK
95
11
1
100

2634


EXP
GVSSKKKNK
32
9
1
100
0.0002
2635


EXP
GVSSKKKNKK
32
10
1
100
0.0002
2636


EXP
HDLISDMIK
51
9
1
100
0.0002
2637


EXP
HDLISDMIKK
51
10
1
100
0.0002
2638


EXP
IFNKESLAEK
15
10
1
100
0.0003
2639


EXP
IIFNKESLAEK
14
11
1
100

2640


EXP
KGSGEPLIDVH
41
11
1
100

2641


EXP
KGTGSGVSSK
27
10
1
100
0.0009
2642


EXP
KGTGSGVSSKK
27
11
1
100

2643


EXP
LALFFIIFNK
9
10
1
100
0.0530
2644


EXP
LFFIIFNK
11
8
1
100

2645


EXP
LGGVGLVLY
93
9
1
100
0.0002
2646


EXP
LISDMIKK
53
8
1
100

2647


EXP
LLGGVGLVLY
92
10
1
100
0.0003
2648


EXP
LVEVNKRK
64
8
1
100

2649


EXP
LVEVNKRKSK
64
10
1
100
0.0002
2650


EXP
LVEVNKRKSKY
64
11
1
100

2651


EXP
LVLYNTEK
98
8
1
100

2652


EXP
LVLYNTEKGR
98
10
1
100
0.0002
2653


EXP
LVLYNTEKGRH
98
11
1
100

2654


EXP
NLVSGPEH
155
8
1
100

2655


EXP
NNLVSGPEH
154
9
1
100

2656


EXP
NTEKGRHPFK
102
10
1
100
0.0080
2657


EXP
SGEPLIDVH
43
9
1
100
0.0002
2658


EXP
SGVSSKKK
31
8
1
100

2659


EXP
SGVSSKKKNK
31
10
1
100
0.0002
2660


EXP
SGVSSKKKNKK
31
11
1
100

2661


EXP
SLAEKTNK
20
8
1
100

2662


EXP
SSKKKNKK
34
8
1
100

2663


EXP
TGSGVSSK
29
8
1
100

2664


EXP
TGSGVSSKK
29
9
1
100
0.0016
2665


EXP
TGSGVSSKKK
29
10
1
100
0.0002
2666


EXP
VGLVLYNTEK
96
10
1
100
0.0052
2667


EXP
VLLGGVGLVLY
91
11
1
100

2668


EXP
VLYNTEKGR
99
9
1
100
0.0007
2669


EXP
VLYNTEKGRH
99
10
1
100
0.0002
2670


EXP
VNKRKSKY
67
8
1
100

2671


EXP
VNKRKSKYK
67
9
1
100

2672


EXP
VSSKKKNK
33
8
1
100

2673


EXP
VSSKKKNKK
33
9
1
100
0.0002
2674


EXP
YNTEKGRH
101
8
1
100

2675


EXP
YNTEKGRHPFK
101
11
1
100

2676


LSA
ADTKKNLER 
1632
9
1
100

2677


LSA
ADTKKNLERK
1632
10
1
100
0.0003
2678


LSA
ADTKKNLERKK
1632
11
1
100

2679


LSA
AIELPSENER
1660
10
1
100
0.0002
2680


LSA
ANEKLQEQQR
1531
10
1
100

2681


LSA
DDDDKKKY
130
8
1
100

2682


LSA
DDDDKKKYIK
130
10
1
100
0.0002
2683


LSA
DDDKKKYIK
131
9
1
100
0.0002
2684


LSA
DDEDLDEFK
1778
9
1
100
0.0002
2685


LSA
DDKKKYIK
132
8
1
100

2686


LSA
DDLDEGIEK
1817
9
1
100
0.0002
2687


LSA
DGSIKPEQK
1724
9
1
100
0.0002
2688


LSA
DIHKGHLEEK
1713
10
1
100
0.0002
2689


LSA
DIHKGHLEEKK
1713
11
1
100

2690


LSA
DITKYFMK
1901
8
1
100

2691


LSA
DLDEFKPIVQY
1781
11
1
100

2692


LSA
DLDEGIEK
1818
8
1
100

2693


LSA
DLEEKAAK
148
8
1
100

2694


LSA
DLEQDRLAK
1388
9
1
100
0.0002
2695


LSA
DLEQDRLAKEK
1388
11
1
100

2696


LSA
DLEQERLAK
1609
9
1
100
0.0002
2697


LSA
DLEQERLAKEK
1609
11
1
100

2698


LSA
DLEQERLANEK
1524
11
1
100

2699


LSA
DLEQERRAK
1575
9
1
100
0.0002
2700


LSA
DLEQERRAKEK
1575
11
1
100

2701


LSA
DLEQRKADTK
1626
10
1
100
0.0002
2702


LSA
DLEQRKADTKK
1626
11
1
100

2703


LSA
DLERTKASK
1184
9
1
100
0.0002
2704


LSA
DNNFKPNDK
1846
9
1
100

2705


LSA
DNRGNSRDSK
1682
10
1
100

2706


LSA
DSEQERLAK
521
9
1
100
0.0002
2707


LSA
DSEQERLAKEK
521
11
1
100

2708


LSA
DSKEISIIEK
1689
10
1
100
0.0002
2709


LSA
DTKKNLER
1633
8
1
100

2710


LSA
DTKKNLERK
1633
9
1
100
0.0002
2711


LSA
DTKKNLERKK
1633
10
1
100
0.0002
2712


LSA
DVLAEDLY
1646
8
1
100

2713


LSA
DVLAEDLYGR
1646
10
1
100
0.0002
2714


LSA
DVNDFQISK
1751
9
1
100
0.0018
2715


LSA
DVNDFQISKY
1751
10
1
100
0.0002
2716


LSA
EDDEDLDEFK
1777
10
1
100
0.0002
2717


LSA
EDEISAEY
1761
8
1
100

2718


LSA
EDITKYFMK
1900
9
1
100
0.0003
2719


LSA
EDKSADIQNH
1733
10
1
100

2720


LSA
EDLEEKAAK
147
9
1
100
0.0002
2721


LSA
EFKPIVQY
1784
8
1
100

2722


LSA
EGRRDIHK
1709
8
1
100

2723


LSA
EGRRDIHKGH
1709
10
1
100
0.0002
2724


LSA
EIIKSNLR
33
8
1
100

2725


LSA
EISIIEKTNR
1692
10
1
100
0.0002
2726


LSA
ELEDLIEK
1805
8
1
100

2727


LSA
ELPSENER
1662
8
1
100

2728


LSA
ELPSENERGY
1662
10
1
100
0.0002
2729


LSA
ELPSENERGYY
1662
11
1
100

2730


LSA
ELSEDITK
1897
8
1
100

2731


LSA
ELSEDITKY
1897
9
1
100
0.0002
2732


LSA
ELSEEKIK
1829
8
1
100

2733


LSA
ELSEEKIKK
1829
9
1
100
0.0002
2734


LSA
ELSEEKIKKGK
1829
11
1
100

2735


LSA
ELTMSNVK
83
8
1
100

2736


LSA
ENERGYYIPH
1666
10
1
100

2737


LSA
ENIFLKENK
108
9
1
100

2738


LSA
ENKLNKEGK
114
9
1
100

2739


LSA
ENNKFFDK
73
8
1
100

2740


LSA
ENNKFFDKDK
73
10
1
100

2741


LSA
ENRQEDLEEK
143
10
1
100

2742


LSA
ESITTNVEGR
1702
10
1
100
0.0002
2743


LSA
ESITTNVEGRR
1702
11
1
100

2744


LSA
FILVNLLIFH
11
10
1
100
0.0060
2745


LSA
FLKENKLNK
111
9
1
100
0.0005
2746


LSA
GDVLAEDLY
1645
9
1
100

2747


LSA
GDVLAEDLYGR
1645
11
1
100

2748


LSA
GSIKPEQK
1725
8
1
100

2749


LSA
GSIKPEQKEDK
1725
11
1
100

2750


LSA
GSSNSRNR
42
8
1
100

2751


LSA
GVSENIFLK
105
9
1
100
0.6600
2752


LSA
HGDVLAEDLY
1644
10
1
100
0.0002
2753


LSA
HIINDDDDK
126
9
1
100
0.0002
2754


LSA
HIINDDDDKK
126
10
1
100
0.0002
2755


LSA
HIINDDDDKKK
126
11
1
100

2756


LSA
HIKKYKNDK
1860
9
1
100
0.0002
2757


LSA
HILYISFY
3
8
1
100

2758


LSA
HINGKIIK
20
8
1
100

2759


LSA
HLEEKKDGSIK
1718
11
1
100

2760


LSA
HNSYEKTK
63
8
1
100

2761


LSA
HVLSHNSY
59
8
1
100

2762


LSA
HVLSHNSYEK
59
10
1
100
0.0140
2763


LSA
IFHINGKIIK
18
10
1
100
0.0006
2764


LSA
IFLKENKLNK
110
10
1
100
0.0002
2765


LSA
IINDDDDK
127
8
1
100

2766


LSA
IINDDDDKK
127
9
1
100
0.0002
2767


LSA
IINDDDDKKK
127
10
1
100
0.0002
2768


LSA
IINDDDDKKKY
127
11
1
100

2769


LSA
ILVNLLIFH
12
9
1
100
0.0008
2770


LSA
INDDDDKK
128
8
1
100

2771


LSA
INDDDDKKK
128
9
1
100

2772


LSA
INDDDDKKKY
128
10
1
100

2773


LSA
INEEKHEK
50
8
1
100

2774


LSA
INEEKHEKK
50
9
1
100

2775


LSA
INEEKHEKKH
50
10
1
100

2776


LSA
INGKIIKNSEK
21
11
1
100

2777


LSA
ISDVNDFQISK
1749
11
1
100

2778


LSA
ISIIEKTNR
1693
9
1
100
0.0008
2779


LSA
ITTNVEGR
1704
8
1
100

2780


LSA
ITTNVEGRR
1704
9
1
100
0.0007
2781


LSA
IVDELSEDITK
1894
11
1
100

2782


LSA
KADTKKNLER
1631
10
1
100
0.0002
2783


LSA
KADTKKNLERK
1631
11
1
100

2784


LSA
KDEIIKSNLR
31
10
1
100

2785


LSA
KDGSIKPEQK
1723
10
1
100
0.0002
2786


LSA
KDKELTMSNVK
80
11
1
100

2787


LSA
KDNNFKPNDK
1845
10
1
100
0.0002
2788


LSA
KFIKSLFH
1876
8
1
100

2789


LSA
KGHLEEKK
1716
8
1
100

2790


LSA
KGKKYEKTK
1837
9
1
100
0.0002
2791


LSA
KIIKNSEK
24
8
1
100

2792


LSA
KIKKGKKY
1834
8
1
100

2793


LSA
KIKKGKKYEK
1834
10
1
100
0.0007
2794


LSA
KLNKEGKLIEH
116
11
1
100

2795


LSA
KLQEQQSDLER
1177
11
1
100

2796


LSA
KNDKQVNK
1865
8
1
100

2797


LSA
KNDKQVNKEK
1865
10
1
100

2798


LSA
KNLERKKEH
1636
9
1
100

2799


LSA
KNNENNKFFDK
70
11
1
100

2800


LSA
KNSEKDEIIK
27
10
1
100

2801


LSA
KNVSQTNFK
90
9
1
100

2802


LSA
KSADIQNH
1735
8
1
100

2803


LSA
KSLYDEHIK
1854
9
1
100
0.0340
2804


LSA
KSLYDEHIKK
1854
10
1
100
0.0490
2805


LSA
KSLYDEHIKKY
1854
11
1
100

2806


LSA
KSSEELSEEK
1825
10
1
100
0.0009
2807


LSA
KTKDNNFK
1843
8
1
100

2808


LSA
KTKNNENNK
68
9
1
100
0.0038
2809


LSA
LAEDLYGR
1648
8
1
100

2810


LSA
LAKEKLQEQQR
1615
11
1
100

2811


LSA
LANEKLQEQQR
1530
11
1
100

2812


LSA
LDDLDEGIEK
1816
10
1
100
0.0002
2813


LSA
LDEFKPIVQY
1782
10
1
100

2814


LSA
LGVSENIFLK
104
10
1
100
0.0063
2815


LSA
LIFHINGK
17
8
1
100

2816


LSA
LIFHINGKIIK
17
11
1
100

2817


LSA
LLIFHINGK
16
9
1
100
0.0100
2818


LSA
LNKEGKLIEH
117
10
1
100

2819


LSA
LSEDITKY
1898
8
1
100

2820


LSA
LSEDITKYFMK
1898
11
1
100

2821


LSA
LSEEKIKK
1830
8
1
100

2822


LSA
LSEEKIKKGK
1830
10
1
100
0.0002
2823


LSA
LSEEKIKKGKK
1830
11
1
100

2824


LSA
LSHNSYEK
61
8
1
100

2825


LSA
LSHNSYEKTK
61
10
1
100
0.0002
2826


LSA
LVNLLIFH
13
8
1
100

2827


LSA
NDDDDKKK
129
8
1
100

2828


LSA
NDDDDKKKY
129
9
1
100

2829


LSA
NDDDDKKKYIK
129
11
1
100

2830


LSA
NDFQISKY
1753
8
1
100

2831


LSA
NDKQVNKEK
1866
9
1
100
0.0002
2832


LSA
NDKQVNKEKEK
1866
11
1
100

2833


LSA
NDKSLYDEH
1852
9
1
100

2834


LSA
NDKSLYDEHIK
1852
11
1
100

2835


LSA
NFKPNDKSLY
1848
10
1
100

2836


LSA
NFQDEENIGIY
1793
11
1
100

2837


LSA
NGKIIKNSEK
22
10
1
100
0.0002
2838


LSA
NIFLKENK
109
8
1
100

2839


LSA
NIFLKENKLNK
109
11
1
100

2840


LSA
NLDDLDEGIEK
1815
11
1
100

2841


LSA
NLERKKEH
1637
8
1
100

2842


LSA
NLGVSENIFLK
103
11
1
100

2843


LSA
NLLIFHINGK
15
10
1
100
0.0008
2844


LSA
NLRSGSSNSR
38
10
1
100
0.0002
2845


LSA
NNENNKFFDK
71
10
1
100

2846


LSA
NNFKPNDK
1847
8
1
100

2847


LSA
NNFKPNDKSLY
1847
11
1
100

2848


LSA
NNKFFDKDK
74
9
1
100

2849


LSA
NSEKDEIIK
28
9
1
100
0.0002
2850


LSA
NSRNRINEEK
45
10
1
100
0.0002
2851


LSA
NSRNRINEEKH
45
11
1
100

2852


LSA
NVEGRRDIH
1707
9
1
100
0.0002
2853


LSA
NVEGRRDIHK
1707
10
1
100
0.0002
2854


LSA
NVKNVSQTNFK
88
11
1
100

2855


LSA
NVSQTNFK
91
8
1
100

2856


LSA
PAIELPSENER
1659
11
1
100

2857


LSA
PNDKSLYDEH
1851
10
1
100

2858


LSA
PSENERGY
1664
8
1
100

2859


LSA
PSENERGYY
1664
9
1
100
0.0002
2860


LSA
QDEENIGIY
1795
9
1
100

2861


LSA
QDEENIGIYK
1795
10
1
100
0.0002
2862


LSA
QDNRGNSR
1681
8
1
100

2863


LSA
QDNRGNSRDSK
1681
11
1
100

2864


LSA
QDRLAKEK
1391
8
1
100

2865


LSA
QGQQSDLEQER
1128
11
1
100

2866


LSA
QSDLEQDR
1386
8
1
100

2867


LSA
QSDLEQDRLAK
1386
11
1
100

2868


LSA
QSDLEQER
1590
8
1
100

2869


LSA
QSDLEQERLAK
1590
11
1
100

2870


LSA
QSDLEQERR
1573
9
1
100
0.0002
2871


LSA
QSDLEQERRAK
1573
11
1
100

2872


LSA
QSDLERTK
1182
8
1
100

2873


LSA
QSDLERTKASK
1182
11
1
100

2874


LSA
QSDSEQER
519
8
1
100

2875


LSA
QSDSEQERLAK
519
11
1
100

2876


LSA
QSSLPQDNR
1676
9
1
100
0.0013
2877


LSA
QTNFKSLLR
94
9
1
100
0.0440
2878


LSA
QVNKEKEK
1869
8
1
100

2879


LSA
QVNKEKEKFIK
1869
11
1
100

2880


LSA
RDIHKGHLEEK
1712
11
1
100

2881


LSA
RDLEQERLAK
1608
10
1
100
0.0002
2882


LSA
RDLEQERR
1540
8
1
100

2883


LSA
RDLEQERRAK
1540
10
1
100
0.0002
2884


LSA
RDLEQRKADTK
1625
11
1
100

2885


LSA
RDSKEISIIEK
1688
11
1
100

2886


LSA
RGNSRDSK
1684
8
1
100

2887


LSA
RINEEKHEK
49
9
1
100
0.0370
2888


LSA
RINEEKHEKK
49
10
1
100
0.0018
2889


LSA
RINEEKHEKKH
49
11
1
100

2890


LSA
RNRINEEK
47
8
1
100

2891


LSA
RNRINEEKH
47
9
1
100

2892


LSA
RNRINEEKHEK
47
11
1
100

2893


LSA
RSGSSNSR
40
8
1
100

2894


LSA
RSGSSNSRNR
40
10
1
100
0.0002
2895


LSA
SDLEQDRLAK
1387
10
1
100
0.0002
2896


LSA
SDLEQERLAK
1591
10
1
100
0.0002
2897


LSA
SDLEQERR
1574
8
1
100

2898


LSA
SDLEQERRAK
1574
10
1
100
0.0002
2899


LSA
SDLERTKASK
1183
10
1
100
0.0002
2900


LSA
SDSEQERLAK
520
10
1
100
0.0002
2901


LSA
SDVNDFQISK
1750
10
1
100
0.0002
2902


LSA
SDVNDFQISKY
1750
11
1
100

2903


LSA
SGSSNSRNR
41
9
1
100
0.0030
2904


LSA
SIIEKTNR
1694
8
1
100

2905


LSA
SIKPEQKEDK
1726
10
1
100
0.0002
2906


LSA
SITTNVEGR
1703
9
1
100
0.0027
2907


LSA
SITTNVEGRR
1703
10
1
100
0.0002
2908


LSA
SLPQDNRGNSR
1678
11
1
100

2909


LSA
SLYDEHIK
1855
8
1
100

2910


LSA
SLYDEHIKK
1855
9
1
100
0.4100
2911


LSA
SLYDEHIKKY
1855
10
1
100
0.0045
2912


LSA
SLYDEHIKKYK
1855
11
1
100

2913


LSA
SNLRSGSSNSR
37
11
1
100

2914


LSA
SNSRNRINEEK
44
11
1
100

2915


LSA
SSEELSEEK
1826
9
1
100
0.0017
2916


LSA
SSEELSEEKIK
1826
11
1
100

2917


LSA
SSLPQDNR
1677
8
1
100

2918


LSA
TNFKSLLR
95
8
1
100

2919


LSA
TNVEGRRDIH
1706
10
1
100

2920


LSA
TNVEGRRDIHK
1706
11
1
100

2921


LSA
TTNVEGRR
1705
8
1
100

2922


LSA
TTNVEGRRDIH
1705
11
1
100

2923


LSA
VDELSEDITK
1895
10
1
100
0.0002
2924


LSA
VDELSEDITKY
1895
11
1
100

2925


LSA
VLAEDLYGR
1647
9
1
100
0.0004
2926


LSA
VLSHNSYEK
60
9
1
100
0.0280
2927


LSA
VLSHNSYEKTK
60
11
1
100

2928


LSA
VNDFQISK
1752
8
1
100

2929


LSA
VNDFQISKY
1752
9
1
100

2930


LSA
VNKEKEKFIK
1870
10
1
100

2931


LSA
VNLLIFHINGK
14
11
1
100

2932


LSA
VSENIFLK
106
8
1
100

2933


LSA
VSENIFLKENK
106
11
1
100

2934


LSA
VSQTNFKSLLR
92
11
1
100

2935


LSA
YDEHIKKY
1857
8
1
100

2936


LSA
YDEHIKKYK
1857
9
1
100
0.0002
2937


LSA
YFILVNLLIFH
10
11
1
100

2938


LSA
YIKGQDENR
137
9
1
100
0.0002
2939


SSP2
ACAGLAYK
512
8
10
100

2940


SSP2
ADSAWENVK
216
9
10
100
0.0009
2941


SSP2
AFNRFLVGCH
197
10
10
100

2942


SSP2
ALLACAGLAY
509
10
10
100
0.0110
2943


SSP2
ALLACAGLAYK
509
11
10
100

2944


SSP2
ALLQVRKH
136
8
9
90

2945


SSP2
AVCVEVEK
233
8
10
100

2946


SSP2
CGKGTRSR
257
8
10
100

2947


SSP2
CGKGTRSRK
257
9
10
100
0.0002
2948


SSP2
CGKGTRSRKR
257
10
10
100
0.0002
2949


SSP2
CNDEVDLY
43
8
8
80

2950


SSP2
CSGSIRRH
55
8
10
100

2951


SSP2
CSVTCGKGTR
253
10
10
100
0.0002
2952


SSP2
DALLQVRK
135
8
9
90

2953


SSP2
DALLQVRKH
135
9
9
90
0.0002
2954


SSP2
DASKNKEK
106
8
10
100

2955


SSP2
DCSGSIRR
54
8
10
100

2956


SSP2
DCSGSIRRH
54
9
10
100

2957


SSP2
DDREENFDIPK
385
11
10
100

2958


SSP2
DIPKKPENK
392
9
10
100
0.0002
2959


SSP2
DIPKKPENKH
392
10
10
100
0.0002
2960


SSP2
DLDEPEQFR
546
9
10
100
0.0002
2961


SSP2
DLFLVNGR
19
8
10
100

2962


SSP2
DNQNNLPNDK
402
10
10
100

2963


SSP2
DSAWENVK
217
8
10
100

2964


SSP2
DSIQDSLK
166
8
10
100

2965


SSP2
DSIQDSLKESR
166
11
10
100

2966


SSP2
DSLKESRK
170
8
9
90

2967


SSP2
DVPKNPEDDR
378
10
10
100
0.0002
2968


SSP2
DVQNNIVDEIK
27
11
10
100

2969


SSP2
EDDQPRPR
300
8
10
100

2970


SSP2
EDRETRPH
450
8
9
90

2971


SSP2
EDRETRPHGR
450
10
9
90

2972


SSP2
EIIRLHSDASK
99
11
10
100

2973


SSP2
ELQEQCEEER
276
10
8
80
0.0002
2974


SSP2
ENFDIPKK
389
8
10
100

2975


SSP2
ENRSYNRK
462
8
10
100

2976


SSP2
ETLGEEDK
538
8
10
100

2977


SSP2
EVCNDEVDLY
41
10
8
80
0.0002
2978


SSP2
EVPSDVPK
374
8
10
100

2979


SSP2
FDETLGEEDK
536
10
10
100
0.0002
2980


SSP2
FDIPKKPENK
391
10
10
100
0.0002
2981


SSP2
FDIPKKPENKH
391
11
10
100

2982


SSP2
FDLFLVNGR
18
9
10
100

2983


SSP2
FFDLFLVNGR
17
10
10
100

2984


SSP2
FLVGCHPSDGK
201
11
10
100

2985


SSP2
FMKAVCVEVEK
230
11
10
100

2986


SSP2
FNRFLVGCH
198
9
10
100

2987


SSP2
FVVPGAATPY
520
10
8
80
0.0002
2988


SSP2
GCHPSDGK
204
8
10
100

2989


SSP2
GDNFAVEK
308
8
9
90

2990


SSP2
GINVAFNR
193
8
10
100

2991


SSP2
GIPDSIQDSLK
163
11
10
100

2992


SSP2
GNRHVPNSEDR
442
11
10
100

2993


SSP2
GSIRRHNWVNH
57
11
8
80

2994


SSP2
GTRSRKREILH
260
11
10
100

2995


SSP2
HAVPLAMK
67
8
10
100

2996


SSP2
HDNQNNLPNDK
401
11
10
100

2997


SSP2
HGRNNENR
457
8
10
100

2998


SSP2
HGRNNENRSY
457
10
10
100
0.0002
2999


SSP2
HLNDRINR
143
8
10
100

3000


SSP2
HSDASKNK
104
8
10
100

3001


SSP2
HSDASKNKEK
104
10
10
100
0.0002
3002


SSP2
HVPNSEDR
445
8
10
100

3003


SSP2
HVPNSEDRETR
445
11
9
90

3004


SSP2
IFFDLFLVNGR
16
11
10
100

3005


SSP2
IGQGINVAFNR
190
11
10
100

3006


SSP2
IIRLHSDASK
100
10
10
100
0.0002
3007


SSP2
IVDEIKYR
32
8
9
90

3008


SSP2
KAVCVEVEK
232
9
10
100
0.0076
3009


SSP2
KDLDEPEQFR
545
10
10
100

3010


SSP2
KFVVPGAATPY
519
11
8
80

3011


SSP2
KGTRSRKR
259
8
10
100

3012


SSP2
KNVIGPFMK
224
9
10
100

3013


SSP2
KVLDNERK
421
8
8
80

3014


SSP2
LACAGLAY
511
8
10
100

3015


SSP2
LACAGLAYK
511
9
10
100
0.0290
3016


SSP2
LALLACAGLAY
508
11
10
100

3017


SSP2
LDEPEQFR
547
8
10
100

3018


SSP2
LLACAGLAY
510
9
10
100
0.0005
3019


SSP2
LLACAGLAYK
510
10
10
100
0.0870
3020


SSP2
LLMDCSGSIR
51
10
10
100
0.0005
3021


SSP2
LLMDCSGSIRR
51
11
10
100

3022


SSP2
LLQVRKHLNDR
137
11
9
90

3023


SSP2
LLSTNLPY
121
8
9
90

3024


SSP2
LLSTNLPYGR
121
10
8
80
0.0025
3025


SSP2
LMDCSGSIR
52
9
10
100
0.0002
3026


SSP2
LMDCSGSIRR
52
10
10
100
0.0002
3027


SSP2
LMDCSGSIRRH
52
11
10
100

3028


SSP2
LSTNLPYGR
122
9
8
80
0.0100
3029


SSP2
LVGCHPSDGK
202
10
10
100
0.0002
3030


SSP2
MDCSGSIR
53
8
10
100

3031


SSP2
MDCSGSIRR
53
9
10
100

3032


SSP2
MDCSGSIRRH
53
10
10
100

3033


SSP2
MNHLGNVK
1
8
10
100

3034


SSP2
MNHLGNVKY
1
9
10
100

3035


SSP2
NFDIPKKPENK
390
11
10
100

3036


SSP2
NIPEDSEK
366
8
10
100

3037


SSP2
NIVDEIKY
31
8
10
100

3038


SSP2
NIVDEIKYR
31
9
9
90
0.0002
3039


SSP2
NLPNDKSDR
406
9
10
100
0.0002
3040


SSP2
NNENRSYNR
460
9
10
100

3041


SSP2
NNENRSYNRK
460
10
10
100

3042


SSP2
NNIVDEIK
30
8
10
100

3043


SSP2
NNIVDEIKY
30
9
10
100

3044


SSP2
NNIVDEIKYR
30
10
9
90

3045


SSP2
NNLPNDKSDR
405
10
10
100

3046


SSP2
NSEDRETR
448
8
9
90

3047


SSP2
NSEDRETRPH
448
10
9
90
0.0002
3048


SSP2
NVIGPFMK
225
8
10
100

3049


SSP2
NVKNVIGPFMK
222
11
10
100

3050


SSP2
PCSVTCGK
252
8
10
100

3051


SSP2
PCSVTCGKGTR
252
11
10
100

3052


SSP2
PDSIQDSLK
165
9
10
100
0.0002
3053


SSP2
PFDETLGEEDK
535
11
10
100

3054


SSP2
PNIPEDSEK
365
9
10
100

3055


SSP2
PNSEDRETR
447
9
9
90

3056


SSP2
PNSEDRETRPH
447
11
9
90

3057


SSP2
PSDGKCNLY
207
9
10
100
0.0002
3058


SSP2
PSPNPEEGK
328
9
10
100
0.0002
3059


SSP2
QCEEERCPPK
280
10
8
80
0.0002
3060


SSP2
QDNNGNRH
438
8
10
100

3061


SSP2
QDSLKESR
169
8
10
100

3062


SSP2
QDSLKESRK
169
9
9
90
0.0002
3063


SSP2
QGINVAFNR
192
9
10
100
0.0780
3064


SSP2
QNNIVDEIK
29
9
10
100

3065


SSP2
QNNIVDEIKY
29
10
10
100

3066


SSP2
QNNIVDEIKYR
29
11
9
90

3067


SSP2
QNNLPNDK
404
8
10
100

3068


SSP2
QNNLPNDKSDR
404
11
10
100

3069


SSP2
QSQDNNGNR
436
9
10
100
0.0002
3070


SSP2
QSQDNNGNRH
436
10
10
100
0.0002
3071


SSP2
QVRKHLNDR
139
9
9
90
0.0002
3072


SSP2
RGDNFAVEK
307
9
9
90
0.0240
3073


SSP2
RLHSDASK
102
8
10
100

3074


SSP2
RLHSDASKNK
102
10
10
100
0.0002
3075


SSP2
RNNENRSY
459
8
10
100

3076


SSP2
RNNENRSYNR
459
10
10
100

3077


SSP2
RNNENRSYNRK
459
11
10
100

3078


SSP2
RSRKREILH
262
9
10
100
0.0002
3079


SSP2
SDASKNKEK
105
9
10
100
0.0002
3080


SSP2
SDGKCNLY
208
8
10
100

3081


SSP2
SDVPKNPEDDR
377
11
10
100

3082


SSP2
SIQDSLKESR
167
10
10
100
0.0009
3083


SSP2
SIQDSLKESRK
167
11
9
90

3084


SSP2
SIRRHNWVNH
58
10
8
80
0.0002
3085


SSP2
SLLSTNLPY
120
9
9
90
0.0046
3086


SSP2
SLLSTNLPYGR
120
11
8
80

3087


SSP2
STNLPYGR
123
8
8
80

3088


SSP2
SVTCGKGTR
254
9
10
100
0.0009
3089


SSP2
SVTCGKGTRSR
254
11
10
100

3090


SSP2
TCGKGTRSR
256
9
10
100

3091


SSP2
TCGKGTRSRK
256
10
10
100
0.0002
3092


SSP2
TCGKGTRSRKR
256
11
10
100

3093


SSP2
VAFNRFLVGCH
196
11
10
100

3094


SSP2
VCNDEVDLY
42
9
8
80

3095


SSP2
VGCHPSDGK
203
9
10
100
0.0003
3096


SSP2
VNHAVPLAMK
65
10
8
80

3097


SSP2
VTCGKGTR
255
8
10
100

3098


SSP2
VTCGKGTRSR
255
10
10
100
0.0017
3099


SSP2
VTCGKGTRSRK
255
11
10
100

3100


SSP2
VVPGAATPY
521
9
8
80
0.0002
3101


SSP2
WSPCSVTCGK
250
10
10
100
0.0002
3102


SSP2
WVNHAVPLAMK
64
11
8
80

3103


SSP2
YADSAWENVK
215
10
10
100
0.0002
3104


SSP2
YLLMDCSGSIR
50
11
10
100

3105
















TABLE XVIII







Malaria A24 Motif Peptides With Binding Information

















No. of
Sequence
Conservancy




Protein
Sequence
Position
Amino Acids
Frequency
(%)
A*02401
Seq. Id

















CSP
CYGSSSNTRVL
25
11
19
100

3106


CSP
DYENDIEKKI
398
10
18
95

3107


CSP
EMNYYGKQENW
52
11
19
100

3108


CSP
IMVLSFLF
427
8
19
100

3109


CSP
IMVLSFLFL
427
9
19
100
0.0008
3110


CSP
KMEKCSSVF
409
9
19
100

3111


CSP
MMRKLAIL
1
8
19
100

3112


CSP
NYDNAGINL
39
9
18
95
0.0004
3113


CSP
NYYGKQENW
54
9
19
100

3114


CSP
SFLFVEAL
12
8
19
100

3115


CSP
SFLFVEALF
12
9
19
100

3116


CSP
VFNVVNSSI
416
9
19
100

3117


CSP
VFNVVNSSIGL
416
11
19
100

3118


CSP
WYSLKKNSRSL
62
11
19
100

3119


CSP
YYGKQENW
55
8
19
100

3120


CSP
YYGKQENWYSL
55
11
19
100

3121


EXP
DMIKKEEEL
56
9
1
100

3122


EXP
FFIIFNKESL
12
10
1
100

3123


EXP
FFLALFFI
7
8
1
100

3124


EXP
FFLALFFII
7
9
1
100

3125


EXP
FFLALFFIIF
7
10
1
100

3126


EXP
KYKLATSVL
73
9
1
100
0.0960
3127


EXP
LFFIIFNKESL
11
11
1
100

3128


EXP
LYNTEKGRHPF
100
11
1
100

3129


EXP
VFFLALFF
6
8
1
100

3130


EXP
VFFLALFFI
6
9
1
100

3131


EXP
VFFLALFFII
6
10
1
100

3132


EXP
VFFLALFFIIF
6
11
1
100

3133


LSA
DFQISKYEDEI
1754
11
1
100

3134


LSA
EFKPIVQYDNF
1784
11
1
100

3135


LSA
FFDKDKEL
77
8
1
100

3136


LSA
FYFILVNL
9
8
1
100

3137


LSA
FYFILVNLL
9
9
1
100
7.5000
3138


LSA
FYFILVNLLI
9
10
1
100

3139


LSA
FYFILVNLLIF
9
11
1
100

3140


LSA
GYYIPHQSSL
1670
10
1
100
0.0074
3141


LSA
IFDGDNEI
1884
8
1
100

3142


LSA
IFDGDNEIL
1884
9
1
100

3143


LSA
IFDGDNEILQI
1884
11
1
100

3144


LSA
IFHINGKI
18
8
1
100

3145


LSA
IFHINGKII
18
9
1
100

3146


LSA
IFLKENKL
110
8
1
100

3147


LSA
IYKELEDL
1802
8
1
100

3148


LSA
IYKELEDLI
1802
9
1
100

3149


LSA
KFFDKDKEL
76
9
1
100

3150


LSA
KFIKSLFHI
1876
9
1
100

3151


LSA
KFIKSLFHIF
1876
10
1
100

3152


LSA
KYEKTKDNNF
1840
10
1
100
0.0004
3153


LSA
LFHIFDGDNEI
1881
11
1
100

3154


LSA
LYGRLEIPAI
1652
10
1
100

3155


LSA
LYISFYFI
5
8
1
100

3156


LSA
LYISFYFIL
5
9
1
100
0.0088
3157


LSA
NFKPNDKSL
1848
9
1
100

3158


LSA
NFKSLLRNL
96
9
1
100

3159


LSA
NFQDEENI
1793
8
1
100

3160


LSA
NFQDEENIGI
1793
10
1
100

3161


LSA
QYDNFQDEENI
1790
11
1
100

3162


LSA
SFYFILVNL
8
9
1
100

3163


LSA
SFYFILVNLL
8
10
1
100

3164


LSA
SFYFILVNLLI
8
11
1
100

3165


LSA
YFILVNLL
10
8
1
100

3166


LSA
YFILVNLLI
10
9
1
100

3167


LSA
YFILVNLLIF
10
10
1
100

3168


LSA
YYIPHQSSL
1671
9
1
100
4.3000
3169


SSP2
AMKLIQQL
72
8
10
100

3170


SSP2
AMKLIQQLNL
72
10
10
100
0.0006
3171


SSP2
AWENVKNVI
219
9
10
100

3172


SSP2
KYKIAGGI
497
8
9
90

3173


SSP2
KYLVIVFL
8
8
10
100

3174


SSP2
KYLVIVFLI
8
9
10
100
4.6000
3175


SSP2
KYLVIVFLIF
8
10
10
100
0.0003
3176


SSP2
KYLVIVFLIFF
8
11
10
100

3177


SSP2
LMDCSGSI
52
8
10
100

3178


SSP2
LYLLMDCSGSI
49
11
9
90

3179


SSP2
NWVNHAVPL
63
9
8
80

3180


SSP2
PYAGEPAPF
528
9
8
80
0.0370
3181


SSP2
QFRLPEENEW
552
10
10
100

3182


SSP2
VFGIGQGI
187
8
10
100

3183


SSP2
VFLIFFDL
13
8
10
100

3184


SSP2
VFLIFFDLF
13
9
10
100

3185


SSP2
VFLIFFDLFL
13
10
10
100

3186
















TABLE XIXa







Malaria DR Super Motif Peptide


















Core

Core

Exemplary
Position In
Exemplary
Exemplary 




SeqID
Core
Conser-
Exemplary
SeqID
PF Poly-
Sequence
Sequence


Protein
Core Sequence
Num
Frequency
vancy (%)
Sequence
Num
Protein
Frequency
Conservancy (%)



















CSP
FLFVEALFQ
3187
19
100
VSSFLFVEALFQEYQ
3291
10
19
100


CSP
FNVVNSSIG
3188
19
100
SSVFNVVNSSIGLIM
3292
440
19
100


CSP
FQEYQCYGS
3189
19
100
EALFQEYQCYGSSSN
3293
17
19
100


CSP
IEKKICKME
3190
19
100
ENDIEKKICKMEKCS
3294
426
19
100


CSP
IGLIMVLSF
3191
19
100
NSSIGLIMVLSFLFL
3295
447
19
100


CSP
ILSVSSFLF
3192
19
100
KLAILSVSSFLFVEA
3296
4
19
100


CSP
LAILSVSSF
3193
19
100
MRKLAILSVSSFLFV
3297
2
19
100


CSP
MEKCSSVFN
3194
19
100
ICKMEKCSSVFNVVN
3298
433
19
100


CSP
VVNSSIGLI
3195
19
100
VFNVVNSSIGLIMVL
3299
442
19
100


CSP
YQCYGSSSN
3196
19
100
FQEYQCYGSSSNTRV
3300
20
19
100


CSP
YNELEMNYY
3197
19
100
INLYNELEMNYYGKQ
3301
45
18
95


CSP
YDNAGINLY
3198
18
95
ELNYDNAGINLYNEL
3302
37
18
95


CSP
IQNSLSTEW
3199
15
79
LKKIQNSLSTEWSPC
3303
385
15
79


CSP
WSPCSVTCG
3200
10
100
STEWSPCSVTCGNGI
3304
393
19
100


LSA
FILVNLLIF
3201
1
100
SFYFILVNLLIFHIN
3305
8
1
100


LSA
FYFILVNLL
3202
1
100
YISFYFILVNLLIFH
3306
6
1
100


LSA
IHKGHLEEK
3203
1
100
RRDIHKGHLEEKKDG
3307
1711
1
100


LSA
IIKSNLRSG
3204
1
100
KDEIIKSNLRSGSSN
3308
31
1
100


LSA
ILVNLLIFH
3205
1
100
FYFILVNLLIFHING
3309
9
1
100


LSA
INGKIIKNS
3206
1
100
IFHINGKIIKNSEKD
3310
18
1
100


LSA
IPAIELPSE
3207
1
100
RLEIPAIELPSENER
3311
1655
1
100


LSA
IPHQSSLPQ
3208
1
100
GYYIPHQSSLPQDNR
3312
1670
1
100


LSA
IQNHTLETV
3209
1
100
SADIQNHTLETVNIS
3313
1736
1
100


LSA
ISFYFILVN
3210
1
100
ILYISFYFILVNLLI
3314
4
1
100


LSA
LDEFKPIVQ
3211
1
100
DEDLDEFKPIVQYDN
3315
1779
1
100


LSA
LEEKAAKET
3212
1
100
QEDLEEKAAKETLQG
3316
146
1
100


LSA
LEIPAIELP
3213
1
100
YGRLEIPAIELPSEN
3317
1653
1
100


LSA
LEQRKADTK
3214
1
100
QRDLEQRKADTKKNL
3318
1624
1
100


LSA
LERTKASKE
3215
1
100
QSDLERTKASKETLQ
3319
1182
1
100


LSA
LETVNISDV
3216
1
100
NHTLETVNISDVNDF
3320
1741
1
100


LSA
LIEHIINDD
3217
1
100
EGKLIEHIINDDDDK
3321
120
1
100


LSA
LKENKLNKE
3218
1
100
NIFLKENKLNKEGKL
3322
109
1
100


LSA
LLIFHINGK
3219
1
100
LVNLLIFHINGKIIK
3323
13
1
100


LSA
LQEQQSDLE
3220
1
100
KETLQEQQSDLEQER
3324
1192
1
100


LSA
LQEQQSDSE
3221
1
100
KEKLQEQQSDSEQER
3325
512
1
100


LSA
LQGQQSDLE
3222
1
100
KETLQEQQSDLEQER
3326
155
1
100


LSA
LRNLGVSEN
3223
1
100
KSLLRNLGVSENIFL
3327
98
1
100


LSA
LRSGSSNSR
3224
1
100
KSNLRSGSSNSRNRI
3328
36
1
100


LSA
LTMSNVKNV
3225
1
100
DKELTMSNVKNVSQT
3329
81
1
100


LSA
LVNLLIFHI
3226
1
100
YFILVNLLIFHINGK
3330
10
1
100


LSA
VLSHNSYEK
3227
1
100
KKHVLSHNSYEKTKN
3331
57
1
100


LSA
VNDFQISKY
3228
1
100
ISDVNDFQISKYEDE
3332
1749
1
100


LSA
VNISDVNDF
3229
1
100
LETVNISDVNDFQIS
3333
1744
1
100


LSA
YDDSLIDEE
3230
1
100
SAEYDDSLIDEEEDD
3334
1765
1
100


LSA
YGRLEIPAI
3231
1
100
EDLYGRLEIPAIELP
3335
1650
1
100


LSA
YIPHQSSLP
3232
1
100
RGYYIPHQSSLPQDN
3336
1669
1
100


EXP
FKIGSSDPA
3233
1
100
RHPFKIGSSDPADNA
3337
107
1
100


EXP
IDVHDLISD
3234
1
100
EPLIDVHDLISDMIK
3338
45
1
100


EXP
IFNKESLAE
3235
1
100
FFIIFNKESLAEKTN
3339
12
1
100


EXP
IGSSDPADN
3236
1
100
PFKIGSSDPADNANP
3340
109
1
100


EXP
LALFFIIFN
3237
1
100
VFFLALFFIIFNKES
3341
6
1
100


EXP
LATSVLAGL
3238
1
100
KYKLATSVLAGLLGN
3342
73
1
100


EXP
LGGVGLVLY
3239
1
100
TVLLGGVGLVLYNTE
3343
90
1
100


EXP
LGNVSTVLL
3240
1
100
AGLLGNVSTVLLGGV
3344
82
1
100


EXP
LLGNVSTVL
3241
1
100
LAGLLGNVSTVLLGG
3345
81
1
100


EXP
LSVFFLALF
3242
1
100
MKILSVFFLALFFII
3346
1
1
100


EXP
LVLYNTEKG
3243
1
100
GVGLVLYNTEKGRHP
3347
95
1
100


EXP
VFFLALFFI
3244
1
100
ILSVFFLALFFIIFN
3348
3
1
100


EXP
VHDLISDMI
3245
1
100
LIDVHDLISDMIKKE
3349
47
1
100


EXP
VLAGLLGNV
3246
1
100
ATSVLAGLLGNVSTV
3350
77
1
100


EXP
VLLGGVGLV
3247
1
100
VSTVLLGGVGLVLYN
3351
88
1
100


EXP
VNKRKSKYK
3248
1
100
LVEVNKRKSKYKLAT
3352
64
1
100


EXP
VSTVLLGGV
3249
1
100
LGNVSTVLLGGVGLV
3353
85
1
100


EXP
VTAQDVTPE
3250
1
100
DPQVTAQDVTPEQPQ
3574
136
1
100


EXP
YKLATSVLA
3251
1
100
KSKYKLATSVLAGLL
3354
71
1
100


SSP2
FDLFLVNGR
3252
10
100
LIFFDLFLVNGRDVQ
3355
15
10
100


SSP2
FFDLFLVNG
3253
10
100
FLIFFDLFLVNGRDV
3356
14
10
100


SSP2
FMKAVCVEV
3254
10
100
IGPFMKAVCVEVEKT
3357
227
10
100


SSP2
FNRFLVGCH
3255
10
100
NVAFNRFLVGCHPSD
3358
195
10
100


SSP2
IAGGLALLA
3256
10
100
AGGIAGGLALLACAG
3359
513
10
100


SSP2
IAVFGIGQG
3257
10
100
GVKIAVFGIGQGINV
3360
182
10
100


SSP2
LACAGLAYK
3258
10
100
LALLACAGLAYKFVV
3361
520
10
100


SSP2
LALLACAGL
3259
10
100
AGGLALLACAGLAYK
3362
517
10
100


SSP2
LAMKLIQQL
3260
10
100
AVPLAMKLIQQLNLN
3363
68
10
100


SSP2
LAYKFVVPG
3261
10
100
CAGLAYKFVVPGAAT
3364
525
10
100


SSP2
LIFFDLFLV
3262
10
100
IVFLIFFDLFLVNGR
3365
12
10
100


SSP2
LTDGIPDSI
3263
10
100
VVILTDGIPDSIQDS
3366
157
10
100


SSP2
LVGCHPSDG
3264
10
100
NRFLVGCHPSDGKCN
3367
199
10
100


SSP2
LVIVFLIFF
3265
10
100
VKYLVIVFLIFFDLF
3368
7
10
100


SSP2
LVVILTDGI
3266
10
100
ANQLVVILTDGIPDS
3369
153
10
100


SSP2
MDCSGSIRR
3267
10
100
YLLMDCSGSIRRHNW
3370
50
10
100


SSP2
MKAVCVEVE
3268
10
100
GPFMKAVCVEVEKTA
3371
228
10
100


SSP2
VEKTASCGV
3269
10
100
CVEVEKTASCGVWDE
3372
235
10
100


SSP2
VGCHPSDGK
3270
10
100
RFLVGCHPSDGKCNL
3373
200
10
100


SSP2
VIGPFMKAV
3271
10
100
VKNVIGPFMKAVCVE
3374
223
10
100


SSP2
VIVFLIFFD
3272
10
100
KYLVIVFLIFFDLFL
3375
8
10
100


SSP2
VKYLVTVFL
3273
10
100
LGNVKYLVTVFLIFF
3376
4
10
100


SSP2
VNGRDVQNN
3274
10
100
LFLVNGRDVQNNIVD
3377
20
10
100


SSP2
WDEWSPCSV
3275
10
100
CGVWDEWSPCSVTCG
3378
244
10
100


SSP2
IAGGIAGGL
3276
10
100
KYKIAGGIAGGLALL
3379
509
9
90


SSP2
VQNNIVDEI
3277
10
100
GRDVQNNIVDEIKYR
3380
25
9
90


SSP2
YLLMDCSGS
3278
10
100
VDLYLLMDCSGSIRR
3381
47
9
90


SSP2
FVVPGAATP
3279
10
100
AYKFVVPGAATPYAG
3382
529
8
80


SSP2
YKFVVPGAA
3280
10
100
GLAYKFVVPGAATPY
3383
527
8
80


SSP2
IIRLHSDAS
3281
10
100
AKEIIRLHSDASKNK
3384
97
6
60


SSP2
IIDNNPQEP
3282
10
100
EENIIDNNPQEPSPN
3385
317
4
40


SSP2
VDLYLLMDC
3283
9
90
NDEVDLYLLMDCSGS
3386
44
8
80


SSP2
LLSTNLPYG
3284
9
90
IKSLLSTNLPYGRTN
3387
118
5
50


SSP2
LHEGCTSEL
3285
8
80
REILHEGCTSELQEQ
3388
266
8
80


SSP2
VNHAVPLAM
3286
8
80
HNWVNHAVPLAMKLI
3389
62
8
80


SSP2
VPGAATPYA
3287
8
80
KFVVPGAATPYAGEP
3390
531
8
80


SSP2
VVPGAATPY
3288
8
80
YKFVVPGAATPYAGE
3391
530
8
80


SSP2
WVNHAVPLA
3289
8
80
RHNWVNHAVPLAMKL
3392
61
8
80


SSP2
LSTNLPYGR
3290
8
80
KSLLSTNLPYGRTNL
3393
119
5
50
















TABLE XIXb





Malaria DR Super Motif Peptide With Binding Data


























Core

Exemplary










SeqID
Exemplary
SeqID









Core Sequence
Num
Sequence
Num
DR 1
DR2w2β1
DR2w2β2
DR3
DR4w4
DR4w15
DR5w11





FLFVEALFQ
3187
VSSFLFVEALFQEYQ
3291









FNVVNSSIG
3188
SSVFNVVNSSIGLIM
3292
0.1200
0.0290
0.0080 
−0.0043
0.1000
0.0230
0.0170


FQEYQCYGS
3189
EALFQEYQCYGSSSN
3293
0.0001

−0.0005

0.0053
−0.0009
−0.0002


IEKKICKME
3190
ENDIEKKICKMEKCS
3294









IGLIMVLSF
3191
NSSIGLIMVLSFLFL
3295
0.0040 
0.0250
0.0024
−0.0043
0.0120
0.0035
−0.0005


ILSVSSFLF
3192
KLAILSVSSFLFVEA
3296









LAILSVSSF
3193
MRKLAILSVSSFLFV
3297
0.1000 
0.5000
0.0130
−0.0043
0.0078
0.0270
0.0370


MEKCSSVFN
3194
ICKMEKCSSVFNVVN
3298









VVNSSIGLI
3195
VFNVVNSSIGLIMVL
3299
0.0310
0.0021
0.0006 
0.0021
0.0079
0.0056
0.0002


YQCYGSSSN
3196
FQEYQCYGSSSNTRV
3300









YNELEMNYY
3197
INLYNELEMNYYGKQ
3301









YDNAGINLY
3198
ELNYDNAGINLYNEL
3302
0.0003

−0.0005
0.0091
−0.0009
−0.0009
−0.0002


IQNSLSTEW
3199
LKKIQNSLSTEWSPC
3303









WSPCSVTCG
3200
STEWSPCSVTCGNGI
3304









FILVNLLIF
3201
SFYFILVNLLIFHIN
3305
0.0009
0.0100
−0.0020 
−0.0043
0.0250
0.0038
−0.0005


FYFILVNLL
3202
YISFYFILVNLLIFH
3306
0.0029
0.0040
0.0044 
−0.0008
0.0210
−0.0009
0.0011


IHKGHLEEK
3203
RRDIHKGHLEEKKDG
3307









IIKSNLRSG
3204
KDEIIKSNLRSGSSN
3308









ILVNLLIFH
3205
FYFILVNLLIFHING
3309









INGKIIKNS
3206
IFHINGKIIKNSEKD
3310
0.0320
0.0220
0.0660 
0.0120
−0.0007
0.0038
0.0380


IPAIELPSE
3207
RLEIPAIELPSENER
3311









IPHQSSLPQ
3208
GYYIPHQSSLPQDNR
3312









IQNHTLETV
3209
SADIQNHTLETVNIS
3313
0.0001

−0.0005 
−0.0041
−0.0007
−0.0014
−0.0002


ISFYFILVN
3210
ILYISFYFILVNLLI
3314









LDEFKPIVQ
3211
DEDLDEFKPIVQYDN
3315









LEEKAAKET
3212
QEDLEEKAAKETLQG
3316
0.0001

−0.0005

−0.0009
−0.0009
−0.0002


LEIPAIELP
3213
YGRLEIPAIELPSEN
3317









LEQRKADTK
3214
QRDLEQRKADTKKNL
3318









LERTKASKE
3215
QSDLERTKASKETLQ
3319









LETVNISDV
3216
NHTLETVNISDVNDF
3320
0.0001

−0.0005

−0.0007
0.0016
−0.0002


LIEHIINDD
3217
EGKLIEHIINDDDDK
3321









LKENKLNKE
3218
NIFLKENKLNKEGKL
3322









LLIFHINGK
3219
LVNLLIFHINGKIIK
3323
0.0640 
0.7100
0.0070
−0.0043
0.0110
−0.0030
0.2700


LQEQQSDLE
3220
KETLQEQQSDLEQER
3324









LQEQQSDSE
3221
KEKLQEQQSDSEQER
3325









LQGQQSDLE
3222
KETLQEQQSDLEQER
3326









LRNLGVSEN
3223
KSLLRNLGVSENIFL
3327
0.0150
0.0088
0.0006

0.0210
0.0810
0.0033


LRSGSSNSR
3224
KSNLRSGSSNSRNRI
3328









LTMSNVKNV
3225
DKELTMSNVKNVSQT
3329
0.0018
0.0003
0.0009 
0.0058
0.0023
0.0074
0.0030


LVNLLIFHI
3226
YFILVNLLIFHINGK
3330
0.0018
0.0004
0.0120 
−0.0008
0.0160
0.0027
0.0015


VLSHNSYEK
3227
KKHVLSHNSYEKTKN
3331









VNDFQISKY
3228
ISDVNDFQISKYEDE
3332
0.0001

−0.0005

−0.0007
−0.0014
−0.0002


VNISDVNDF
3229
LETVNISDVNDFQIS
3333









YDDSLIDEE
3230
SAEYDDSLIDEEEDD
3334









YGRLEIPAI
3231
EDLYGRLEIPAIELP
3335
0.0004

−0.0005

−0.0007
−0.0170
−0.0002


YIPHQSSLP
3232
RGYYIPHQSSLPQDN
3336
0.2900
0.0004
0.0029

4.1000
0.2800
0.0064


FKIGSSDPA
3233
RHPFKIGSSDPADNA
3337
0.0044 
−0.0004
−0.0005 
−0.0008
0.4700
0.0029
0.0056


IDVHDLISD
3234
EPLIDVHDLISDMIK
3338









IFNKESLAE
3235
FFIIFNKESLAEKTN
3339









IGSSDPADN
3236
PFKIGSSDPADNANP
3340









LALFFIIFN
3237
VFFLALFFIIFNKES
3341
0.0006 
0.0180
−0.0021
−0.0043
0.0047
0.0100
−0.0005


LATSVLAGL
3238
KYKLATSVLAGLLGN
3342
1.2000
0.0018
0.0700 
0.0010
3.2000
0.1200
0.0210


LGGVGLVLY
3239
TVLLGGVGLVLYNTE
3343
0.4900

−0.0005

0.0032
−0.0009
−0.0002


LGNVSTVLL
3240
AGLLGNVSTVLLGGV
3344
0.0430
0.0240
0.0013 
0.0069
0.0065
0.0360
0.0005


LLGNVSTVL
3241
LAGLLGNVSTVLLGG
3345
0.0420
0.0110
0.0006 
0.0078
0.0160
0.0230
0.0004


LSVFFLALF
3242
MKILSVFFLALFFII
3346
0.0017
0.0170
−0.0021
−0.0043
0.0370
−0.0047
−0.0010


LVLYNTEKG
3243
GVGLVLYNTEKGRHP
3347









VFFLALFFI
3244
ILSVFFLALFFIIFN
3348
0.0016
0.0036
0.0091
−0.0008
0.0130
−0.0009
0.0012


VHDLISDMI
3245
LIDVHDLISDMIKKE
3349
0.0130

0.0061
0.0100
0.0310
0.0076
0.0037


VLAGLLGNV
3246
ATSVLAGLLGNVSTV
3350
0.2600

−0.0005

0.0021
−0.0014
0.0008


VLLGGVGLV
3247
VSTVLLGGVGLVLYN
3351
0.8800
0.0080
0.0005
−0.0008
0.0067
−0.0009
0.0003


VNKRKSKYK
3248
LVEVNKRKSKYKLAT
3352









VSTVLLGGV
3249
LGNVSTVLLGGVGLV
3353
0.0140
0.0001
−0.0005
−0.0008
0.0016
−0.0014
−0.0002


VTAQDVTPE
3250
DPQVTAQDVTPEQPQ
3574









YKLATSVLA
3251
KSKYKLATSVLAGLL
3354
1.4000
0.0073
0.8500
−0.0008
6.3000
0.8100
0.6700


FDLFLVNGR
3252
LIFFDLFLVNGRDVQ
3355
0.0042



0.0036




FFDLFLVNG
3253
FLIFFDLFLVNGRDV
3356









FMKAVCVEV
3254
IGPFMKAVCVEVEKT
3357
0.0072
0.0003
0.0430 
−0.0008
−0.0006
0.0086
−0.0004


FNRFLVGCH
3255
NVAFNRFLVGCHPSD
3358









IAGGLALLA
3256
AGGIAGGLALLACAG
3359
0.0160

0.0013

0.0014
−0.0014
−0.0002


IAVFGIGQG
3257
GVKIAVFGIGQGINV
3360









LACAGLAYK
3258
LALLACAGLAYKFVV
3361









LALLACAGL
3259
AGGLALLACAGLAYK
3362
0.0018

0.0013

−0.0007
−0.0014
−0.0002


LAMKLIQQL
3260
AVPLAMKLIQQLNLN
3363
0.0015

−0.0006

0.0023
0.0013
0.0002


LAYKFVVPG
3261
CAGLAYKFVVPGAAT
3364

0.0048







LIFFDLFLV
3262
IVFLIFFDLFLVNGR
3365
0.0006

0.0019
−0.0008
0.0130
−0.0009
0.0019


LTDGIPDSI
3263
VVILTDGIPDSIQDS
3366
0.0001

−0.0006

0.1200
−0.0014
−0.0004


LVGCHPSDG
3264
NRFLVGCHPSDGKCN
3367









LVIVFLIFF
3265
VKYLVIVFLIFFDLF
3368
0.0001



0.0030




LVVILTDGI
3266
ANQLVVILTDGIPDS
3369
0.0038
0.0008
−0.0005
0.0019
0.0460
0.0062
−0.0002


MDCSGSIRR
3267
YLLMDCSGSIRRHNW
3370









MKAVCVEVE
3268
GPFMKAVCVEVEKTA
3371









VEKTASCGV
3269
CVEVEKTASCGVWDE
3372
0.0004

−0.0005

0.0021
−0.0009
−0.0002


VGCHPSDGK
3270
RFLVGCHPSDGKCNL
3373









VIGPFMKAV
3271
VKNVIGPFMKAVCVE
3374
0.0900
0.0430
0.0800
−0.0026
−0.0020
−0.0030
0.3420


VIVFLIFFD
3272
KYLVIVFLIFFDLFL
3375
0.0012
0.0057
−0.0020 
−0.0043
0.0680
−0.0030
−0.0009


VKYLVTVFL
3273
LGNVKYLVTVFLIFF
3376
0.0006
0.0033
0.0012
−0.0008
0.0120
0.0045
0.0018


VNGRDVQNN
3274
LFLVNGRDVQNNIVD
3377









WDEWSPCSV
3275
CGVWDEWSPCSVTCG
3378
0.0001

−0.0006

−0.0007
−0.0014
−0.0002


IAGGIAGGL
3276
KYKIAGGIAGGLALL
3379
0.0380
0.0001
0.0480
0.0250
0.0120
0.0017
0.2300


VQNNIVDEI
3277
GRDVQNNIVDEIKYR
3380
0.0001
0.0001
−0.0006 
0.0026
−0.0006
−0.0014
−0.0004


YLLMDCSGS
3278
VDLYLLMDCSGSIRR
3381
0.0016

0.0096

0.0150
−0.0014
−0.0004


FVVPGAATP
3279
AYKFVVPGAATPYAG
3382
0.3600
−0.0009
0.0620 
0.0160
0.1600
0.0036
0.6400


YKFVVPGAA
3280
GLAYKFVVPGAATPY
3383
1.6000
0.0001
0.7000
−0.0008
1.0000
0.0270
1.9000


IIRLHSDAS
3281
AKEIIRLHSDASKNK
3384









IIDNNPQEP
3282
EENIIDNNPQEPSPN
3385









VDLYLLMDC
3283
NDEVDLYLLMDCSGS
3386
0.0001

−0.0005

0.0028
−0.0009
−0.0002


LLSTNLPYG
3284
IKSLLSTNLPYGRTN
3387









LHEGCTSEL
3285
REILHEGCTSELQEQ
3388
0.0001

−0.0005 
−0.0041
−0.0009
−0.0014
−0.0002


VNHAVPLAM
3286
HNWVNHAVPLAMKLI
3389
0.3500
0.0250
0.1400
0.2300
3.9000
0.0400
0.0074


VPGAATPYA
3287
KFVVPGAATPYAGEP
3390
0.0230
0.0001
0.0010
0.0620
0.1200
0.0067
0.0010


VVPGAATPY
3288
YKFVVPGAATPYAGE
3391
0.1100
0.0008
0.0053
−0.0008
0.0057
−0.0014
0.0036


WVNHAVPLA
3289
RHNWVNHAVPLAMKL
3392
0.1900
0.0350
0.1600 
0.4000
5.0000
0.0360
0.0079


LSTNLPYGR
3290
KSLLSTNLPYGRTNL
3393
0.0012



0.0120






Core

Exemplary










SeqID
Exemplary
SeqID









Core Sequence
Num
Sequence
Num
DR5w12
DR6w19
DR7
DR8w2
DR9
DRw53





FLFVEALFQ
3187
VSSFLFVEALFQEYQ
3291

0.3600
0.7600
0.0550
1.2000




FNVVNSSIG
3188
SSVFNVVNSSIGLIM
3292
0.0051

−0.0003
0.0005





FQEYQCYGS
3189
EALFQEYQCYGSSSN
3293
0.0001








IEKKICKME
3190
ENDIEKKICKMEKCS
3294









IGLIMVLSF
3191
NSSIGLIMVLSFLFL
3295
0.0340
0.0009
0.0690
−0.0010
0.0042




ILSVSSFLF
3192
KLAILSVSSFLFVEA
3296









LAILSVSSF
3193
MRKLAILSVSSFLFV
3297
0.1200
0.0930
0.0500
0.0013
0.1100




MEKCSSVFN
3194
ICKMEKCSSVFNVVN
3298









VVNSSIGLI
3195
VFNVVNSSIGLIMVL
3299
0.0015
0.2600
0.1800
0.0012
0.5000




YQCYGSSSN
3196
FQEYQCYGSSSNTRV
3300









YNELEMNYY
3197
INLYNELEMNYYGKQ
3301









YDNAGINLY
3198
ELNYDNAGINLYNEL
3302
0.0001

−0.0003
−0.0003





IQNSLSTEW
3199
LKKIQNSLSTEWSPC
3303









WSPCSVTCG
3200
STEWSPCSVTCGNGI
3304









FILVNLLIF
3201
SFYFILVNLLIFHIN
3305
0.0009
0.0004
0.0084
−0.0007
−0.0018




FYFILVNLL
3202
YISFYFILVNLLIFH
3306
0.0006
0.0003
0.0020
0.0010
−0.0003




IHKGHLEEK
3203
RRDIHKGHLEEKKDG
3307









IIKSNLRSG
3204
KDEIIKSNLRSGSSN
3308









ILVNLLIFH
3205
FYFILVNLLIFHING
3309









INGKIIKNS
3206
IFHINGKIIKNSEKD
3310
0.0055
0.0120
0.0160
0.0400
0.0093
0.0020



IPAIELPSE
3207
RLEIPAIELPSENER
3311









IPHQSSLPQ
3208
GYYIPHQSSLPQDNR
3312









IQNHTLETV
3209
SADIQNHTLETVNIS
3313
0.0001

−0.0003
−0.0003

0.0012



ISFYFILVN
3210
ILYISFYFILVNLLI
3314









LDEFKPIVQ
3211
DEDLDEFKPIVQYDN
3315









LEEKAAKET
3212
QEDLEEKAAKETLQG
3316
0.0001

−0.0003
−0.0002





LEIPAIELP
3213
YGRLEIPAIELPSEN
3317









LEQRKADTK
3214
QRDLEQRKADTKKNL
3318









LERTKASKE
3215
QSDLERTKASKETLQ
3319









LETVNISDV
3216
NHTLETVNISDVNDF
3320
0.0015

0.0010
−0.0003

−0.0005



LIEHIINDD
3217
EGKLIEHIINDDDDK
3321









LKENKLNKE
3218
NIFLKENKLNKEGKL
3322









LLIFHINGK
3219
LVNLLIFHINGKIIK
3323
0.0410
0.0530
0.1200
0.0290
0.1800




LQEQQSDLE
3220
KETLQEQQSDLEQER
3324









LQEQQSDSE
3221
KEKLQEQQSDSEQER
3325









LQGQQSDLE
3222
KETLQEQQSDLEQER
3326









LRNLGVSEN
3223
KSLLRNLGVSENIFL
3327

0.5700
0.0770
0.0021
1.6000




LRSGSSNSR
3224
KSNLRSGSSNSRNRI
3328









LTMSNVKNV
3225
DKELTMSNVKNVSQT
3329
0.0001
0.0430
0.0410
0.0110
0.0710
0.0024



LVNLLIFHI
3226
YFILVNLLIFHINGK
3330
0.0006
0.0013
0.0059
0.0005
0.0040
0.0290



VLSHNSYEK
3227
KKHVLSHNSYEKTKN
3331









VNDFQISKY
3228
ISDVNDFQISKYEDE
3332
0.0001

−0.0003
−0.0003

−0.0005



VNISDVNDF
3229
LETVNISDVNDFQIS
3333









YDDSLIDEE
3230
SAEYDDSLIDEEEDD
3334









YGRLEIPAI
3231
EDLYGRLEIPAIELP
3335
0.0002

−0.0003
0.0021

−0.0005



YIPHQSSLP
3232
RGYYIPHQSSLPQDN
3336

0.0004
0.1700
0.0150
0.1500




FKIGSSDPA
3233
RHPFKIGSSDPADNA
3337
0.0001
0.0003
−0.0003
0.0380
0.0950




IDVHDLISD
3234
EPLIDVHDLISDMIK
3338









IFNKESLAE
3235
FFIIFNKESLAEKTN
3339









IGSSDPADN
3236
PFKIGSSDPADNANP
3340









LALFFIIFN
3237
VFFLALFFIIFNKES
3341
0.0002
−0.0002
0.0056
−0.0007
−0.0018




LATSVLAGL
3238
KYKLATSVLAGLLGN
3342
0.0073
0.0075
0.6500
0.1300
2.6000




LGGVGLVLY
3239
TVLLGGVGLVLYNTE
3343
0.0004

0.0007
−0.0002





LGNVSTVLL
3240
AGLLGNVSTVLLGGV
3344
0.0001
4.6000
0.4300
0.0012
0.5300
0.0012



LLGNVSTVL
3241
LAGLLGNVSTVLLGG
3345
0.0003
0.6400
0.3800
0.0006
0.5500




LSVFFLALF
3242
MKILSVFFLALFFII
3346
0.0023
0.0019
0.0360
0.0023
0.0060




LVLYNTEKG
3243
GVGLVLYNTEKGRHP
3347









VFFLALFFI
3244
ILSVFFLALFFIIFN
3348
0.0008
0.0005
0.0110
0.0031
−0.0003




VHDLISDMI
3245
LIDVHDLISDMIKKE
3349
0.0001
0.0004
0.0100
0.0096
0.0430
0.0940



VLAGLLGNV
3246
ATSVLAGLLGNVSTV
3350
0.0043

−0.0003
0.0005

0.0039



VLLGGVGLV
3247
VSTVLLGGVGLVLYN
3351
0.0011
0.0002
0.0020
−0.0002
0.0120




VNKRKSKYK
3248
LVEVNKRKSKYKLAT
3352









VSTVLLGGV
3249
LGNVSTVLLGGVGLV
3353
0.0005
0.0006
−0.0003
−0.0003
−0.0005
−0.0005



VTAQDVTPE
3250
DPQVTAQDVTPEQPQ
3574









YKLATSVLA
3251
KSKYKLATSVLAGLL
3354
0.0009
0.0082
1.9000
1.1000
2.7000
0.0150



FDLFLVNGR
3252
LIFFDLFLVNGRDVQ
3355


0.0470






FFDLFLVNG
3253
FLIFFDLFLVNGRDV
3356









FMKAVCVEV
3254
IGPFMKAVCVEVEKT
3357
0.0038
0.0003
0.0019
−0.0003
0.0820
0.0700



FNRFLVGCH
3255
NVAFNRFLVGCHPSD
3358









IAGGLALLA
3256
AGGIAGGLALLACAG
3359
0.0007

−0.0003
0.0004

−0.0005



IAVFGIGQG
3257
GVKIAVFGIGQGINV
3360









LACAGLAYK
3258
LALLACAGLAYKFVV
3361









LALLACAGL
3259
AGGLALLACAGLAYK
3362
0.0051

0.0009
0.0003

−0.0005



LAMKLIQQL
3260
AVPLAMKLIQQLNLN
3363
0.1300

0.0770
0.0400

0.0350



LAYKFVVPG
3261
CAGLAYKFVVPGAAT
3364









LIFFDLFLV
3262
IVFLIFFDLFLVNGR
3365
0.0016
0.0006
0.0028
0.0007
−0.0003




LTDGIPDSI
3263
VVILTDGIPDSIQDS
3366
0.0001

−0.0003
−0.0003

0.0114



LVGCHPSDG
3264
NRFLVGCHPSDGKCN
3367









LVIVFLIFF
3265
VKYLVIVFLIFFDLF
3368


0.0010






LVVILTDGI
3266
ANQLVVILTDGIPDS
3369
0.0003
0.0070
0.0054
−0.0002
0.0420




MDCSGSIRR
3267
YLLMDCSGSIRRHNW
3370









MKAVCVEVE
3268
GPFMKAVCVEVEKTA
3371









VEKTASCGV
3269
CVEVEKTASCGVWDE
3372
0.0001

0.0095
0.0005





VGCHPSDGK
3270
RFLVGCHPSDGKCNL
3373









VIGPFMKAV
3271
VKNVIGPFMKAVCVE
3374
0.0920
0.1100
0.0590
0.0230
0.0870




VIVFLIFFD
3272
KYLVIVFLIFFDLFL
3375
0.0021
0.0034
0.0130
0.0065
−0.0018




VKYLVTVFL
3273
LGNVKYLVTVFLIFF
3376
0.0011
0.0016
0.0040
0.0050
0.0012




VNGRDVQNN
3274
LFLVNGRDVQNNIVD
3377









WDEWSPCSV
3275
CGVWDEWSPCSVTCG
3378
0.0001

−0.0003
−0.0003

−0.0006



IAGGIAGGL
3276
KYKIAGGIAGGLALL
3379
0.3600
0.2400
0.0063
1.6000
0.2600
−0.0010



VQNNIVDEI
3277
GRDVQNNIVDEIKYR
3380
0.0001
0.0810
−0.0003
−0.0003
−0.0005
0.0850



YLLMDCSGS
3278
VDLYLLMDCSGSIRR
3381
0.0001

0.0046
0.0007

−0.0010



FVVPGAATP
3279
AYKFVVPGAATPYAG
3382
0.1200
0.1700
0.1800
0.9200
0.1300




YKFVVPGAA
3280
GLAYKFVVPGAATPY
3383
0.3500
0.4900
0.1500
2.5000
0.6000
0.0190



IIRLHSDAS
3281
AKEIIRLHSDASKNK
3384









IIDNNPQEP
3282
EENIIDNNPQEPSPN
3385









VDLYLLMDC
3283
NDEVDLYLLMDCSGS
3386
0.0001

−0.0003
−0.0003





LLSTNLPYG
3284
IKSLLSTNLPYGRTN
3387









LHEGCTSEL
3285
REILHEGCTSELQEQ
3388
0.0001

−0.0003
−0.0003





VNHAVPLAM
3286
HNWVNHAVPLAMKLI
3389
0.6000
0.9400
0.3800
0.7200
4.0000
0.0250



VPGAATPYA
3287
KFVVPGAATPYAGEP
3390
0.0860
0.0460
0.0017
0.0064
0.2500




VVPGAATPY
3288
YKFVVPGAATPYAGE
3391
0.0001
0.0017
0.0160
0.0026
0.0200




WVNHAVPLA
3289
RHNWVNHAVPLAMKL
3392
0.0240
0.8900
0.4400
1.8000
4.6000
0.0430



LSTNLPYGR
3290
KSLLSTNLPYGRTNL
3393


0.0005
















TABLE XXa







Malaria DR3a Motif Peptides


















Core
Core


Exemplary
Position in
Exemplary
Exemplary




SeqID
Sequence
Core Sequence

SeqID
Pf 
Sequence
Conservancy 


Protein
Core Sequence
Num
Frequency
Conservancy (%)
Exemplary Sequence
Num
Poly-Protein
Frequency
(%)



















CSP
LFQEYQCYG
3394
19
100
VEALFQEYQCYGSSS
3449
16
19
100


CSP
LFVEALFQE
3395
19
100
SSFLFVEALFQEYQC
3450
11
19
100


CSP
MPNDPNRNV
3396
19
100
GHNMPNDPNRNVDEN
3451
347
19
100


CSP
LYNELEMNY
3397
19
100
GINLYNELEMNYYGK
3452
44
18
95


CSP
VLNELNYDN
3398
19
100
NTRVLNELNYDNAGI
3453
31
18
95


CSP
YENDIEKKI
3399
19
100
ELDYENDIEKKICKM
3454
422
12
63


CSP
LNYDNAGIN
3400
18
95
LNELNYDNAGINLYN
3455
35
18
95


CSP
LSTEWSPCS
3401
18
95
QNSLSTEWSPCSVTC
3456
389
15
79


CSP
LDYENDIEK
3402
18
95
KDELDYENDIEKKIC
3457
420
12
63


LSA
FDGDNEILQ
3403
1
100
FHIFDGDNEILQIVD
3458
1882
1
100


LSA
FDKDKELTM
3404
1
100
NKFFDKDKELTMSNV
3459
75
1
100


LSA
FQDEENIGI
3405
1
100
YDNFQDEENIGIYKE
3460
1791
1
100


LSA
IDEEEDDED
3406
1
100
DSLIDEEEDDEDLDE
3461
1770
1
100


LSA
IINDDDDKK
3407
1
100
IEHIINDDDDKKKYI
3462
124
1
100


LSA
INDDDDKKK
3408
1
100
EHIINDDDDKKKYIK
3463
125
1
100


LSA
ISAEYDDSL
3409
1
100
EDEISAEYDDSLIDE
3464
1761
1
100


LSA
IVDELSEDI
3410
1
100
ILQIVDELSEDITKY
3465
1891
1
100


LSA
IYKELEDLI
3411
1
100
NIGIYKELEDLIEKN
3466
1799
1
100


LSA
LAEDLYGRL
3412
1
100
GDVLAEDLYGRLEIP
3467
1645
1
100


LSA
LAKEKLQEQ
3413
1
100
QERLAKEKLQEQQSD
3468
1357
1
100


LSA
LAKEKLQGQ
3414
1
100
QERLAKEKLQGQQSD
3469
1119
1
100


LSA
LANEKLQEQ
3415
1
100
QERLANEKLQEQQRD
3470
1527
1
100


LSA
LEQDRLAKE
3416
1
100
QSDLEQDRLAKEKLQ
3471
1386
1
100


LSA
LEQERLAKE
3417
1
100
QSDLEQERLAKEKLQ
3472
1590
1
100


LSA
LEQERLANE
3418
1
100
QSDLEQERLANEKLQ
3473
1522
1
100


LSA
LIDEEEDDE
3419
1
100
DDSLIDEEEDDEDLD
3474
1769
1
100


LSA
LPSENERGY
3420
1
100
AIELPSENERGYYIP
3475
1660
1
100


LSA
LSEDITKYF
3421
1
100
VDELSEDITKYFMKL
3476
1895
1
100


LSA
LSEEKIKKG
3422
1
100
SEELSEEKIKKGKKY
3477
1827
1
100


LSA
LYDEHIKKY
3423
1
100
DKSLYDEHIKKYKND
3478
1853
1
100


LSA
VLAEDLYGR
3424
1
100
HGDVLAEDLYGRLEI
3479
1644
1
100


LSA
VNKEKEKFI
3425
1
100
DKQVNKEKEKFIKSL
3480
1867
1
100


LSA
VQYDNFQDE
3426
1
100
KPIVQYDNFQDEENI
3481
1786
1
100


LSA
YEDEISAEY
3427
1
100
ISKYEDEISAEYDDS
3482
1757
1
100


LSA
YKNDKQVNK
3428
1
100
IKKYKNDKQVNKEKE
3483
1861
1
100


PfEXP
FNKESLAEK
3429
1
100
FIIFNKESLAEKTNK
3484
13
1
100


PfEXP
IKKEEELVE
3430
1
100
SDMIKKEEELVEVNK
3485
55
1
100


PfEXP
LISDMIKKE
3431
1
100
VHDLISDMIKKEEEL
3486
50
1
100


PfEXP
VTPEQPQGD
3432
1
100
AQDVTPEQPQGDDNN
3487
141
1
100


PfEXP
YNTEKGRHP
3433
1
100
LVLYNTEKGRHPFKI
3488
98
1
100


SSP2
IFFDLFLVN
3434
10
100
VFLIFFDLFLVNGRD
3489
13
10
100


SSP2
ILTDGIPDS
3435
10
100
LVVILTDGIPDSIQD
3490
156
10
100


SSP2
INRENANQL
3436
10
100
NDRINRENANQLVVI
3491
145
10
100


SSP2
LHSDASKNK
3437
10
100
IIRLHSDASKNKEKA
3492
100
10
100


SSP2
LYADSAWEN
3438
10
100
KCNLYADSAWENVKN
3493
211
10
100


SSP2
VCVEVEKTA
3439
10
100
MKAVCVEVEKTASCG
3494
231
10
100


SSP2
VEVEKTASC
3440
10
100
AVCVEVEKTASCGVW
3495
233
10
100


SSP2
VPSDVPKNP
3441
10
100
EKEVPSDVPKNPEDD
3496
384
10
100


SSP2
VWDEWSPCS
3442
10
100
SCGVWDEWSPCSVTC
3497
243
10
100


SSP2
LLMDCSGSI
3443
10
90
DLYLLMDCSGSIRRH
3498
48
9
90


SSP2
ILHEGCTSE
3444
10
80
KREILHEGCTSELQE
3499
265
8
80


SSP2
IPEDSEKEV
3445
10
80
EPNIPEDSEKEVPSD
3500
376
8
80


SSP2
YREEVCNDE
3446
9
80
EIKYREEVCNDEVDL
3501
35
8
80


SSP2
VCNDEVDLY
3447
8
80
REEVCNDEVDLYLLM
3502
39
8
80


SSP2
YAGEPAPFD
3448
8
80
ATPYAGEPAPFDETL
3503
538
8
80
















TABLE XXb





DR3a Motif Peptides With Binding Information




























Exem-










Core

plary










SeqID

SeqID









Core Sequence
Num
Exemplary Sequence
Num
DR 1
DR2w2β
DR2wβ2
DR3
DR4w4
DR4w15
DR5w11





LFQEYQCYG
3394
VEALFQEYQCYGSSS
3449



 0.0082





LFVEALFQE
3395
SSFLFVEALFQEYQC
3450



 0.0051





MPNDPNRNV
3396
GHNMPNDPNRNVDEN
3451



−0.0033





LYNELEMNY
3397
GINLYNELEMNYYGK
3452



 0.0270





VLNELNYDN
3398
NTRVLNELNYDNAGI
3453



−0.0033





YENDIEKKI
3399
ELDYENDIEKKICKM
3454









LNYDNAGIN
3400
LNELNYDNAGINLYN
3455









LSTEWSPCS
3401
QNSLSTEWSPCSVTC
3456



−0.0033





LDYENDIEK
3402
KDELDYENDIEKKIC
3457









FDGDNEILQ
3403
FHIFDGDNEILQIVD
3458



 0.0640





FDKDKELTM
3404
NKFFDKDKELTMSNV
3459









FQDEENIGI
3405
YDNFQDEENIGIYKE
3460



−0.0033





IDEEEDDED
3406
DSLIDEEEDDEDLDE
3461









IINDDDDKK
3407
IEHIINDDDDKKKYI
3462









INDDDDKKK
3408
EHIINDDDDKKKYIK
3463









ISAEYDDSL
3409
EDEISAEYDDSLIDE
3464



−0.0033





IVDELSEDI
3410
ILQIVDELSEDITKY
3465
0.0001

−0.0005
−0.0041
 0.0027
 0.0017
−0.0002


IYKELEDLI
3411
NIGIYKELEDLIEKN
3466



−0.0033





LAEDLYGRL
3412
GDVLAEDLYGRLEIP
3467









LAKEKLQEQ
3413
QERLAKEKLQEQQSD
3468









LAKEKLQGQ
3414
QERLAKEKLQGQQSD
3469









LANEKLQEQ
3415
QERLANEKLQEQQRD
3470



−0.0033





LEQDRLAKE
3416
QSDLEQDRLAKEKLQ
3471



 0.0038





LEQERLAKE
3417
QSDLEQERLAKEKLQ
3472



−0.0033





LEQERLANE
3418
QSDLEQERLANEKLQ
3473









LIDEEEDDE
3419
DDSLIDEEEDDEDLD
3474









LPSENERGY
3420
AIELPSENERGYYIP
3475



−0.0033





LSEDITKYF
3421
VDELSEDITKYFMKL
3476









LSEEKIKKG
3422
SEELSEEKIKKGKKY
3477



−0.0033





LYDEHIKKY
3423
DKSLYDEHIKKYKND
3478
0.0001

−0.0005
−0.0041
−0.0007
−0.0014
−0.0002


VLAEDLYGR
3424
HGDVLAEDLYGRLEI
3479









VNKEKEKFI
3425
DKQVNKEKEKFIKSL
3480



−0.0033





VQYDNFQDE
3426
KPIVQYDNFQDEENI
3481



−0.0033





YEDEISAEY
3427
ISKYEDEISAEYDDS
3482
0.0001

−0.0005
−0.0041
 0.0008
−0.0014
−0.0002


YKNDKQVNK
3428
IKKYKNDKQVNKEKE
3483



−0.0033





FNKESLAEK
3429
FIIFNKESLAEKTNK
3484



 0.0040





IKKEEELVE
3430
SDMIKKEEELVEVNK
3485



−0.0033





LISDMIKKE
3431
VHDLISDMIKKEEEL
3486









VTPEQPQGD
3432
AQDVTPEQPQGDDNN
3487



−0.0033





YNTEKGRHP
3433
LVLYNTEKGRHPFKI
3488









IFFDLFLVN
3434
VFLIFFDLFLVNGRD
3489









ILTDGIPDS
3435
LVVILTDGIPDSIQD
3490
0.0002
0.0001
−0.0006
 0.1400
 0.3600
−0.0014
−0.0004


INRENANQL
3436
NDRINRENANQLVVI
3491
0.0770

 0.0015
 0.0092
 0.0011
 0.0010
−0.0004


LHSDASKNK
3437
IIRLHSDASKNKEKA
3492



−0.0033





LYADSAWEN
3438
KCNLYADSAWENVKN
3493
0.0002
0.0005
−0.0010
 0.3500
−0.0055

−0.0006


VCVEVEKTA
3439
MKAVCVEVEKTASCG
3494









VEVEKTASC
3440
AVCVEVEKTASCGVW
3495
0.0001

−0.0006
−0.0041
 0.0030
−0.0014
 0.0003


VPSDVPKNP
3441
EKEVPSDVPKNPEDD
3496



−0.0130





VWDEWSPCS
3442
SCGVWDEWSPCSVTC
3497
0.0001

−0.0005
−0.0041
−0.0009
−0.0009
−0.0002


LLMDCSGSI
3443
DLYLLMDCSGSIRRH
3498
0.0041

 0.0250
 0.0300
 0.0340
 0.0028
−0.0002


ILHEGCTSE
3444
KREILHEGCTSELQE
3499









IPEDSEKEV
3445
EPNIPEDSEKEVPSD
3500



−0.0130





YREEVCNDE
3446
EIKYREEVCNDEVDL
3501



−0.0033





VCNDEVDLY
3447
REEVCNDEVDLYLLM
3502
0.0003

−0.0006
 0.1300
−0.0006
−0.0014
−0.0004


YAGEPAPFD
3448
ATPYAGEPAPFDETL
3503



−0.0130




















Core SeqID

Exemplary








Core Sequence
Num
Exemplary Sequence
SeqID Num
DR5w12
DR6w19
DR7
DR8w2
DR9
DRw53





LFQEYQCYG
3394
VEALFQEYQCYGSSS
3449








LFVEALFQE
3395
SSFLFVEALFQEYQC
3450








MPNDPNRNV
3396
GHNMPNDPNRNVDEN
3451








LYNELEMNY
3397
GINLYNELEMNYYGK
3452








VLNELNYDN
3398
NTRVLNELNYDNAGI
3453








YENDIEKKI
3399
ELDYENDIEKKICKM
3454








LNYDNAGIN
3400
LNELNYDNAGINLYN
3455








LSTEWSPCS
3401
QNSLSTEWSPCSVTC
3456








LDYENDIEK
3402
KDELDYENDIEKKIC
3457








FDGDNEILQ
3403
FHIFDGDNEILQIVD
3458








FDKDKELTM
3404
NKFFDKDKELTMSNV
3459








FQDEENIGI
3405
YDNFQDEENIGIYKE
3460








IDEEEDDED
3406
DSLIDEEEDDEDLDE
3461








IINDDDDKK
3407
IEHIINDDDDKKKYI
3462








INDDDDKKK
3408
EHIINDDDDKKKYIK
3463








ISAEYDDSL
3409
EDEISAEYDDSLIDE
3464








IVDELSEDI
3410
ILQIVDELSEDITKY
3465
0.0001

−0.0003
−0.0003

0.0290


IYKELEDLI
3411
NIGIYKELEDLIEKN
3466








LAEDLYGRL
3412
GDVLAEDLYGRLEIP
3467








LAKEKLQEQ
3413
QERLAKEKLQEQQSD
3468








LAKEKLQGQ
3414
QERLAKEKLQGQQSD
3469








LANEKLQEQ
3415
QERLANEKLQEQQRD
3470








LEQDRLAKE
3416
QSDLEQDRLAKEKLQ
3471








LEQERLAKE
3417
QSDLEQERLAKEKLQ
3472








LEQERLANE
3418
QSDLEQERLANEKLQ
3473








LIDEEEDDE
3419
DDSLIDEEEDDEDLD
3474








LPSENERGY
3420
AIELPSENERGYYIP
3475








LSEDITKYF
3421
VDELSEDITKYFMKL
3476








LSEEKIKKG
3422
SEELSEEKIKKGKKY
3477








LYDEHIKKY
3423
DKSLYDEHIKKYKND
3478
0.0001

−0.0003
−0.0003

0.0006


VLAEDLYGR
3424
HGDVLAEDLYGRLEI
3479








VNKEKEKFI
3425
DKQVNKEKEKFIKSL
3480








VQYDNFQDE
3426
KPIVQYDNFQDEENI
3481








YEDEISAEY
3427
ISKYEDEISAEYDDS
3482
0.0001

−0.0003
−0.0003

−0.0005


YKNDKQVNK
3428
IKKYKNDKQVNKEKE
3483








FNKESLAEK
3429
FIIFNKESLAEKTNK
3484








IKKEEELVE
3430
SDMIKKEEELVEVNK
3485








LISDMIKKE
3431
VHDLISDMIKKEEEL
3486








VTPEQPQGD
3432
AQDVTPEQPQGDDNN
3487








YNTEKGRHP
3433
LVLYNTEKGRHPFKI
3488








IFFDLFLVN
3434
VFLIFFDLFLVNGRD
3489








ILTDGIPDS
3435
LVVILTDGIPDSIQD
3490
0.0002
0.0002
0.0046
−0.0003
0.0014
0.0480


INRENANQL
3436
NDRINRENANQLVVI
3491
0.0001

−0.0003
−0.0003

0.0096


LHSDASKNK
3437
IIRLHSDASKNKEKA
3492








LYADSAWEN
3438
KCNLYADSAWENVKN
3493

0.0003
−0.0014
−0.0009




VCVEVEKTA
3439
MKAVCVEVEKTASCG
3494








VEVEKTASC
3440
AVCVEVEKTASCGVW
3495
0.0001

0.0073
0.0006

0.0022


VPSDVPKNP
3441
EKEVPSDVPKNPEDD
3496








VWDEWSPCS
3442
SCGVWDEWSPCSVTC
3497
0.0001

−0.0003
−0.0003




LLMDCSGSI
3443
DLYLLMDCSGSIRRH
3498
0.0001

0.0072
0.0014

0.0057


ILHEGCTSE
3444
KREILHEGCTSELQE
3499








IPEDSEKEV
3445
EPNIPEDSEKEVPSD
3500








YREEVCNDE
3446
EIKYREEVCNDEVDL
3501








VCNDEVDLY
3447
REEVCNDEVDLYLLM
3502
0.0001

−0.0003
−0.0003

−0.0010


YAGEPAPFD
3448
ATPYAGEPAPFDETL
3503
















TABLE XXc







Malaria DR3b Motif Peptides


















Core
Core


Exemplary
Position
Exemplary
Exemplary




SeqID
Sequence
Core Sequence

SeqID
in Pf
Sequence
Conservancy 


Protein
Core Sequence
Num
Frequency
Conservancy (%)
Exemplary Sequence
Num
Poly-Protein
Frequency
(%)



















CSP
LKKNSRSLG
3504
19
100
WYSLKKNSRSLGEND
3539
62
19
100


CSP
ANNDVKNNN
3505
3
16
NANANNDVKNNNNEE
3540
361
3
16


LSA
ADIQNHTLE
3506
1
100
DKSADIQNHTLETVN
3541
1734
1
100


LSA
FHINGKIIK
3507
1
100
LLIFHINGKIIKNSE
3542
16
1
100


LSA
FKPNDKSLY
3508
1
100
DNNFKPNDKSLYDEH
3543
1846
1
100


LSA
FLKENKLNK
3509
1
100
ENIFLKENKLNKEGK
3544
108
1
100


LSA
IEKTNRESI
3510
1
100
ISIIEKTNRESITTN
3545
1693
1
100


LSA
IKNSEKDEI
3511
1
100
GKIIKNSEKDEIIKS
3546
23
1
100


LSA
IKPEQKEDK
3512
1
100
DGSIKPEQKEDKSAD
3547
1724
1
100


LSA
IKSNLRSGS
3513
1
100
DEIIKSNLRSGSSNS
3548
32
1
100


LSA
INEEKHEKK
3514
1
100
RNRINEEKHEKKHVL
3549
47
1
100


LSA
LEQERRAKE
3515
1
100
QSDLEQERRAKEKLQ
3550
1573
1
100


LSA
LNKEGKLIE
3516
1
100
ENKLNKEGKLIEHII
3551
114
1
100


LSA
LPQDNRGNS
3517
1
100
QSSLPQDNRGNSRDS
3552
1676
1
100


LSA
LQEQQRDLE
3518
1
100
NEKLQEQQRDLEQER
3553
1532
1
100


PfEXP
AEKTNKGTG
3519
1
100
ESLAEKTNKGTGSGV
3554
19
1
I00


PfEXP
LYNTEKGRH
3520
1
100
GLVLYNTEKGRHPFK
3555
97
1
100


PfEXP
VEVNKRKSK
3521
1
100
EELVEVNKRKSKYKL
3556
62
1
100


SSP2
AWENVKNVI
3522
10
100
ADSAWENVKNVIGPF
3557
216
10
100


SSP2
FLVNGRDVQ
3523
10
100
FDLFLVNGRDVQNNI
3558
18
10
100


SSP2
LGEEDKDLD
3524
10
100
DETLGEEDKDLDEPE
3559
549
10
100


SSP2
LDNERKQSD
3525
10
80
PKVLDNERKQSDPQS
3560
435
8
80


SSP2
VLDNERKQS
3526
10
70
PPKVLDNERKQSDPQ
3561
434
7
70


SSP2
IQDSLKESR
3527
10
60
PDSIQDSLKESRKLN
3562
165
6
60


SSP2
IVDEIKYRE
3528
9
90
QNNIVDEIKYREEVC
3563
29
9
90


SSP2
ALLQVRKHL
3529
9
60
LTDALLQVRKHLNDR
3564
133
6
60


SSP2
LKESRKLND
3530
6
50
QDSLKESRKLNDRGV
3565
169
5
50


SSP2
FSNNAKEII
3531
6
40
VNVFSNNAKEIIRLH
3566
90
4
40


SSP2
YNDTPKHPE
3532
5
50
NRKYNDTPKHPEREE
3567
479
5
50


SSP2
FSNNAREII
3533
4
20
LNIFSNNAREIIRLH
3568
90
2
20


SSP2
LKESRKLSD
3534
3
30
QDSLKESRKLSDRGV
3569
169
3
30


SSP2
YNDTPKYPE
3535
2
20
NRKYNDTPKYPEREE
3570
479
2
20


SSP2
AGSDNKYKI
3536
1
10
KKKAGSDNKYKIAGG
3571
501
1
10


SSP2
ALLEVRKHL
3537
1
10
LTDALLEVRKHLNDR
3572
133
1
10


SSP2
IVDEIKYSE
3538
1
10
QNNIVDEIKYSEEVC
3573
29
1
10
















TABLE XXd





Malaria DR3b Motif Peptides With Binding Information




























Exem-










Core

plary









Core Sequence
SeqID

SeqID









Num
Num
Exemplary Sequence
Num
DR 1
DR2w2β1
DR2w2β2
DR3
DR4w4
DR4w15
DR5w11





LKKNSRSLG
3504
WYSLKKNSRSLGEND
3539









ANNDVKNNN
3505
NANANNDVKNNNNEE
3540









ADIQNHTLE
3506
DKSADIQNHTLETVN
3541









FHINGKIIK
3507
LLIFHINGKIIKNSE
3542
 0.5700
0.2900
 0.2500
 0.5300
 0.0060
−0.0030
 0.3600


FKPNDKSLY
3508
DNNFKPNDKSLYDEH
3543



 0.1700





FLKENKLNK
3509
ENIFLKENKLNKEGK
3544



 0.0950





IEKTNRESI
3510
ISIIEKTNRESITTN
3545



 0.1300





IKNSEKDEI
3511
GKIIKNSEKDEIIKS
3546
 0.0002

−0.0021
−0.0160
−0.0017
 0.0030
−0.0010


IKPEQKEDK
3512
DGSIKPEQKEDKSAD
3547



−0.0033





IKSNLRSGS
3513
DEIIKSNLRSGSSNS
3548



 0.0050





INEEKHEKK
3514
RNRINEEKHEKKHVL
3549



 0.0420





LEQERRAKE
3515
QSDLEQERRAKEKLQ
3550









LNKEGKLIE
3516
ENKLNKEGKLIEHII
3551
 0.0001

−0.0021
−0.0140
−0.0017
−0.0047
−0.0005


LPQDNRGNS
3517
QSSLPQDNRGNSRDS
3552



−0.0033





LQEQQRDLE
3518
NEKLQEQQRDLEQER
3553









AEKTNKGTG
3519
ESLAEKTNKGTGSGV
3554



−0.0033





LYNTEKGRH
3520
GLVLYNTEKGRHPFK
3555









VEVNKRKSK
3521
EELVEVNKRKSKYKL
3556



 0.0880





AWENVKNVI
3522
ADSAWENVKNVIGPF
3557



−0.0130





FLVNGRDVQ
3523
FDLFLVNGRDVQNNI
3558



−0.0033





LGEEDKDLD
3524
DETLGEEDKDLDEPE
3559



−0.0130





LDNERKQSD
3525
PKVLDNERKQSDPQS
3560



−0.0130





VLDNERKQS
3526
PPKVLDNERKQSDPQ
3561



−0.0130





IQDSLKESR
3527
PDSIQDSLKESRKLN
3562
−0.0001
0.0040
−0.0018
 0.8400
−0.0055

−0.0006


IVDEIKYRE
3528
QNNIVDEIKYREEVC
3563









ALLQVRKHL
3529
LTDALLQVRKHLNDR
3564



−0.0033





LKESRKLND
3530
QDSLKESRKLNDRGV
3565









FSNNAKEII
3531
VNVFSNNAKEIIRLH
3566









YNDTPKHPE
3532
NRKYNDTPKHPEREE
3567









FSNNAREII
3533
LNIFSNNAREIIRLH
3568









LKESRKLSD
3534
QDSLKESRKLNDRGV
3569









YNDTPKYPE
3535
NRKYNDTPKYPEREE
3570









AGSDNKYKI
3536
KKKAGSDNKYKIAGG
3571









ALLEVRKHL
3537
LTDALLEVRKHLNDR
3572









IVDEIKYSE
3538
QNNIVDEIKYSEEVC
3573




















Core

Exemplary 









SeqID

SeqID








Core Sequence
Num
Exemplary Sequence
Num
DR5w12
DR6w19
DR7
DR8w2
DR9
DRw53





LKKNSRSLG
3504
WYSLKKNSRSLGEND
3539








ANNDVKNNN
3505
NANANNDVKNNNNEE
3540








ADIQNHTLE
3506
DKSADIQNHTLETVN
3541








FHINGKIIK
3507
LLIFHINGKIIKNSE
3542
0.0230
0.0330
0.1300
0.1400
0.1500



FKPNDKSLY
3508
DNNFKPNDKSLYDEH
3543








FLKENKLNK
3509
ENIFLKENKLNKEGK
3544








IEKTNRESI
3510
ISIIEKTNRESITTN
3545








IKNSEKDEI
3511
GKIIKNSEKDEIIKS
3546
−0.0003

−0.0011
−0.0007




IKPEQKEDK
3512
DGSIKPEQKEDKSAD
3547








IKSNLRSGS
3513
DEIIKSNLRSGSSNS
3548








INEEKHEKK
3514
RNRINEEKHEKKHVL
3549








LEQERRAKE
3515
QSDLEQERRAKEKLQ
3550








LNKEGKLIE
3516
ENKLNKEGKLIEHII
3551
−0.0003

−0.0009
−0.0007




LPQDNRGNS
3517
QSSLPQDNRQNSRDS
3552








LQEQQRDLE
3518
NEKLQEQQRDLEQER
3553








AEKTNKGTG
3519
ESLAEKTNKGTGSGV
3554








LYNTEKGRH
3520
GLVLYNTEKGRHPFK
3555








VEVNKRKSK
3521
EELVEVNKRKSKYKL
3556








AWENVKNVI
3522
ADSAWENVKNVIGPF
3557








FLVNGRDVQ
3523
FDLFLVNGRDVQNNI
3558








LGEEDKDLD
3524
DETLGEEDKDLDEPE
3559








LDNERKQSD
3525
PKVLDNERKQSDPQS
3560








VLDNERKQS
3526
PPKVLDNERKQSDPQ
3561








IQDSLKESR
3527
PDSIQDSLKESRKLN
3562

−0.0002
−0.0014
0.0012




IVDEIKYRE
3528
QNNIVDEIKYREEVC
3563








ALLQVRKHL
3529
LTDALLQVRKHLNDR
3564








LKESRKLND
3530
QDSLKESRKLNDRGV
3565








FSNNAKEII
3531
VNVFSNNAKEIIRLH
3566








YNDTPKHPE
3532
NRKYNDTPKHPEREE
3567








FSNNAREII
3533
LNIFSNNAREIIRLH
3568








LKESRKLSD
3534
QDSLKESRKLSDRGV
3569








YNDTPKYPE
3535
NRKYNDTPKYPEREE
3570








AGSDNKYKI
3536
KKKAGSDNKYKIAGG
3571








ALLEVRKHL
3537
LTDALLEVRKHLNDR
3572








IVDEIKYSE
3538
QNNIVDEIKYREEVC
3573
















TABLE XXI







Population coverage with combined HLA Supertypes









PHENOTYPIC FREQUENCY















North







Cau-
American
Japa-
Chi-
His-
Av-


HLA-SUPERTYPES
casian
Black
nese
nese
panic
erage
















a. Individual Supertypes








A2
45.8
39.0
42.4
45.9
43.0
43.2


A3
37.5
42.1
45.8
52.7
43.1
44.2


B7
38.6
52.7
48.8
35.5
47.1
44.7


A1
47.1
16.1
21.8
14.7
26.3
25.2


A24
23.9
38.9
58.6
40.1
38.3
40.0


B44
43.0
21.2
42.9
39.1
39.0
37.0


B27
28.4
26.1
13.3
13.9
35.3
23.4


B62
12.6
4.8
36.5
25.4
11.1
18.1


B58
10.0
25.1
1.6
9.0
5.9
10.3


b. Combined Supertypes








A2, A3, B7
83.0
86.1
87.5
88.4
86.3
86.2


A2, A3, B7, A24, B44,
99.5
98.1
100.0
99.5
99.4
99.3


A1








A2, A3, B7, A24, B44,
99.9
99.6
100.0
99.8
99.9
99.8


A1, B27, B62, B58
















TABLE XXII







Fixed analogs of P. falciparum CTL epitopes


















SEQ




SEQ


Supertype


ID

Alleles
Fixing
Fixed
ID


(or allele)
Peptide
Sequence
NO:
Source
bounds
strategy
sequence
NO:


















A2
1167.21
FLIFFDLFLV
3610
Pf SSP2 14
5
V2
FVIFFDLFLV
3803


supertype
1167.16
FMKAVCVEV
3611
Pf SSP2 230
5
V2
FVKAVCVEV
3804



1167.08
GLIMVLSFL
3612
Pf CSP 425
4
Vc
GLIMVLSFV
3805








V2
GVIMVLSFL
3806








V2/Vc
GVIMVLSFV
3807



1167.12
VLAGLLGNV
3613
Pf EXP1 80
4
V2
VVAGLLGNV
3808



1167.13
KILSVFFLA
3614
Pf EXP1 2
3
L2
KLLSVFFLA
3809








V2
KVLSVFFLA
3810








Vc
KILSVFFLV
3811








L2/Vc
KLLSVFFLV
3812








V2/Vc
KVLSVFFLV
3813



1167.10
GLLGNVSTV
3615
Pf EXP1 83
3
V2
GVLGNVSTV
3814



1167.18
ILSVSSFLFV
3616
Pf CSP 7
2
V2
IVSVSSFLFV
3815



1167.19
VLLGGVGLVL
3617
Pf EXP1 91
2
Vc
VLLGGVGLVV
3816








V2
VVLGGVGLVL
3817








V2/Vc
VVLGGVGLVV
3818


A3-
1167.36
LACAGLAYK
3718
Pf SSP2 511
4
V2
LVCAGLAYK
3819


supertype
1167.32
QTNFKSLLR
3619
Pf LSA1 94
4
V2
QVNFKSLLR
3820



1167.43
VTCGNGIQVR
3620
Pf CSP 375
4
V2
VVCGNGIQVR
3821



1167.24
ALFFIIFNK
3621
Pf EXP1 10
3
V2
AVFFIIFNK
3822



1167.28
GVSENIFLK
3622
Pf LSA1 105
3
—





1167.47
HVLSHNSYEK
3623
Pf LSA1 59
3
—





1167.51
LLACAGLAYK
3624
Pf SSP2 510
3
V2
LVACAGLAYK
3823



1167.46
FILVNLLIFH
3625
Pf LSA1 11
2
V2
FVLVNLLIFH
3824








Rc
FILVNLLIFR
3825








Kc
FILVNLLIFK
3826








V2/Rc
FVLVNLLIFR
3827








V2/Kc
FVLVNLLIFK
3828


B7-
1167.61
TPYAGEPAPF
3626
Pf SSP2 539
4
Ic
TPYAGEPAPI
3829


supertype
19.0051
LPYGRTNL
3627
Pf SSP2 126
3
Ic
LPYGRTNI
3830


A1
16.0245
FQDEENIGIY
3628
Pf LSA1 1794
1
T2
FTDEENIGIY
3831



16.0040
FVEALFQEY
3629
Pf CSP 15
1
D3
FVDALFQEY
3832








T2
FTEALFQEY
3833



15.0184
LPSENERGY
3630
Pf LSA1 1663
1
D3
LPDENERGY
3834








T2
LTSENERGY
3835



16.0130
PSDGKCNLY
3631
Pf SSP2 207
1
T2
PTDGKCNLY
3836


A24
1167.54
FYFILVNLL
3632
Pf LSA1 9
1
Fc
FYFILVNLF
3837



1167.53
KYKLATSVL
3633
Pf EXP1 73
1
Fc
KYKLATSVF
3838



1167.56
KYLVIVFLI
3634
Pf SSP2 8
1
Fc
KYLVIVFLF
3839



1167.55
YYIPHQSSL
3635
Pf LSA1 1671
1
Fc
YYIPHQSSF
3840





aA2-supertype peptides are tested for binding to A*0201, A*0202, A*0203, A*0206, and A*6802. A3-supertype peptides are tested for binding to A*03, A*11, A*31011, A*3301, and A*6801. B7-supertype peptides are tested for binding to B*0702, B*3501, B*5101, B*5301, and B*5401. A1 and A24 peptides are tested for binding to A*0101 and A*2402, respectively.













TABLE XXIII







Plasmodium falciparum CTL-inducing epitopes












SEQ






ID
Anti-
Resi-
HLA-


Epitope
NO:
gen
dues
restriction





GLIMVLSFL
3636
CSP
386-394
A2-supertype


ILSVSSFLFV
3637
CSP
 7-16
A2-supertype


VLAGLLGNV
3638
Exp-1
80-88
A2-supertype


KILSVFFLA
3639
Exp-1
 2-10
A2-supertype


GLLGNVSTV
3640
Exp-1
83-91
A2-supertype


VLLGGVGLVL
3641
Exp-1
 91-100
A2-supertype


FLIFFDLFLV
3642
SSP2
14-23
A2-supertype


VTCGNGIQVR
3643
CSP
336-345
A3 -supertype


ALFFIIFNK
3644
Exp-1
10-18
A3 -supertype


QTNFKSLLR
3645
LSA-1
 94-102
A3-supertype


GVSENIFLK
3646
LSA-1
105-113
A3 -supertype


HVLSHNSYEK
3647
LSA-1
59-68
A3 -supertype


FILVNLLIFH
3648
LSA-1
11-20
A3 -supertype


TPYAGELPAPF
3649
SSP2
539-548
B7-supertype


MPLETQLAI
3650
s16
77-85
B7-supertype


MRKLAILSVSSFLVF
3651
CSP
 2-16
DR-supermotif


MNYYGKQENWYSLKK
3652
CSP
53-67
DR-supermotif


RHNWVNHAVPLAMKLI
3653
SSP2
61-76
DR-supermotif


VKNVIGPFMKAVCVE
3654
SSP2
223-237
DR-supermotif


SSVFNVVNSSIGLIM
3655
CSP
410-424
DR-supermotif


AGLLGNVSTVSTVLLGGV
3656
EXP1
82-96
DR-supermotif


KSKYKLATSVLAGLL
3657
EXP1
71-85
DR-supermotif


GLAYKFVVPGAATPY
3658
SSP2
512-526
DR-supermotif


KYKIAGGIAGGLALL
3659
SSP2
494-508
DR-supermotif
















TABLE XXIV







MHC-peptide binding assays: cell lines and radiolabeled ligands.















Radiolabeled peptide



















SEQ ID


Species
Antigen
Allele
Cell line
Source
Sequence
NO:










A. Class I binding assays













Human
A1
A*0101
Steinlin
Hu. J chain 102-110
YTAVVPLVY
3660



A2
A*0201
PI
HBVc 18-27 F6->Y
FLPSDYFPSV
3661



A2
A*0202
P815 (transfected)
HBVc 18-27 F6->Y
FLPSDYFPSV
3662



A2
A*0203
FUN
HBVc 18-27 F6->Y
FLPSDYFPSV
3663



A2
A*0206
CLA
HBVc 18-27 F6->Y
FLPSDYFPSV
3664



A2
A*0207
721.221 (transfected)
HBVc 18-27 F6->Y
FLPSDYFPSV
3665



A3

GM3107
non-natural (A3CON1)
KVFPYALINK
3666



A11

BVR
non-natural (A3CON1)
KVFPYALINK
3667



A24
A*2402
KAS116
non-natural (A24CON1)
AYIDNYNKF
3668



A31
A*3101
SPACH
non-natural (A3CON1)
KVFPYALINK
3669



A33
A*3301
LWAGS
non-natural (A3CON1)
KVFPYALINK
3670



A28/68
A*6801
C1R
HBVc 141-151 T7->Y
STLPETYVVRR
3671



A28/68
A*6802
AMAI
HBV pol 646-654 C4->A
FTQAGYPAL
3672



B7
B*0702
GM3107
A2 sigal seq. 5-13 (L7->Y)
APRTLVYLL
3673



B8
B*0801
Steinlin
HIVgp 586-593 Y1->F, Q5->Y
FLKDYQLL
3674



B27
B*2705
LG2
R 60s
FRYNGLIHR
3675



B35
B*3501
C1R, BVR
non-natural (B35CON2)
FPFKYAAAF
3676



B35
B*3502
TISI
non-natural (B35CON2)
FPFKYAAAF
3677



B35
B*3503
EHM
non-natural (B35CON2)
FPFKYAAAF
3678



B44
B*4403
PITQUT
EF-1 G6->Y
AEMGKYSFY
3679



B51

KAS116
non-natural (B35CON2)
FPFKYAAAF
3680



B53
B*5301
AMAI
non-natural (B35CON2)
FPFKYAAAF
3681



B54
B*5401
KT3
non-natural (B35CON2)
FPFKYAAAF
3682



Cw4
Cw*0401
C1R
non-natural (C4CON1)
QYDDAVYKL
3683



Cw6
Cw*0602
721.221 transfected
non-natural (C6CON1)
YRHDGGNVL
3684



Cw7
CW*0702
721.221 transfected
non-natural (C6CON1)
YRHDGGNVL
3685


Mouse
Db

EL4
Adenovirus E1A P7->Y
SGPSNTYPEI
3686



Kb

EL4
VSV NP 52-59
RGYVFQGL
3687



Dd

P815
HIV-IIIB ENV G4->Y
RGPYRAFVTI
3688



Kd

P815
non-natural (KdCON1)
KFNPMKTYI
3689



Ld

P815
HBVs 28-39
IPQSLDSYWTSL
3690







B. Class II binding assays













Human
DR1
DRB1*0101
LG2
HA Y307-319
YPKYVKQNTLKLAT
3691



DR2
DRB1*1501
L466.1
MBP 88-102Y
VVHFFKNIVTPRTPPY
3692



DR2
DRB1*1601
L242.5
non-natural (760.16)
YAAFAAAKTAAAFA
3693



DR3
DRB1*0301
MAT
MT 65 kD Y3-13
YKTIAFDEEARR
3694



DR4w4
DRB1*0401
Preiss
non-natural (717.01)
YARFQSQTTLKQKT
3695



DR4w10
DRB1*0402
YAR
non-natural (717.10)
YARFQRQTTLKAAA
3696



DR4w14
DRB1*0404
BIN 40
non-natural (717.01)
YARFQSQTTLKQKT
3697



DR4w15
DRB1*0405
KT3
non-natural (717.01)
YARFQSQTTLKQKT
3698



DR7
DRB1*0701
Pitout
Tet. tox. 830-843
QYIKANSKFIGITE
3699



DR8
DRB1*0802
QLL
Tet. tox. 830-843
QYIKANSKFIGITE
3700



DR8
DRB1*0803
LUY
Tet. tox. 830-843
QYIKANSKFIGITE
3701



DR9
DRB1*0901
HID
Tet. tox. 830-843
QYIKANSKFIGITE
3702



DR11
DRB1*1101
Sweig
Tet. tox. 830-843
QYIKANSKFIGITE
3703



DR12
DRB1*1201
Herluf
unknown eluted peptide
EALIHQLKINPYVLS
3704



DR13
DRB1*1302
H0301
Tet. tox. 830-843 S->A
QYIKANAKFIGITE
3705



DR51
DRB5*0101
GM3107 or L416.3
Tet. tox. 830-843
QYIKANAKFIGITE
3706



DR51
DRB5*0201
L255.1
HA 307-319
PKYVKQNTLKLAT
3707



DR52
DRB3*0101
MAT
Tet. tox. 830-843
NGQIGNDPNRDIL
3708



DR53
DRB4*0101
L257.6
non-natural (717.01)
YARFQSQTTLKQKT
3709



DQ3.1
QA1*0301/DQB1.03(
PF
non-natural (ROIV)
YAHAAHAAHAAHAAHAA
3710


Mouse
IAb

DB27.4
non-natural (ROIV)
YAHAAHAAHAAHAAHAA
3711



IAd

A20
non-natural (ROIV)
YAHAAHAAHAAHAAHAA
3712



IAk

CH-12
HEL 46-61
YNTDGSTDYGILQINSR
3713



IAs

LS102.9
non-natural (ROIV)
YAHAAHAAHAAHAAHAA
3714



IAu

91.7
non-natural (ROIV)
YAHAAHAAHAAHAAHAA
3715



IEd

A20
Lambda repressor 12-26
YLEDARRKKAIYEKKK
3716



IEk

CH-12
Lambda repressor 12-26
YLEDARRKKAIYEKKK
3717
















TABLE XXV







Monoclonal antibodies 


used in MEC purification.










Monoclonal 




antibody
Specificity







W6/32
HLA-class I



B123.2
HLA-B and C



IVD12
HLA-DQ



LB3.1
HLA-DR



M1/42
H-2 class I



28-14-8S
H-2 Db and Ld



34-5-8S
H-2 Dd



B8-24-3
H-2 Kb



SF1-1.1.1
H-2 Kd



Y-3
H-2 Kb



10.3.6
H-2 IAk



14.4.4
H-2IEd, IEK



MKD6
H-2 IAd



Y3JP
H-2 IAb, IAS, IAu

















TABLE XXVI







P. falciparum A2-supermotif CTL epitopes
















SEQ ID

A2-supertype binding capacity (IC50 nM)
Alleles

















Peptide
AA
Sequence
NO:
Source
A*0201
A*0202
A*0203
A*0206
A*6802
bounda




















1167.21
10
FLIFFDLFLV
3718
Pf SSP2 14
12
10
5.9
11
333
5


1167.16
9
FMKAVCVEV
3719
Pf SSP2 230
63
307
2.9
389
143
5


1167.12
9
VLAGLLGNV
3720
Pf EXP1 80
19
24
0.67
31
606
4


1167.08
9
GLIMVLSFL
3721
Pf CSP 425
22
20
3.6
74
4396
4


1167.13
9
KILSVFFLA
3722
Pf EXP1 2
5.0
172
3448
8.0
9524
3


1167.10
9
GLLGNVSTV
3723
Pf EXP1 83
24
1194
1.2
25
21053
3


1167.19
10
VLLGGVGLVL
3724
Pf EXP1 91
94
—
2500
420
16000
2


1167.18
10
ILSVSSFLFV
3725
Pf CSP 7
208
3583
19
587
2105
2





*A dash indicates IC50 nM > 30000.













TABLE XXVII







P. falciparum A3-supermotif CTL epitopes
















SEQ ID

A3-supertype binding capacity (IC50 nM)
Alleles

















Peptide
AA
Sequence
NO:
Source
A*0301
A*1101
A*3101
A*3301
A*6801
bounda




















1167.32
9
QTNFKSLLR
3726
Pf LSA1 94
50
14
180
617
4
4


1167.36
9
LACAGLAYK
3727
Pf SSP2 511
423
143
5294
64
32
4


1167.43
10
VTCGNGIQVR
3728
Pf CSP 375
6875
11
15
64
444
4


1167.24
9
ALFFIIFNK
3729
Pf EXP1 10
9.2
2.2
720
1261
73
3


1167.51
10
LLACAGLAYK
3730
Pf SSP2 510
22
73
692
1526
24
3


1167.28
9
GVSENIFLK
3731
Pf LSA1 105
151
5.0
2250
8286
10
3


1167.47
10
HVLSHNSYEK
3732
Pf LSA1 59
407
200
—
—
114
3


1167.46
10
FILVNLLIFH
3733
Pf LSA1 11
733
1333
1957
397
154
2





*A dash indicates IC50 nM > 30000.













TABLE XXVIII







P. falciparum B7-supermotif CTL epitopes
















SEQ ID

B7-supertype binding capacity (IC50 nM)
Alleles

















Peptide
AA
Sequence
NO:
Source
B*0702
B*3501
B*5101
B*5301
B*5401
bounda




















1167.61
10
TPYAGEPAPF
3734
Pf SSP2 539
31
14
15
158
25000
4


19.0051
8
LPYGRTNL
3735
Pf SSP2 126
50
—
32
15500
417
3





* A dash indicates 1050 nM > 30000.













TABLE XXIX







P. falciparum HLA-A*0101 and A*2402 binding peptides



















Binding capacity (IC50 nM)














Motif
Peptide
AA
Sequence
SEQ ID NO:
Source
A*0101
A*2401

















A1 
16.0040
9
FVEALFQEY
3736
Pf CSP 15
7.4




16.0245
10
FQDEENIGIY
3737
Pf LSA1 1794
23




15.0184
9
LPSENERGY
3738

37




16.0130
9
PSDGKCNLY
3739
Pf SSP2 207
46



A24
1167.55
9
YYIPHQSSL
3740
Pf LSA1 1671

2.4



1167.54
9
FYFILVNLL
3741
Pf LSA1 9

25



1167.56
9
KYLVIVFLI
3742
Pf SSP2 8

34



1167.53
9
KYKLATSVL
3743
Pf EXP1 73

75
















TABLE XXX







HLA-DR screening panels











Screening


Representative Assay
Phenotypic Frequencies

















Panel
Antigen
Alleles
Allele
Alias
Cauc.
Blk.
Jpn.
Chn.
Hisp.
Avg.




















Primary
DR1
DRB1*0101-03
DRB1*0101
(DR1)
18.5
8.4
10.7
4.5
10.1
10.4



DR4
DRB1*0401-12
DRB1*0401
(DR4w4)
23.6
6.1
40.4
21.9
29.8
24.4



DR7
DRB1*0701-02
DRB1*0701
(DR7)
26.2
11.1
1.0
15.0
16.6
14.0



Panel total



59.6
24.5
49.3
38.7
51.1
44.6


Secondary
DR2
DRB1*1501-03
DRB1*1501
(DR2w2 β1)
19.9
14.8
30.9
22.0
15.0
20.5



DR2
DR135*0101
DRB5*0101
(DR2w2 β2)
—
—
—
—
—
—



DR9
DRB1*09011,09012
DRB1*0901
(DR9)
3.6
4.7
24.5
19.9
6.7
11.9



 DR13
DRB1*1301-06
DRB1*1302
(DR6w19)
21.7
16.5
14.6
12.2
10.5
15.1



Panel total



42.0
33.9
61.0
48.9
30.5
43.2


Tertiary
DR4
DRB1*0405
DRB1*0405
(DR4w15)
—
—
—
—
—
—



DR8
DRB1*0801-5
DRB1*0802
(DR8w2)
5.5
10.9
25.0
10.7
23.3
15.1



 DR11
DRB1*1101-05
DRB1*1101
(DR5w11)
17.0
18.0
4.9
19.4
18.1
15.5



Panel total



22.0
27.8
29.2
29.0
39.0
29.4


Quarternary
DR3
DRB1*0301-2
DRB1*0301
(DR3w17)
17.7
19.5
0.4
7.3
14.4
11.9



 DR12
DRB1*1201-02
DRB1*1201
(DR5w12)
2.8
5.5
13.1
17.6
5.7
8.9



Panel total



20.2
24.4
13.5
24.2
19.7
20.4
















TABLE XXXI





P. falciparum derived HTL candidate epitopes





















SEQ ID

Binding capacity (IC50 nM)















Peptide
Sequence
NO:
Source
DR1
DR2wβ1
DR2w2β2
DR4w4
DR4w15





F125.04
RHNWVNHAVPLAMKLI
3744
Pf SSP2 61
26
260
83
14
317


1188.34
HNWVNHAVPLAMKLI
3745
Pf SSP2 62
14
364
143
12
950


1188.16
KSKYKLATSVLAGLL
3746
Pf EXP1 71
3.6
1247
24
7.1
47



LVNLLIFHINGKIIKNSE
3747
Pf LSA1 13







F125.02
LVNLLIFHINGKIIKNS
3748
Pf LSA1 13
78
13
426
—
1810


27.0402
LLIFHINGKIIKNSE
3749
Pf LSA1 16
8.8

80
7500



1188.32
GLAYKFVVPGAATPY
3750
Pf SSP2 512
3.1
—
29
45
1407


27.0392
SSVFNVVNSSIGLIM
3751
Pf CSP 410
42
314
2500
450
1652


27.0417
VKNVIGPFMKAVCVE
3752
Pf SSP2 223
56
212
250
—
—


27.0388
MRKLAILSVSSFLFV
3753
Pf CSP 2
50
18
1538
5769
1407


27.0387
MNYYGKQENWYSLKK
3754
Pf CSP 53
6.4
9100
435
21
292


1188.38
KYKIAGGIAGGLALL
3755
Pf SSP2 494
132
—
417
3750
22353


1188.13
AGLLGNVSTVLLGGV
3756
Pf EXP1 82
116
379
15,385
6923
1056


27.0408
QTNFKSLLRNLGVSE
3757
Pf LSA1 94
91
8273
5405
2500
1900


35.0171
PDSIQDSLKESRKLN
3758
Pf SSP2 165
—
2285
—
—



35.0172
KCNLYADSAWENVKN
3759
Pf SSP2 211
23425
18200
—
—
















Binding capacity (IC50 nM)
Alleles

















Peptide
DR5w11
DR6w19
DR7
DR8w2
DR9
DR3
DR5w12
bound2






F125.04
282
3.9
23
41
33
8751
441
11



1188.34
2703
3.7
66
68
19
1304
497
10



1188.16
30
427
13
45
28
—
—
9



F125.02
408
66
260
766
625
19722
11610
8



27.0402
56
106
192
350
500
566
12957
8



1188.32
11
7.1
167
20
125
—
851
9



27.0392
1176
9.7
33
891
63
—
—
7



27.0417
476
32
424
2130
862
—
3239
7



27.0388
541
38
500
—
682


6



27.0387
351
3182
3788
538
22059


6



1188.38
87
15
3968
31
288


6



1188.13
—
0.76
58
—
142


5



27.0408
51
47
7813
69
—


4



35.0171
—
—
—
—
—
357

1



35.0172
—
11061
—
—
—
857

1





A dash (—) indicates IC50 > 20 μM.













TABLE XXXII







PBMC responses of individuals 


from the Irian Java endemic malaria region.









Percent individuals yielding positive responses (n)










Peptide 
1FNγ
TNFa
Proliferation
















CSP.2
11%
(7) 
59% 
(39)
9% 
(11)


LSA1.13 
16% 
(9)
30% 
(21)
8% 
(10)


CSP.53 
7% 
(4)
53% 
(40)
3% 
(4)


SSP2.61 
7% 
(4)
45% 
(36)
7% 
(9)


SSP2.223
15% 
(9) 
42% 
(31)
5% 
(6)


CSP.410 
16% 
(9) 
47% 
(33)
12%
(14)


EXP1.82 
29% 
(17)
43% 
(32)
6% 
(7)


EXP1.71 
9% 
(5)
49% 
(36)
12% 
(14)


SSP2.512
14% 
(8)
41% 
(30)
3% 
(4)


SSP2.62 
11% 
(6)
42% 
(31)
12%
(14)


SSP2.494
7% 
(4)
36% 
(26)
2% 
(3)
















TABLE XXXIII







P. falciparum CTL epitopes













Supertype





Alleles


(or allele)
Peptide
AA
Sequence
SEQ ID NO:
Source
bounda
















A2-supertype
1167.08
9
GLIMVLSFL
3760
Pf CSP 425
4



1167.10
9
GLLGNVSTV
3761
Pf EXP1 83
3



1167.12
9
VLAGLLGNV
3762
Pf EXP1 80
4



1167.13
9
KILSVFFLA
3763
Pf EXP1 2
3



1167.16
9
FMKAVCVEV
3764
Pf SSP2 230
5



1167.18
10
ILSVSSFLFV
3765
Pf CSP 7
2



1167.19
10
VLLGGVGLVL
3766
Pf EXP1 91
2



1167.21
10
FLIFFDLFLV
3767
Pf SSP2 14
5


A3-supertype
1167.24
9
ALFFIIFNK
3768
PF EXP1 10
3



1167.28
9
GVSENIFLK
3769
Pf LSA1 105
3



1167.32
9
QTNFKSLLR
3770
Pf LSA1 94
4



1167.36
9
LACAGLAYK
3771
Pf SSP2 511
4



1167.43
10
VTCGNGIQVR
3772
Pf CSP 375
4



1167.46
10
FILVNLLIFH
3773
Pf LSA1 11
2



1167.47
10
HVLSHNSYEK
3774
Pf LSA1 59
3



1167.51
10
LLACAGLAYK
3775
Pf SSP2 510
3


B7-supertype
19.0051
8
LPYGRTNL
3776
Pf SSP2 126
3



1167.61
10
TPYAGEPAPF
3777
Pf SSP2 539
4


A1
15.0184
9
LPSENERGY
3778
Pf LSA1 1663
1



16.0040
9
FVEALFQEY
3779
Pf CSP 15
1



16.0130
9
PSDGKCNLY
3780
Pf SSP2 207
1



16.0245
10
FQDEENIGIY
3781
Pf LSA1 1794
1


A24
1167.53
9
KYKLATSVL
3782
Pf EXP1 73
1



1167.54
9
FYFILVNLL
3783
Pf LSA1 9
1



1167.55
9
YYIPHQSSL
3784
Pf LSA1 1671
1



1167.56
9
KYLVIVFLI
3785
Pf SSP2 8
1





aA2-supertype peptides are tested for binding to A*0201, A*0202, A*0203, A*0206, and A*6802. A3-supertype peptides are tested for binding to A*03, A*11, A*31011, A*3301, and A*6801. B7-supertype peptides are tested for binding to B*0702, B*3501, B*5101, B*5301, and B*5401. A1 and A24 peptides are tested for binding to A*0101 and A*2402, respectively.













TABLE XXXIV







P. falciparum HTL epitopes















SEQ 

Alleles


Motif
Peptide
Sequence
ID NO:
Source
bounda















DR-
F125.04
RHNWVNHAVPLAMKLI
3786
Pf SSP2 61
11


supermotif








1188.16
KSKYKLATSVLAGLL
3787
Pf EXP1 71
 9



27.0402
LLIFHINGKIIKNSE
3788
Pf LSA1 16
 9







(DR3)



1188.32
GLAYKFVVPGAATPY
3789
Pf SSP2 512
9



27.0392
SSVFNVVNSSIGLIM
3790
Pf CSP 410
 7



27.0417
VKNVIGPFMKAVCVE
3791
Pf SSP2 223
 7



27.0388
MRKLAILSVSSFLFV
3792
Pf CSP 2
 6



27.0387
MNYYGKQENWYSLKK
3793
Pf CSP53
 6



1188.38
KYKIAGGIAGGLALL
3794
Pf SSP2 494
 6



1188.13
AGLLGNVSTVLLGGV
3795
Pf EXP1 82
 5



27.0408
QTNFKSLLRNLGVSE
3796
Pf LSA1 94
 4


DR3
35.0171
PDSIQDSLKESRKLN
3797
Pf SSP2 165
DR3



35.0172
KCNLYADSAWENVKN
3798
Pf SSP2 211
DR3





aHLA-DR supermotif peptides are screened for binding to a panel alleles representing the 10 most common HLA antigens, including DR1, DR2w2 β1, DR2w2 β2, DR4w4, DR4w15, DR5w11, DR6w19, DR7, DR8w2, and DR9. Additional alleles that are tested include DR3, DR5w12, DR52a, and DR53. DR3-motif peptides are tested for binding to DR3.













TABLE XXXV







Estimated population coverage by a panel of P. falciparum derived HTL epitopes













Representative
No. of
Population coverage (phenotypic frequency)
















Antigen
Alleles
assay
epitopes2
Cauc.
Blk.
Jpn.
Chn.
Hisp.
Avg.



















DR1
DRB1*0101-03
DR1
11
18.5
8.4
10.7
4.5
10.1
10.4


DR2
DRB1*1501-03
DR2w2 β1
6
19.9
14.8
30.9
22.0
15.0
20.5


DR2
DRB5*0101
DR2w2 β2
7
—
—
—
—
—
—


DR3
DRB1*0301-2
DR3
3
17.7
19.5
0.40
7.3
14.4
11.9


DR4
DRB1*0401-12
DR4w4
5
23.6
6.1
40.4
21.9
29.8
24.4


DR4
DRB1*0401-12
DR4w15
3
—
—
—
—
—
—


DR7
DRB1*0701-02
DR7
8
26.2
11.1
1.0
15.0
16.6
14.0


DR8
DRB1*0801-5
DR8w2
8
5.5
10.9
25.0
10.7
23.3
15.1


DR9
DRB1*09011,09012
DR9
9
3.6
4.7
24.5
19.9
6.7
11.9


 DR11
DRB1*1101-05
DR5w11
9
17.0
18.0
4.9
19.4
18.1
15.5


 DR12
DRB1*1201-2
DR5w12
2
2.8
5.5
13.1
17.6
5.7
8.9


 DR13
DRB1*1301-06
DR6w19
10
21.7
16.5
14.6
12.2
10.5
15.1


Total



97.0
83.9
98.8
95.5
95.6
94.7

## Claims

1. A conjugate of an isolated peptide less than 13 amino acids in length comprising the oligopeptide GVSENIFLK (SEQ ID NO:3731) and a T helper peptide; wherein said T helper peptide is less than about 50 amino acids in length and wherein said T helper peptide comprises a pan-DR binding epitope.

2. A composition comprising the conjugate of claim 1 and a carrier.

3. The conjugate of claim 1, wherein the isolated peptide is GVSENIFLK (SEQ ID NO:3731).

4. The conjugate of claim 1, wherein said pan-DR binding epitope is aKXVWANTLKAAa (SEQ ID NO:3802), where “X” is either cyclohexylalanine, phenylalanine, or tyrosine, and “a” is either D-alanine or L-alanine.