# Patent

## Title
Spider silk fusion protein structures for binding to an organic target

## Abstract

A protein structure capable of selective interaction with an organic target is provided. The protein structure is a polymer comprising as a repeating structural unit a recombinant fusion protein that is capable of selective interaction with the organic target. The fusion protein is comprising the moieties B, REP and CT, and optionally NT. B is a non-spidroin moiety of more than 30 amino acid residues, which provides the capacity of selective interaction with the organic target. REP is a moiety of from 70 to 300 amino acid residues and is derived from the repetitive fragment of a spider silk protein. CT is a moiety of from 70 to 120 amino acid residues and is derived from the C-terminal fragment of a spider silk protein. NT is an optional moiety of from 100 to 160 amino acid residues and is derived from the N-terminal fragment of a spider silk protein. The fusion protein and protein structure thereof is useful as an affinity medium and a cell scaffold material.

## Background
This application is a Continuation of U.S. patent application Ser. No. 13/880,628 filed on Aug. 6, 2013, which is the National Phase of PCT International Application No. PCT/EP2011/068626 filed on Oct. 25, 2011 and claims priority under 35 U.S.C. §119(a) to patent application Ser. No. 10/189,059.8 filed in Europe on Oct. 27, 2010, all of which are hereby expressly incorporated by reference into the present application.


TECHNICAL FIELD OF THE INVENTION
The present invention relates to the field of recombinant fusion proteins, and more specifically to fusion proteins comprising moieties derived from spider silk proteins (spidroins). The present invention provides methods for providing a protein structure which is a polymer comprising a recombinant fusion protein, which is comprising moieties derived from spidroins. There is also provided novel protein structures for binding to an organic target.
BACKGROUND TO THE INVENTION
In applied protein chemistry, it is a common problem how to formulate or present a biologically active peptide or protein to the relevant site of activity, typically an organic target, such as a nucleic acid, a protein, a complex of proteins, or a complex of a protein(s) and/or lipids and/or carbohydrates and/or a nucleic acid(s). The simplest solution is simply to provide an aqueous solution of the biologically active peptide or protein. Many applications do however require some further means to achieve the desired goal. For instance, the peptides/proteins may be associated with a lipid mixture or chemically immobilized to a support structure.
Applications for peptides/proteins immobilized to a support structure include preparative and analytical separation procedures, such as bioprocesses, chromatography, cell capture and culture, active filters, and diagnostics. Structures based on extracellular matrix proteins, e.g. collagen, are disclosed in EP 704 532 and EP 985 732.
It has also been suggested to use spider silk proteins in a supporting structure. Spider silks are nature's high-performance polymers, obtaining extraordinary toughness and extensibility due to a combination of strength and elasticity. Spiders have up to seven different glands which produce a variety of silk types with different mechanical properties and functions. Dragline silk, produced by the major ampullate gland, is the toughest fiber. It consists of two main polypeptides, mostly referred to as major ampullate spidroin (MaSp) 1 and 2, but e.g. as ADF-3 and ADF-4 in Araneus diadematus. These proteins have molecular masses in the range of 200-720 kDa. Spider dragline silk proteins, or MaSps, have a tripartite composition; a non-repetitive N-terminal domain, a central repetitive region comprised of many iterated poly-Ala/Gly segments, and a non-repetitive C-terminal domain. It is generally believed that the repetitive region forms intermolecular contacts in the silk fibers, while the precise functions of the terminal domains are less clear. It is also believed that in association with fiber formation, the repetitive region undergoes a structural conversion from random coil and α-helical conformation to β-sheet structure. The C-terminal region of spidroins is generally conserved between spider species and silk types.
WO 07/078239 and Stark, M. et al., Biomacromolecules 8: 1695-1701, (2007) disclose a miniature spider silk protein consisting of a repetitive fragment with a high content of Ala and Gly and a C-terminal fragment of a protein, as well as soluble fusion proteins comprising the spider silk protein. Fibers of the spider silk protein are obtained spontaneously upon liberation of the spider silk protein from its fusion partner.
Rising, A. et al., CMLS 68(2): 169-184 (2010) reviews advances in the production of spider silk proteins.
US 2009/0263430 discloses chemical coupling of the enzyme β-galactosidase to films of a miniature spider silk protein. However, chemical coupling may require conditions which are unfavourable for protein stability and/or function. Proteins containing multiple repeats of a segment derived from the repetitive region of spider silk proteins have been designed to include a RGD cell-binding segment (Bini, E et al., Biomacromolecules 7:3139-3145 (2006)) and/or a R5 peptide (Wong Po Foo, C et al., Proc Natl Acad Sci 103 (25): 9428-9433 (2006)) or other protein segments involved in mineralization (Huang, J et al., Biomaterials 28: 2358-2367 (2007); WO 2006/076711). In these prior art documents, films are formed by solubilizing the fusion proteins in the denaturing organic solvent hexafluoroisopropanol (HFIP) and drying.
US 2005/261479 A1 discloses a method of for purification of recombinant silk proteins having an affinity tag, involving magnetic affinity separation of individual silk proteins from complex mixtures without formation of silk protein fibers or other polymer structures.
Known supporting structures and associated techniques have certain drawbacks with regard to e.g. economy, efficiency, stability, regenerating capacity, bioactivity and biocompatibility.
SUMMARY OF THE INVENTION
It is an object of the present invention to provide a novel protein structure that is capable of selective interaction with an organic target.
It is also an object of the present invention to provide a protein structure that is capable of selective interaction with an organic target, wherein the structure is formed without use of harsh solvents which may have an unpredictable effect on the secondary structure or activity of the protein and/or remain in the protein structure.
It is one object of the present invention to provide a stable protein structure that is capable of selective interaction with an organic target, which protein structure can readily be regenerated after use, e.g. with chemical treatment.
It is another object of the present invention to provide a stable protein structure that is biocompatible and suitable for cell culture and as an implant.
It is yet another object of the invention to provide a protein structure with a high density of evenly spaced functionalities that are capable of selective interaction with an organic target.
It is a further object of the invention to provide a protein structure which maintains its selective binding ability upon storage at +4° C. or at room temperature for months.
It is also an object of the invention to provide a protein structure which is autoclavable, i.e. maintains its selective binding ability after sterilizing heat treatment.
For these and other objects that will be evident from the following disclosure, the present invention provides according to a first aspect a fusion protein and a protein structure consisting of polymers comprising as a repeating structural unit the fusion protein as set out in the claims.
According to a related aspect, the present invention provides an isolated polynucleic acid encoding the fusion protein and a method of producing the fusion protein as set out in the claims.
The present invention provides according to another aspect a method for providing a protein structure as set out in the claims.
The present invention provides according to a further aspect an affinity medium as set out in the claims.
The present invention provides according to one aspect a cell scaffold material as set out in the claims. According to a related aspect, the present invention also provides a combination of cells and a cell scaffold material according to the claims.
The present invention provides according to an aspect novel uses of a protein structure and a fusion protein as set out in the claims.
The present invention provides according to another aspect a method for separation of an organic target from a sample as set out in the claims.
The present invention provides according to a further aspect a method for immobilization and optionally cultivation of cells as set out in the claims.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 shows a sequence alignment of spidroin C-terminal domains.
FIG. 2 shows a sequence alignment of spidroin N-terminal domains.
FIG. 3 shows a macroscopic fiber of a fusion protein comprising a Z domain.
FIG. 4 shows a SDS-PAGE gel from purification and analysis of a fusion protein comprising a Z domain.
FIG. 5 shows fibers made of fusion proteins and control fibers that illustrate functionality of the Z domain in a fusion protein.
FIG. 6 shows part of a casted film made of fusion proteins at the bottom of a tissue culture plate.
FIGS. 7-12 show non-reducing SDS-PAGE gels illustrating the functionality of the Z domain in fusion protein structures.
FIGS. 13-15 show non-reducing SDS-PAGE gels illustrating the IgG-binding capacity of the Z domain in a fusion protein structures compared to a commercial protein A matrix.
FIGS. 16-17 show non-reducing SDS-PAGE gels of cleaning-in-place (CIP) procedures of fusion protein structures compared to a commercial protein A matrix.
FIG. 18 shows fluorescence intensities from protein films soaked with biotinylated Atto-565.
FIG. 19 shows a graph and a linear fit of fluorescence intensity values for different concentrations of biotinylated Atto-565 upon binding to a fusion protein film.
FIG. 20 shows graphs of fluorescence intensity values before (−) and after (+) addition of biotinylated Atto-565 to wells with films made of fusion protein or control.
FIG. 21 is a graph showing a standard curve and a linear fit of resulting reaction velocities in catalysis by biotinylated HRP free in solution.
FIG. 22 is a graph showing the reaction velocity in catalysis by biotinylated HRP immobilised to a fusion protein film compared to control.
FIG. 23 shows a reducing SDS-PAGE gel of solubilized fusion protein structures.
FIG. 24-26 shows graphs illustrating binding of IgG-HRP to a fusion protein film comprising Z domains.
FIG. 27 shows graphs illustrating binding of IgG-Alexa Fluor 633 to a fusion protein film comprising Z domains.
FIG. 28 shows a non-reducing SDS-PAGE gel illustrating the functionality of the Z domain in a fusion protein after autoclaving.
FIG. 29 shows a SDS-PAGE gel of cleavage products from Protease 3C treatment of a fusion protein fiber comprising Z domains.
FIG. 30 shows a non-reducing SDS-PAGE gel illustrating the functionality of the Z domain in fusion protein structures formed in the presence of an organic target (IgG).
FIG. 31-32 shows non-reducing SDS-PAGE gels illustrating the functionality of the Abd domain in fusion protein structures.
FIG. 33-34 shows non-reducing SDS-PAGE gels illustrating the functionality of the C2 domain in fusion protein structures.













List of appended sequences
















SEQ ID NO



1
4Rep


2
4RepCT


3
NT4Rep


4
NT5Rep


5
NT4RepCTHis


6
NT


7
CT


8
consensus NT sequence


9
consensus CT sequence


10
repetitive sequence from Euprosthenops australis MaSp1


11
consensus G segment sequence 1


12
consensus G segment sequence 2


13
consensus G segment sequence 3


14
HisZQG4Rep4CT


15
HisZQG4Rep4CT (DNA)


16
HisAbdQG4RepCT


17
HisAbdQG4RepCT (DNA)


18
HisC2QG4RepCT


19
HisC2QG4RepCT (DNA)


SEQ ID NO



20
4RepCT 2


21
4RepCT 2 (DNA)


22
M44RepCT


23
M44RepCT (DNA)


24
modM44RepCT


25
modM44RepCT (DNA)


26
4RepCTM4


27
4RepCTM4 (DNA)









DETAILED DESCRIPTION OF THE INVENTION
The present invention is generally based on the insight that solid protein structures capable of selective interaction with an organic target can be prepared in the form of polymers of a recombinant fusion protein as a repeating structural unit. The fusion protein is comprising at least one non-spidroin moiety of more than 30 amino acid residues that is capable of selective interaction with the organic target, and moieties corresponding to at least the repetitive and the C-terminal fragments of a spider silk protein. Surprisingly, the moieties derived from the spider silk protein can be induced to rearrange structurally and as a result form polymeric, solid structures, while the non-spidroin moiety is not structurally rearranged but maintains its desirable structure and function, i.e. capability of selective interaction with the organic target. The protein structures can be obtained without a chemical coupling step or a denaturing method step, which facilitates the procedure and improves the chances of obtaining a fusion protein with maintained functionality of its moieties, in particular when the functions are dependent on the secondary structure of the moieties. The formation of these fusion protein polymers can be tightly controlled, and this insight has been developed into further novel protein structures, methods of producing the protein structures and uses of the protein structures in various applications and methods.
The fusion protein according to the invention thus harbors both the desired selective interaction activity and an internal solid support activity that is employed in the protein structure under physiological conditions. It must be considered as surprising that the binding activity of the fusion protein is maintained although the non-spidroin moiety is covalently attached to the spidroin moiety when the latter is structurally rearranged to form polymeric, solid structures. In fact, the heat and/or chemical stability and/or binding activity of the moiety providing the selective interaction activity may be increased when integrated in a fusion protein structure according to the invention. The protein structure also provides a high and predictable density of the selective interaction activity towards an organic target. Losses of valuable protein moieties with selective interaction activity are minimized, since all expressed protein moieties are associated with the solid support.
The polymers which are formed from the fusion proteins according to the invention are solid structures and are useful for their physical properties, especially the useful combination of high strength, elasticity and light weight. A particularly useful feature is that the spidroin-derived moieties of the fusion protein are biochemically robust and suitable for regeneration, e.g. with acid, base or chaotropic agents, and suitable for heat sterilization, e.g. autoclaving at 120° C. for 20 min. The polymers are also useful for their ability to support cell adherence and growth. The properties derived from dragline silk are attractive in development of new materials for medical or technical purposes. In particular, protein structures according to the invention are useful in preparative and analytical separation procedures, such as chromatography, cell capture, selection and culture, active filters, and diagnostics. Protein structures according to the invention are also useful in medical devices, such as implants and medical products, such as wound closure systems, band-aids, sutures, wound dressings, and scaffolds for cell immobilization, cell culture, tissue engineering and guided cell regeneration.
The present invention provides a recombinant fusion protein that is capable of selective interaction with an organic target, which fusion protein is comprising the moieties B, REP and CT, and optionally NT. The present invention also provides a protein structure that is capable of selective interaction with an organic target, wherein said protein structure is a polymer comprising, and optionally consisting of, the recombinant fusion protein according to the invention, i.e. comprising, and optionally consisting of, the moieties B, REP and CT, and optionally NT.
Although the REP and the CT moieties of the fusion proteins in the examples by necessity relate to specific proteins, e.g. proteins derived from major spidroin 1 (MaSp1) from Euprosthenops australis, it is considered that the present disclosure is applicable to any structurally similar moieties for the purpose of producing fusion protein structures according to the invention. Furthermore, although the B moiety which provides the selective interaction activity of the fusion proteins in the examples by necessity relate to specific protein moieties, e.g. moieties derived from protein A, protein G and streptavidin, it is considered that the present disclosure is applicable to any structurally and/or functionally similar B moiety for the purpose of producing fusion protein structures according to the invention, capable of selective interaction with an organic target.
Specific fusion proteins according to the invention are defined by the formulas Bx—REP-By-CT-Bz and Bz—CT-By-REP-Bz, wherein x, y and z are integers from 0 to 5; and x+y+z 1, optionally further containing one NT moiety at either end of the fusion protein or between any two protein moieties in the fusion protein. If x+y+z>1, i.e. if there are two or more B moieties, they may be identical or different. The two or more B moieties may have capacity of selective interaction with the same organic target or with different organic targets. It is preferred that the two or more B moieties are substantially identical, each having capacity of selective interaction with the same organic target.
In preferred fusion proteins according to the invention, x, y and z are integers from 0 to 2, preferably from 0 to 1. In certain preferred fusion proteins according to the invention, y=0. In more preferred specific fusion proteins according to the invention, y=0 and either x or z are 0, i.e. the fusion proteins are defined by the formulas Bz—REP-CT, Bz-CT-REP, REP-CT-BZ and CT-REP-BZ, wherein x and z are integers from 1 to 5. In preferred fusion proteins according to the invention, y=0, x and z are integers from 0 to 1; and x+z=1. Thus, certain preferred fusion proteins according to the invention are defined by the formulas B-REP-CT, B-CT-REP, REP-CT-B and CT-REP-B. In preferred fusion proteins according to the invention, the optional NT moiety is missing.
The term “fusion protein” implies here a protein that is made by expression from a recombinant nucleic acid, i.e. DNA or RNA that is created artificially by combining two or more nucleic acid sequences that would not normally occur together (genetic engineering). The fusion proteins according to the invention are recombinant proteins, and they are therefore not identical to naturally occurring proteins. In particular, wildtype spidroins are not fusion proteins according to the invention, because they are not expressed from a recombinant nucleic acid as set out above. The combined nucleic acid sequences encode different proteins, partial proteins or polypeptides with certain functional properties. The resulting fusion protein, or recombinant fusion protein, is a single protein with functional properties derived from each of the original proteins, partial proteins or polypeptides. Furthermore, the fusion protein according to the invention and the corresponding genes are chimeric, i.e. the protein/gene moieties are derived from at least two different species. The REP and the CT moieties, as well as the optional NT moiety, are all derived from a spider silk protein. For avoidance of doubt, the B moiety according to the invention is a non-spidroin protein or polypeptide, i.e. it is not derived from a spider silk protein. In particular, the B moiety according to the invention is not derived from the C-terminal, repetitive or N-terminal fragments of a spider silk protein.
The fusion protein typically consists of from 170 to 2000 amino acid residues, such as from 170 to 1000 amino acid residues, such as from 170 to 600 amino acid residues, preferably from 170 to 500 amino acid residues, such as from 170 to 400 amino acid residues. The small size is advantageous because longer proteins containing spider silk protein fragments may form amorphous aggregates, which require use of harsh solvents for solubilisation and polymerisation. The recombinant fusion protein may contain more than 2000 residues, in particular in cases where the spider silk protein more than one B moiety and/or when it contains a NT moiety.
The terms “spidroins” and “spider silk proteins” are used interchangeably throughout the description and encompass all known spider silk proteins, including major ampullate spider silk proteins which typically are abbreviated “MaSp”, or “ADF” in the case of Araneus diadematus. These major ampullate spider silk proteins are generally of two types, 1 and 2. These terms furthermore include non-natural proteins with a high degree of identity and/or similarity to the known spider silk proteins.
Consequently, the term “non-spidroin” implies proteins that are not derived from a spider silk protein, i.e. with a low (or no) degree of identity and/or similarity to spider silk proteins.
The protein structure according to the invention is capable of selective interaction with an organic target. This capacity resides in the fusion protein according to the invention, and more specifically in the B moiety of the fusion protein. Any interactions of the REP and the CT moieties, as well as the optional NT moiety, with organic molecules are not encompassed by the term “capable of selective interaction with an organic target”. For avoidance of doubt, the term “capable of selective interaction with an organic target” does not encompass dimerization, oligomerization or polymerization of the fusion proteins according to the invention that rely on interactions involving the REP and the CT moieties, as well as the optional NT moiety.
The term “organic target” encompasses all chemical molecules containing carbon with the exception of what is traditionally considered inorganic molecules by the skilled person, e.g. carbonates, simple oxides of carbon, cyanides, diamond and graphite. For avoidance of doubt, inorganic molecules, salts and ions, such as silica and calcium chloride, are not organic. The organic target may be a complex containing or consisting of organic molecules, e.g. a receptor complex on a cell surface. The organic target may be a monomer, dimer, oligomer or polymer of one or more organic molecule types, which may be held together by covalent bonds or other types of association. It may of course also simply be a single organic molecule. Preferred organic targets according to the invention include, but are not limited to, nucleic acids, proteins and polypeptides, lipids and carbohydrates, as well as combinations thereof. Further preferred organic targets according to the invention include, but are not limited to, immunoglobulins, molecules comprising immunoglobulin or derivatives thereof, albumin, molecules comprising albumin or derivatives thereof, biotin, and molecules comprising biotin or derivatives or analogues thereof.
In the context of the present invention, “specific” or “selective” interaction of a ligand, e.g. a B moiety of the fusion protein according to the invention with its target means that the interaction is such that a distinction between specific and non-specific, or between selective and non-selective, interaction becomes meaningful. The interaction between two proteins is sometimes measured by the dissociation constant. The dissociation constant describes the strength of binding (or affinity) between two molecules. Typically the dissociation constant between an antibody and its antigen is from 10−7 to 10−11 M. However, high specificity does not necessarily require high affinity. Molecules with low affinity (in the molar range) for its counterpart have been shown to be as specific as molecules with much higher affinity. In the case of the present invention, a specific or selective interaction refers to the extent to which a particular method can be used to determine the presence and/or amount of a specific protein, the target protein or a fragment thereof, under given conditions in the presence of other proteins in a sample of a naturally occurring or processed biological or biochemical fluid. In other words, specificity or selectivity is the capacity to distinguish between related proteins. Specific and selective are sometimes used interchangeably in the present description.
The fusion protein according to the invention may also contain one or more linker peptides. The linker peptide(s) may be arranged between any moieties of the fusion protein, e.g. between the CT and REP moieties, between two B moieties, between B and CT moieties, and between B and REP moieties, or may be arranged at either terminal end of the fusion protein. If the fusion protein contains two or more B moieties, the linker peptide(s) may also be arranged in between two B moieties. The linker(s) may provide a spacer between the functional units of the fusion protein, but may also constitute a handle for identification and purification of the fusion protein, e.g. a His and/or a Trx tag. If the fusion protein contains two or more linker peptides for identification and purification of the fusion protein, it is preferred that they are separated by a spacer sequence, e.g. His6-spacer-His6-. The linker may also constitute a signal peptide, such as a signal recognition particle, which directs the fusion protein to the membrane and/or causes secretion of the fusion protein from the host cell into the surrounding medium. The fusion protein may also include a cleavage site in its amino acid sequence, which allows for cleavage and removal of the linker(s) and/or other relevant moieties, typically the B moiety or moieties. Various cleavage sites are known to the person skilled in the art, e.g. cleavage sites for chemical agents, such as CNBr after Met residues and hydroxylamine between Asn-Gly residues, cleavage sites for proteases, such as thrombin or protease 3C, and self-splicing sequences, such as intein self-splicing sequences.
The REP, CT and B moieties are linked directly or indirectly to one another. A direct linkage implies a direct covalent binding between the moieties without intervening sequences, such as linkers. An indirect linkage also implies that the moieties are linked by covalent bonds, but that there are intervening sequences, such as linkers and/or one or more further moieties, e.g. a NT moiety.
The B moiety or moieties may be arranged internally or at either end of the fusion protein, i.e. C-terminally arranged or N-terminally arranged. It is preferred that the B moiety or moieties are arranged at the N-terminal end of the fusion protein. If the fusion protein contains one or more linker peptide(s) for identification and purification of the fusion protein, e.g. a His or Trx tag(s), it is preferred that it is arranged at the N-terminal end of the fusion protein.
A preferred fusion protein has the form of an N-terminally arranged B moiety, coupled by a linker peptide of 1-30 amino acid residues, such as 1-10 amino acid residues, to C-terminally arranged REP and CT moieties. The linker peptide may contain a cleavage site. Optionally, the fusion protein has an N-terminal or C-terminal linker peptide, which may contain a purification tag, such as a His tag, and a cleavage site.
Another preferred fusion protein has the form of an N-terminally arranged B moiety coupled directly to C-terminally arranged REP and CT moieties. Optionally, the fusion protein has an N-terminal or C-terminal linker peptide, which may contain a purification tag, such as a His tag, and a cleavage site.
The protein structure according to the invention is a polymer comprising as a repeating structural unit recombinant fusion proteins according to the invention, which implies that it contains an ordered plurality of fusion proteins according to the invention, typically well above 100 fusion protein units, e.g. 1000 fusion protein units or more. Optionally, the polymer may comprise as a further repeating structural unit complementary proteins without a B moiety, preferably proteins derived from spider silk. This may be advantageous if the B moiety of the fusion protein is large and/or bulky. These complementary proteins typically comprise a REP moiety and a CT moiety, and optionally an NT moiety. Preferred complementary proteins according to the invention can have any of the structures set out herein with a deleted B moiety. It is preferred that the complementary fusion protein in is substantially identical to the fusion protein with a deleted B moiety. However, it is preferred that the protein structure according to the invention is a polymer consisting of recombinant fusion proteins according to the invention as a repeating structural unit, i.e. that the protein structure according to the invention is a polymer of the recombinant fusion protein according to the invention.
The magnitude of fusion units in the polymer implies that the protein structure obtains a significant size. In a preferred embodiment, the protein structure has a size of at least 0.1 μm in at least two dimensions. Thus, the term “protein structure” as used herein relates to fusion protein polymers having a thickness of at least 0.1 μm, preferably macroscopic polymers that are visible to the human eye, i.e. having a thickness of at least 1 μm. The term “protein structure” does not encompass unstructured aggregates or precipitates. While monomers of the fusion protein are water soluble, it is understood that the protein structures according to the invention are solid structures, i.e. not soluble in water. The protein structures are polymers comprising as a repeating structural unit monomers of the recombinant fusion proteins according to the invention.
It is preferable that the protein structure according to the invention is in a physical form selected from the group consisting of fiber, film, foam, net, mesh, sphere and capsule.
It is preferable that the protein structure according to the invention is a fiber or film with a thickness of at least 0.1 μm, preferably at least 1 μm. It is preferred that the fiber or film has a thickness in the range of 1-400 μm, preferably 60-120 μm. It is preferred that fibers have a length in the range of 0.5-300 cm, preferably 1-100 cm. Other preferred ranges are 0.5-30 cm and 1-20 cm. The fiber has the capacity to remain intact during physical manipulation, i.e. can be used for spinning, weaving, twisting, crocheting and similar procedures. The film is advantageous in that it is coherent and adheres to solid structures, e.g. the plastics in microtiter plates. This property of the film facilitates washing and regeneration procedures and is very useful for separation purposes. A particularly useful protein structure is a film or a fiber wherein the B moiety is the Z domain derived from staphylococcal protein A or a protein fragment having at least 70% identity thereto, see e.g. Examples 1-6.
It is also preferred that the protein structure according to the invention has a tensile strength above 1 MPa, preferably above 2 MPa, more preferably 10 MPa or higher. It is preferred that the protein structure according to the invention has a tensile strength above 100 MPa, more preferably 200 MPa or higher.
The REP moiety is a protein fragment containing from 70 to 300 amino acid residues and is derived from the repetitive fragment of a spider silk protein. This implies that the REP moiety has a repetitive character, alternating between alanine-rich stretches and glycine-rich stretches. The REP moiety generally contains more than 70, such as more than 140, and less than 300, preferably less than 240, such as less than 200, amino acid residues, and can itself be divided into several L (linker) segments, A (alanine-rich) segments and G (glycine-rich) segments, as will be explained in more detail below. Typically, said linker segments, which are optional, are located at the REP moiety terminals, while the remaining segments are in turn alanine-rich and glycine-rich. Thus, the REP moiety can generally have either of the following structures, wherein n is an integer:
L(AG)nL, such as LA1G1A2G2A3G3A4G4A5G5L;
L(AG)nAL, such as LA1G1A2G2A3G3A4G4A5G5A6L;
L(GA)nL, such as LG1A1G2A2G3A3G4A4G5A5L; or
L(GA)nGL, such as LG1A1G2A2G3A3G4A4G5A5G6L.
It follows that it is not critical whether an alanine-rich or a glycine-rich segment is adjacent to the N-terminal or C-terminal linker segments. It is preferred that n is an integer from 2 to 10, preferably from 2 to 8, preferably from 4 to 8, more preferred from 4 to 6, i.e. n=4, n=5 or n=6.
In preferred embodiments, the alanine content of the REP moiety according to the invention is above 20%, preferably above 25%, more preferably above 30%, and below 50%, preferably below 40%, more preferably below 35%. This is advantageous, since it is contemplated that a higher alanine content provides a stiffer and/or stronger and/or less extendible structure.
In certain embodiments, the REP moiety is void of proline residues, i.e. there are no proline residues in the REP moiety.
Now turning to the segments that constitute the REP moiety according to the invention, it shall be emphasized that each segment is individual, i.e. any two A segments, any two G segments or any two L segments of a specific REP moiety may be identical or may not be identical. Thus, it is not a general feature of the invention that each type of segment is identical within a specific REP moiety. Rather, the following disclosure provides the skilled person with guidelines how to design individual segments and gather them into a REP moiety which is thereby considered to be derived from the repetitive fragment of a spider silk protein, and which constitutes a part of a functional fusion protein according to the invention.
Each individual A segment is an amino acid sequence having from 8 to 18 amino acid residues. It is preferred that each individual A segment contains from 13 to 15 amino acid residues. It is also possible that a majority, or more than two, of the A segments contain from 13 to 15 amino acid residues, and that a minority, such as one or two, of the A segments contain from 8 to 18 amino acid residues, such as 8-12 or 16-18 amino acid residues. A vast majority of these amino acid residues are alanine residues. More specifically, from 0 to 3 of the amino acid residues are not alanine residues, and the remaining amino acid residues are alanine residues. Thus, all amino acid residues in each individual A segment are alanine residues, with no exception or the exception of one, two or three amino acid residues, which can be any amino acid. It is preferred that the alanine-replacing amino acid(s) is (are) natural amino acids, preferably individually selected from the group of serine, glutamic acid, cysteine and glycine, more preferably serine. Of course, it is possible that one or more of the A segments are all-alanine segments, while the remaining A segments contain 1-3 non-alanine residues, such as serine, glutamic acid, cysteine or glycine.
In a preferred embodiment, each A segment contains 13-15 amino acid residues, including 10-15 alanine residues and 0-3 non-alanine residues as described above. In a more preferred embodiment, each A segment contains 13-15 amino acid residues, including 12-15 alanine residues and 0-1 non-alanine residues as described above.
It is preferred that each individual A segment has at least 80%, preferably at least 90%, more preferably 95%, most preferably 100% identity to an amino acid sequence selected from the group of amino acid residues 7-19, 43-56, 71-83, 107-120, 135-147, 171-183, 198-211, 235-248, 266-279, 294-306, 330-342, 357-370, 394-406, 421-434, 458-470, 489-502, 517-529, 553-566, 581-594, 618-630, 648-661, 676-688, 712-725, 740-752, 776-789, 804-816, 840-853, 868-880, 904-917, 932-945, 969-981, 999-1013, 1028-1042 and 1060-1073 of SEQ ID NO: 10. Each sequence of this group corresponds to a segment of the naturally occurring sequence of Euprosthenops australis MaSp1 protein, which is deduced from cloning of the corresponding cDNA, see WO 2007/078239. Alternatively, each individual A segment has at least 80%, preferably at least 90%, more preferably 95%, most preferably 100% identity to an amino acid sequence selected from the group of amino acid residues 143-152, 174-186, 204-218, 233-247 and 265-278 of SEQ ID NO: 3. Each sequence of this group corresponds to a segment of expressed, non-natural spider silk proteins, which proteins have capacity to form silk structures under appropriate conditions. Thus, in certain embodiments according to the invention, each individual A segment is identical to an amino acid sequence selected from the above-mentioned amino acid segments. Without wishing to be bound by any particular theory, it is envisaged that A segments according to the invention form helical structures or beta sheets.
The term “% identity”, as used throughout the specification and the appended claims, is calculated as follows. The query sequence is aligned to the target sequence using the CLUSTAL W algorithm (Thompson, J. D., Higgins, D. G. and Gibson, T. J., Nucleic Acids Research, 22: 4673-4680 (1994)). A comparison is made over the window corresponding to the shortest of the aligned sequences. The amino acid residues at each position are compared, and the percentage of positions in the query sequence that have identical correspondences in the target sequence is reported as % identity.
The term “% similarity”, as used throughout the specification and the appended claims, is calculated as described for “% identity”, with the exception that the hydrophobic residues Ala, Val, Phe, Pro, Leu, Ile, Trp, Met and Cys are similar; the basic residues Lys, Arg and His are similar; the acidic residues Glu and Asp are similar; and the hydrophilic, uncharged residues Gln, Asn, Ser, Thr and Tyr are similar. The remaining natural amino acid Gly is not similar to any other amino acid in this context.
Throughout this description, alternative embodiments according to the invention fulfill, instead of the specified percentage of identity, the corresponding percentage of similarity. Other alternative embodiments fulfill the specified percentage of identity as well as another, higher percentage of similarity, selected from the group of preferred percentages of identity for each sequence. For example, a sequence may be 70% similar to another sequence; or it may be 70% identical to another sequence; or it may be 70% identical and 90% similar to another sequence.
Furthermore, it has been concluded from experimental data that each individual G segment is an amino acid sequence of from 12 to 30 amino acid residues. It is preferred that each individual G segment consists of from 14 to 23 amino acid residues. At least 40% of the amino acid residues of each G segment are glycine residues. Typically the glycine content of each individual G segment is in the range of 40-60%.
It is preferred that each individual G segment has at least 80%, preferably at least 90%, more preferably 95%, most preferably 100% identity to an amino acid sequence selected from the group of amino acid residues 20-42, 57-70, 84-106, 121-134, 148-170, 184-197, 212-234, 249-265, 280-293, 307-329, 343-356, 371-393, 407-420, 435-457, 471-488, 503-516, 530-552, 567-580, 595-617, 631-647, 662-675, 689-711, 726-739, 753-775, 790-803, 817-839, 854-867, 881-903, 918-931, 946-968, 982-998, 1014-1027, 1043-1059 and 1074-1092 of SEQ ID NO: 10. Each sequence of this group corresponds to a segment of the naturally occurring sequence of Euprosthenops australis MaSp1 protein, which is deduced from cloning of the corresponding cDNA, see WO 2007/078239. Alternatively, each individual G segment has at least 80%, preferably at least 90%, more preferably 95%, most preferably 100% identity to an amino acid sequence selected from the group of amino acid residues 153-173, 187-203, 219-232, 248-264 and 279-296 of SEQ ID NO: 3. Each sequence of this group corresponds to a segment of expressed, non-natural spider silk proteins, which proteins have capacity to form silk structures under appropriate conditions. Thus, in certain embodiments according to the invention, each individual G segment is identical to an amino acid sequence selected from the above-mentioned amino acid segments.
In certain embodiments, the first two amino acid residues of each G segment according to the invention are not -Gln-Gln-.
There are the three subtypes of the G segment according to the invention. This classification is based upon careful analysis of the Euprosthenops australis MaSp1 protein sequence (WO 2007/078239), and the information has been employed and verified in the construction of novel, non-natural spider silk proteins.
The first subtype of the G segment according to the invention is represented by the amino acid one letter consensus sequence GQG(G/S)QGG(Q/Y)GG (L/Q)GQGGYGQGA GSS (SEQ ID NO: 11). This first, and generally the longest, G segment subtype typically contains 23 amino acid residues, but may contain as little as 17 amino acid residues, and lacks charged residues or contain one charged residue. Thus, it is preferred that this first G segment subtype contains 17-23 amino acid residues, but it is contemplated that it may contain as few as 12 or as many as 30 amino acid residues. Without wishing to be bound by any particular theory, it is envisaged that this subtype forms coil structures or 31-helix structures. Representative G segments of this first subtype are amino acid residues 20-42, 84-106, 148-170, 212-234, 307-329, 371-393, 435-457, 530-552, 595-617, 689-711, 753-775, 817-839, 881-903, 946-968, 1043-1059 and 1074-1092 of SEQ ID NO: 10. In certain embodiments, the first two amino acid residues of each G segment of this first subtype according to the invention are not -Gln-Gln-.
The second subtype of the G segment according to the invention is represented by the amino acid one letter consensus sequence GQGGQGQG(G/R)Y GQG(A/S)G(S/G)S (SEQ ID NO: 12). This second, generally mid-sized, G segment subtype typically contains 17 amino acid residues and lacks charged residues or contain one charged residue. It is preferred that this second G segment subtype contains 14-20 amino acid residues, but it is contemplated that it may contain as few as 12 or as many as 30 amino acid residues. Without wishing to be bound by any particular theory, it is envisaged that this subtype forms coil structures. Representative G segments of this second subtype are amino acid residues 249-265, 471-488, 631-647 and 982-998 of SEQ ID NO: 10; and amino acid residues 187-203 of SEQ ID NO: 3.
The third subtype of the G segment according to the invention is represented by the amino acid one letter consensus sequence G(R/Q)GQG(G/R)YGQG (A/S/V)GGN (SEQ ID NO: 13). This third G segment subtype typically contains 14 amino acid residues, and is generally the shortest of the G segment subtypes according to the invention. It is preferred that this third G segment subtype contains 12-17 amino acid residues, but it is contemplated that it may contain as many as 23 amino acid residues. Without wishing to be bound by any particular theory, it is envisaged that this subtype forms turn structures. Representative G segments of this third subtype are amino acid residues 57-70, 121-134, 184-197, 280-293, 343-356, 407-420, 503-516, 567-580, 662-675, 726-739, 790-803, 854-867, 918-931, 1014-1027 of SEQ ID NO: 10; and amino acid residues 219-232 of SEQ ID NO: 3.
Thus, in preferred embodiments, each individual G segment has at least 80%, preferably 90%, more preferably 95%, identity to an amino acid sequence selected from SEQ ID NO: 11, SEQ ID NO: 12 and SEQ ID NO: 13.
In a preferred embodiment of the alternating sequence of A and G segments of the REP moiety, every second G segment is of the first subtype, while the remaining G segments are of the third subtype, e.g. . . . A1GshortA2GlongA3GshortA4GlongA5Gshort . . . . In another preferred embodiment of the REP moiety, one G segment of the second subtype interrupts the G segment regularity via an insertion, e.g. . . . A1GshortA2GlongA3GmidA4GshortA5Glong . . . .
Each individual L segment represents an optional linker amino acid sequence, which may contain from 0 to 20 amino acid residues, such as from 0 to 10 amino acid residues. While this segment is optional and not functionally critical for the spider silk protein, its presence still allows for fully functional spider silk fusion proteins, forming protein structures according to the invention. There are also linker amino acid sequences present in the repetitive part (SEQ ID NO: 10) of the deduced amino acid sequence of the MaSp1 protein from Euprosthenops australis. In particular, the amino acid sequence of a linker segment may resemble any of the described A or G segments, but usually not sufficiently to meet their criteria as defined herein.
As shown in WO 2007/078239, a linker segment arranged at the C-terminal part of the REP moiety can be represented by the amino acid one letter consensus sequences ASASAAASAA STVANSVS and ASAASAAA, which are rich in alanine. In fact, the second sequence can be considered to be an A segment according to the invention, while the first sequence has a high degree of similarity to A segments according to the invention. Another example of a linker segment according the invention has the one letter amino acid sequence GSAMGQGS, which is rich in glycine and has a high degree of similarity to G segments according to the invention. Another example of a linker segment is SASAG.
Representative L segments are amino acid residues 1-6 and 1093-1110 of SEQ ID NO: 10; and amino acid residues 138-142 of SEQ ID NO: 3, but the skilled person in the art will readily recognize that there are many suitable alternative amino acid sequences for these segments. In one embodiment of the REP moiety according to the invention, one of the L segments contains 0 amino acids, i.e. one of the L segments is void. In another embodiment of the REP moiety according to the invention, both L segments contain 0 amino acids, i.e. both L segments are void. Thus, these embodiments of the REP moieties according to the invention may be schematically represented as follows: (AG)nL, (AG)nAL, (GA)nL, (GA)nGL; L(AG)n, L(AG)nA, L(GA)n, L(GA)nG; and (AG)n, (AG)nA, (GA)n, (GA)nG. Any of these REP moieties are suitable for use with any CT moiety as defined below.
The CT moiety is a protein fragment containing from 70 to 120 amino acid residues and is derived from the C-terminal fragment of a spider silk protein. The expression “derived from” implies in the context of the CT moiety according to the invention that it has a high degree of similarity to the C-terminal amino acid sequence of spider silk proteins. As shown in FIG. 1, this amino acid sequence is well conserved among various species and spider silk proteins, including MaSp1 and MaSp2. A consensus sequence of the C-terminal regions of MaSp1 and MaSp2 is provided as SEQ ID NO: 9. In FIG. 1, the following MaSp proteins are aligned, denoted with GenBank accession entries where applicable:







TABLE 1







Spidroin CT moieties








Species and spidroin protein
Entry





Euprosthenops sp MaSp1 (Pouchkina-Stantcheva, 
Cthyb_Esp


N N & McQueen-Mason, S J, ibid)



Euprosthenops australis MaSp1
CTnat_Eau


Argiope trifasciata MaSp1
AF350266_At1


Cyrtophora moluccensis Sp1
AY666062_Cm1


Latrodectus geometricus MaSp1
AF350273_Lg1


Latrodectus hesperus MaSp1
AY953074_Lh1


Macrothele holsti Sp1
AY666068_Mh1


Nephila clavipes MaSp1
U20329_Nc1


Nephila pilipes MaSp1
AY666076_Np1


Nephila madagascariensis MaSp1
AF350277_Nm1


Nephila senegalensis MaSp1
AF350279_Ns1


Octonoba varians Sp1
AY666057_Ov1


Psechrus sinensis Sp1
AY666064_Ps1


Tetragnatha kauaiensis MaSp1
AF350285_Tk1


Tetragnatha versicolor MaSp1
AF350286_Tv1


Araneus bicentenarius Sp2
ABU20328_Ab2


Argiope amoena MaSp2
AY365016_Aam2


Argiope aurantia MaSp2
AF350263_Aau2


Argiope trifasciata MaSp2
AF350267_At2


Gasteracantha mammosa MaSp2
AF350272_Gm2


Latrodectus geometricus MaSp2
AF350275_Lg2


Latrodectus hesperus MaSp2
AY953075_Lh2


Nephila clavipes MaSp2
AY654293_Nc2


Nephila madagascariensis MaSp2
AF350278_Nm2


Nephila senegalensis MaSp2
AF350280_Ns2


Dolomedes tenebrosus Fb1
AF350269_DtFb1


Dolomedes tenebrosus Fb2
AF350270_DtFb2


Araneus diadematus ADF-1
U47853_ADF1


Araneus diadematus ADF-2
U47854_ADF2


Araneus diadematus ADF-3
U47855_ADF3


Araneus diadematus ADF-4
U47856_ADF4









It is not critical which specific CT moiety is present in spider silk proteins according to the invention, as long as the CT moiety is not entirely missing. Thus, the CT moiety according to the invention can be selected from any of the amino acid sequences shown in FIG. 1 and Table 1 or sequences with a high degree of similarity. A wide variety of C-terminal sequences can be used in the spider silk protein according to the invention.
The sequence of the CT moiety according to the invention has at least 50% identity, preferably at least 60%, more preferably at least 65% identity, or even at least 70% identity, to the consensus amino acid sequence SEQ ID NO: 9, which is based on the amino acid sequences of FIG. 1.
A representative CT moiety according to the invention is the Euprosthenops australis sequence SEQ ID NO: 7, Thus, according to a preferred aspect of the invention, the CT moiety has at least 80%, preferably at least 90%, such as at least 95%, identity to SEQ ID NO: 7 or any individual amino acid sequence of FIG. 1 and Table 1. In preferred aspects of the invention, the CT moiety is identical to SEQ ID NO: 7 or any individual amino acid sequence of FIG. 1 and Table 1.
The CT moiety typically consists of from 70 to 120 amino acid residues. It is preferred that the CT moiety contains at least 70, or more than 80, preferably more than 90, amino acid residues. It is also preferred that the CT moiety contains at most 120, or less than 110 amino acid residues. A typical CT moiety contains approximately 100 amino acid residues.
The optional NT moiety is a protein fragment containing from 100 to 160 amino acid residues and is derived from the N-terminal fragment of a spider silk protein. The expression “derived from” implies in the context of the NT moiety according to the invention that it has a high degree of similarity to the N-terminal amino acid sequence of spider silk proteins. As shown in FIG. 2, this amino acid sequence is well conserved among various species and spider silk proteins, including MaSp1 and MaSp2. In FIG. 2, the following spidroin NT moieties are aligned, denoted with Gen Bank accession entries where applicable:







TABLE 2







Spidroin NT moieties











GenBank


Code
Species and spidroin protein
acc. no.





Ea MaSp1
Euprosthenops australis MaSp 1
AM259067


Lg MaSp1
Latrodectus geometricus MaSp 1
ABY67420


Lh MaSp1
Latrodectus hesperus MaSp 1
ABY67414


Nc MaSp1
Nephila clavipes MaSp 1
ACF19411


At MaSp2
Argiope trifasciata MaSp 2
AAZ15371


Lg MaSp2
Latrodectus geometricus MaSp 2
ABY67417


Lh MaSp2
Latrodectus hesperus MaSp 2
ABR68855


Nim MaSp2
Nephila inaurata madagascariensis
AAZ15322



MaSp 2



Nc MaSp2
Nephila clavipes MaSp 2
ACF19413


Ab CySp1
Argiope bruennichi cylindriform spidroin 1
BAE86855


Ncl CySp1
Nephila clavata cylindriform spidroin 1
BAE54451


Lh TuSp1
Latrodectus hesperus tubuliform spidroin
ABD24296


Nc Flag
Nephila clavipes flagelliform silk protein
AF027972


Nim Flag
Nephila inaurata madagascariensis 
AF218623



flagelliform silk protein
(translated)









Only the part corresponding to the N-terminal moiety is shown for each sequence, omitting the signal peptide. Nc flag and Nlm flag are translated and edited according to Rising A. et al. Biomacromolecules 7, 3120-3124 (2006)).
It is not critical which specific NT moiety is present in spider silk proteins according to the invention. Thus, the NT moiety according to the invention can be selected from any of the amino acid sequences shown in FIG. 2 or sequences with a high degree of similarity. A wide variety of N-terminal sequences can be used in the spider silk protein according to the invention. Based on the homologous sequences of FIG. 2, the following sequence constitutes a consensus NT amino acid sequence:







(SEQ ID NO: 8)


QANTPWSSPNLADAFINSF(M/L)SA(A/I)SSSGAFSADQLDDMSTIG


 


(D/N/Q)TLMSAMD(N/S/K)MGRSG(K/R)STKSKLQALNMAFASSMA


 


EIAAAESGG(G/Q)SVGVKTNAISDALSSAFYQTTGSVNPQFV(N/S)E


 


IRSLI(G/N)M(F/L)(A/S)QASANEV.






The sequence of the NT moiety according to the invention has at least 50% identity, preferably at least 60% identity, to the consensus amino acid sequence SEQ ID NO: 8, which is based on the amino acid sequences of FIG. 2. In a preferred embodiment, the sequence of the NT moiety according to the invention has at least 65% identity, preferably at least 70% identity, to the consensus amino acid sequence SEQ ID NO: 8. In preferred embodiments, the NT moiety according to the invention has furthermore 70%, preferably 80%, similarity to the consensus amino acid sequence SEQ ID NO: 8.
A representative NT moiety according to the invention is the Euprosthenops australis sequence SEQ ID NO: 6. According to a preferred embodiment of the invention, the NT moiety has at least 80% identity to SEQ ID NO: 6 or any individual amino acid sequence in FIG. 1. In preferred embodiments of the invention, the NT moiety has at least 90%, such as at least 95% identity, to SEQ ID NO: 6 or any individual amino acid sequence in FIG. 2. In preferred embodiments of the invention, the NT moiety is identical to SEQ ID NO: 6 or any individual amino acid sequence in FIG. 1, in particular to Ea MaSp1.
The NT moiety contains from 100 to 160 amino acid residues. It is preferred that the NT moiety contains at least 100, or more than 110, preferably more than 120, amino acid residues. It is also preferred that the NT moiety contains at most 160, or less than 140 amino acid residues. A typical NT moiety contains approximately 130-140 amino acid residues.
The B moiety is a protein or polypeptide fragment comprising more than 30 amino acid residues. The B moiety is preferably comprising more than 40 amino acid residues, such as more than 50 amino acid residues. The B moiety is preferably comprising less than 500 amino acid residues, such as less than 200 amino acid residues, more preferably less than 100 amino acid residues, such as less than 100 amino acid residues. It is capable of selective interaction with the organic target, and it is the B moiety in the fusion protein which provides the capacity of selective interaction with the organic target.
The B moiety is a non-spidroin moiety. This implies that it is not derived from a spider silk protein, i.e. it has a low (or no) degree of identity and/or similarity to spider silk proteins. The sequence of the B moiety according to the invention preferably has less than 30% identity, such as less than 20% identity, preferably less than 10% identity, to any of the spidroin amino acid sequences disclosed herein, and specifically to any of SEQ ID NO: 6-10.
It is regarded as within the capabilities of those of ordinary skill in the art to select the B moiety. Nevertheless, examples of affinity ligands that may prove useful as B moieties, as well as examples of formats and conditions for detection and/or quantification, are given below for the sake of illustration.
The biomolecular diversity needed for selection of affinity ligands may be generated by combinatorial engineering of one of a plurality of possible scaffold molecules, and specific and/or selective affinity ligands are then selected using a suitable selection platform. Non-limiting examples of such structures, useful for generating affinity ligands against the organic target, are staphylococcal protein A and domains thereof and derivatives of these domains, such as the Z domain (Nord K et al. (1997) Nat. Biotechnol. 15:772-777); lipocalins (Beste G et al. (1999) Proc. Natl. Acad. Sci. U.S.A. 96:1898-1903); ankyrin repeat domains (Binz H K et al. (2003) J. Mol. Biol. 332:489-503); cellulose binding domains (CBD) (Smith G P et al. (1998) J. Mol. Biol. 277:317-332; Lehtiö J et al. (2000) Proteins 41:316-322); γ crystallines (Fiedler U and Rudolph R, WO01/04144); green fluorescent protein (GFP) (Peelle B et al. (2001) Chem. Biol. 8:521-534); human cytotoxic T lymphocyte-associated antigen 4 (CTLA-4) (Hufton S E et al. (2000) FEBS Lett. 475:225-231; Irving R A et al. (2001) J. Immunol. Meth. 248:31-45); protease inhibitors, such as Knottin proteins (Wentzel A et al. (2001) J. Bacteriol. 183:7273-7284; Baggio R et al. (2002) J. Mol. Recognit. 15:126-134) and Kunitz domains (Roberts B L et al. (1992) Gene 121:9-15; Dennis M S and Lazarus R A (1994) J. Biol. Chem. 269:22137-22144); PDZ domains (Schneider S et al. (1999) Nat. Biotechnol. 17:170-175); peptide aptamers, such as thioredoxin (Lu Z et al. (1995) Biotechnology 13:366-372; Klevenz B et al. (2002) Cell. Mol. Life Sci. 59:1993-1998); staphylococcal nuclease (Norman T C et al. (1999) Science 285:591-595); tendamistats (McConell S J and Hoess R H (1995) J. Mol. Biol. 250:460-479; Li R et al. (2003) Protein Eng. 16:65-72); trinectins based on the fibronectin type III domain (Koide A et al. (1998) J. Mol. Biol. 284:1141-1151; Xu L et al. (2002) Chem. Biol. 9:933-942); and zinc fingers (Bianchi E et al. (1995) J. Mol. Biol. 247:154-160; Klug A (1999) J. Mol. Biol. 293:215-218; Segal D J et al. (2003) Biochemistry 42:2137-2148).
The above-mentioned examples include scaffold proteins presenting a single randomized loop used for the generation of novel binding specificities, protein scaffolds with a rigid secondary structure where side chains protruding from the protein surface are randomized for the generation of novel binding specificities, and scaffolds exhibiting a non-contiguous hyper-variable loop region used for the generation of novel binding specificities.
Oligonucleotides may also be used as affinity ligands. Single stranded nucleic acids, called aptamers or decoys, fold into well-defined three-dimensional structures and bind to their target with high affinity and specificity. (Ellington A D and Szostak J W (1990) Nature 346:818-822; Brody E N and Gold L (2000) J. Biotechnol. 74:5-13; Mayer G and Jenne A (2004) BioDrugs 18:351-359). The oligonucleotide ligands can be either RNA or DNA and can bind to a wide range of target molecule classes.
For selection of the desired affinity ligand from a pool of variants of any of the scaffold structures mentioned above, a number of selection platforms are available for the isolation of a specific novel ligand against a target protein of choice. Selection platforms include, but are not limited to, phage display (Smith G P (1985) Science 228:1315-1317), ribosome display (Hanes J and Plückthun A (1997) Proc. Natl. Acad. Sci. U.S.A. 94:4937-4942), yeast two-hybrid system (Fields S and Song 0 (1989) Nature 340:245-246), yeast display (Gai S A and Wittrup K D (2007) Curr Opin Struct Biol 17:467-473), mRNA display (Roberts R W and Szostak J W (1997) Proc. Natl. Acad. Sci. U.S.A. 94:12297-12302), bacterial display (Daugherty P S (2007) Curr Opin Struct Biol 17:474-480, Kronqvist N et al. (2008) Protein Eng Des Sel 1-9, Harvey B R et al. (2004) PNAS 101(25):913-9198), microbead display (Nord O et al. (2003) J Biotechnol 106:1-13, WO01/05808), SELEX (System Evolution of Ligands by Exponential Enrichment) (Tuerk C and Gold L (1990) Science 249:505-510) and protein fragment complementation assays (PCA) (Remy I and Michnick S W (1999) Proc. Natl. Acad. Sci. U.S.A. 96:5394-5399). A preferred group of B moieties with affinity for immunoglobulins, albumin or other organic targets are bacterial receptin domains or derivatives thereof.
A group of preferred B moieties are capable of selective interaction with immunoglobulins and molecules comprising immunoglobulin or derivatives thereof. A preferred group of immunoglobulin subclasses are the subclasses that are recognized by the Z domain derived from staphylococcal protein A, i.e. IgG1, IgG2, IgG4, IgA and IgM from human, all Ig subclasess from rabbit and cow, IgG1 and IgG2 from guinea pig, and IgG1, IgG2a, IgG2b, IgG3 and IgM from mouse (see Hober, S. et al., J. Chromatogr B. 848:40-47 (2007)), more preferably the immunoglobulin subclasses IgG1, IgG2, IgG4, IgA and IgM from human. Another preferred group of immunoglobulin subclasses are the subclasses that are recognized by the C2 domain streptococcal protein G; i.e. all human subclasses of IgG, including IgG3, and IgG from several animals, including mouse, rabbit and sheep.
One group of preferred B moieties are selected from the group consisting of the Z domain derived from staphylococcal protein A, staphylococcal protein A and domains thereof, preferably the E, D, A, B and C domains, streptococcal protein G and domains thereof, preferably the C1, C2 and C3 domains; and protein fragments having at least 70% identity, such as at least 80% identity, or at least 90% identity, to any of these amino acid sequences. Preferably, the B moiety is selected from the group consisting of the Z domain derived from staphylococcal protein A, the B domain of staphylococcal protein A, and the C2 domain of streptococcal protein G; and protein fragments having at least 70% identity, such as at least 80% identity, or at least 90% identity, to any of these amino acid sequences. Preferably, the B moiety is selected from the group consisting of the Z domain derived from staphylococcal protein A and protein fragments having at least 70% identity, such as at least 80% identity, or at least 90% identity, to this amino acid sequence. It is preferred that the B moiety is selected from the group consisting of the Z domain derived from staphylococcal protein A and the C2 domain of streptococcal protein G, see e.g. Examples 1-6 and 8. A preferred group of B moieties with affinity for immunoglobulins are bacterial receptin domains or derivatives thereof.
Another group of preferred B moieties are capable of selective interaction with albumin and molecules comprising albumin or derivatives thereof. A preferred group of B moieties with affinity for albumin are bacterial receptin domains or derivatives thereof. Preferred B moieties are selected from streptococcal protein G, the albumin-binding domain of streptococcal protein G, GA modules from Finegoldia magna; and protein fragments having at least 70% identity, such as at least 80% identity, or at least 90% identity, to any of these amino acid sequences. Preferably, the B moiety is selected from the albumin-binding domain of streptococcal protein G and protein fragments having at least 70% identity, such as at least 80% identity, or at least 90% identity, thereto. It is preferred that the B moiety is the albumin-binding domain of streptococcal protein G see e.g. Example 7.
A further group of preferred B moieties are capable of selective interaction with biotin and molecules comprising biotin or derivatives or analogues thereof. Preferred B moieties are selected from the group consisting of streptavidin, monomeric streptavidin (M4); and protein fragments having at least 70% identity, such as at least 80% identity, or at least 90% identity to any of these amino acid sequences. It is preferred that the B moiety is monomeric streptavidin (M4) see e.g. Examples 10-12.
Specific fusion proteins and protein structures according to the invention are provided in the Examples. These preferred fusion proteins form the group consisting of SEQ ID NOS 14, 16, 18, 22, 24 and 26. Further preferred fusion proteins are having at least 80%, preferably at least 90%, more preferably at least 95%, identity to any of these sequences.
The present invention further provides isolated polynucleic acids encoding a fusion protein according to the invention. In particular, specific polynucleic acids are provided in the Examples and the appended sequence listing, e.g. SEQ ID NOS 15, 17, 19, 23, 25 and 27. Further preferred polynucleic acids encode fusion proteins having at least 80%, preferably at least 90%, more preferably at least 95%, identity to any of SEQ ID NOS 14, 16, 18, 22, 24 and 26.
The polynucleic acids according to the invention are useful for producing the fusion proteins according to the invention. The present invention provides a method of producing a fusion protein. The first step involves expressing in a suitable host a fusion protein according to the invention. Suitable hosts are well known to a person skilled in the art and include e.g. bacteria and eukaryotic cells, such as yeast, insect cell lines and mammalian cell lines. Typically, this step involves expression of a polynucleic acid molecule which encodes the fusion protein in E. coli. 
The second method step involves obtaining a mixture containing the fusion protein. The mixture may for instance be obtained by lysing or mechanically disrupting the host cells. The mixture may also be obtained by collecting the cell culture medium, if the fusion protein is secreted by the host cell. The thus obtained protein can be isolated using standard procedures. If desired, this mixture can be subjected to centrifugation, and the appropriate fraction (precipitate or supernatant) be collected. The mixture containing the fusion protein can also be subjected to gel filtration, chromatography, e.g. anion exchange chromatography, dialysis, phase separation or filtration to cause separation. Optionally, lipopolysaccharides and other pyrogens are actively removed at this stage. If desired, linker peptides may be removed by cleavage in this step.
Proteins structures according to the invention are assembled spontaneously from the fusion proteins according to the invention under suitable conditions, and the assembly into polymers is promoted by the presence of shearing forces and/or an interface between two different phases e.g. between a solid and a liquid phase, between air and a liquid phase or at a hydrophobic/hydrophilic interface, e.g. a mineral oil-water interface. The presence of the resulting interface stimulates polymerization at the interface or in the region surrounding the interface, which region extends into the liquid medium, such that said polymerizing initiates at said interface or in said interface region. Various protein structures can be produced by adapting the conditions during the assembly. For instance, if the assembly is allowed to occur in a container that is gently wagged from side to side, a fiber is formed at the air-water interface. If the mixture is allowed to stand still, a film is formed at the air-water interface. If the mixture is evaporated, a film is formed at the bottom of the container. If oil is added on top of the aqueous mixture, a film is formed at the oil-water interface, either if allowed to stand still or if wagged. If the mixture is foamed, e.g. by bubbling of air or whipping, the foam is stable and solidifies if allowed to dry.
The present invention thus provides a method for providing a protein structure displaying a binding activity towards an organic target. In the first method step, there is provided a recombinant fusion protein according to the invention. The fusion protein may e.g. be provided by expressing it in a suitable host from a polynucleic acid according to the invention. In the second method step, the fusion protein is subjected to conditions to achieve formation of a polymer comprising the recombinant fusion protein. Notably, although the spontaneously assembled protein structures can be solubilized in hexafluoroisopropanol, the solubilized fusion proteins are then not able to spontaneously reassemble into e.g. fibers.
The protein structure is useful as part of an affinity medium for immobilization of an organic target, wherein the B moiety is capable of selective interaction with the organic target. A sample, e.g. a biological sample, may be applied to a fusion protein or a protein structure according to the invention which is capable of binding to an organic target present in the biological sample, and the fusion protein or protein structure is then useful in separation of the organic target from the sample. A biological sample, such as blood, serum or plasma which has been removed from a subject may be subjected to detection, separation and/or quantification of the organic target.
The present invention thus provides a method for separation of an organic target from a sample. A sample, e.g. a biological sample such as blood, serum or plasma, containing the organic target is provided. The biological sample may be an earlier obtained sample. If using an earlier obtained sample in a method, no steps of the method are practiced on the human or animal body.
An affinity medium according to the invention is provided, comprising a fusion protein or a protein structure according to the invention. In certain embodiments, the affinity medium is consisting of the fusion protein or protein structure according to the invention. The affinity medium is capable of selective interaction with the organic target by means of the B moiety in the fusion protein according to the invention. The affinity medium is contacted with the sample under suitable conditions to achieve binding between the affinity medium and the organic target. Non-bound sample is removed under suitable conditions to maintain selective binding between the affinity medium and the organic target. This method results in an organic target immobilized to the affinity medium, and specifically to the fusion protein, according to the invention.
In a preferred method according to the invention, the fusion protein in the affinity medium is present as a protein structure according to the invention when contacting the affinity medium with the sample to achieve binding between the affinity medium and the organic target.
A particularly useful protein structure in this respect is a film or a fiber wherein the B moiety is the Z domain derived from staphylococcal protein A or a protein fragment having at least 70% identity, such as at least 80% identity, or at least 90% identity, thereto, see e.g. Example 1-6. The film is advantageous in that it adheres to solid structures, e.g. the plastics in microtiter plates. This property of the film facilitates washing and regeneration procedures and is very useful for separation purposes.
It has surprisingly been observed that the alkali stability of the Z domain may even be enhanced when being part of a fusion protein according to the invention in a protein structure according to the invention. This property may be very useful for washing and regeneration purposes, e.g. allowing for high concentrations of NaOH, such as 0.1 M, 0.5 M, 1 M or even above 1 M, e.g. 2 M, and/or for high concentrations of urea, e.g. 6-8 M. The chemical stability may also be useful to allow for repeated cycles of use of the Z domain for affinity purification. This alkali stability may be further increased by utilizing a stabilized mutant of the Z domain. Furthermore, it has advantageously been shown that the fusion proteins according to the invention, including the Z domain, are heat stable. This allows for sterilization by heat with maintained binding ability.
A known problem with traditional affinity matrices with Z domains is leakage of the Z domain from the affinity matrix. Due to the stable incorporation of the Z domain by a peptide bond into the fusion protein of the invention, it is contemplated that the undesirable leakage of the Z domain from the protein structures according to the invention is low or absent. Another advantage of the fusion proteins according to the invention is that the resulting protein structure has a high density of Z domains (or other B moieties). It is contemplated that this high density provides a high binding capacity. Altogether, these properties of the fusions proteins are very attractive for various B moieties, and in particular for affinity purification using protein Z with good production economy. These properties are also useful in other formats than in traditional gel bead affinity columns, e.g. in filter-like formats.
The immobilized organic target is capable of selective interaction with a second organic target. The method is then further comprising the step of contacting said affinity medium and the immobilized organic target with a second organic target, which is capable of selective interaction with the first organic target, under suitable conditions to achieve binding between the first and second organic targets.
The immobilized organic target is detectable and/or quantifiable. The detection and/or quantification of the organic target may be accomplished in any way known to the skilled person for detection and/or quantification of binding reagents in assays based on various biological or non-biological interactions. The organic targets may be labeled themselves with various markers or may in turn be detected by secondary, labeled affinity ligands to allow detection, visualization and/or quantification. This can be accomplished using any one or more of a multitude of labels, which can be conjugated to the organic target or to any secondary affinity ligand, using any one or more of a multitude of techniques known to the skilled person, and not as such involving any undue experimentation. Non-limiting examples of labels that can be conjugated to organic targets and/or secondary affinity ligands include fluorescent dyes or metals (e.g., fluorescein, rhodamine, phycoerythrin, fluorescamine), chromophoric dyes (e.g., rhodopsin), chemiluminescent compounds (e.g., luminal, imidazole) and bioluminescent proteins (e.g., luciferin, luciferase), haptens (e.g., biotin). A variety of other useful fluorescers and chromophores are described in Stryer L (1968) Science 162:526-533 and Brand L and Gohlke J R (1972) Annu. Rev. Biochem. 41:843-868. Organic targets and/or secondary affinity ligands can also be labeled with enzymes (e.g., horseradish peroxidase, alkaline phosphatase, beta-lactamase), radioisotopes (e.g., 3H, 14C, 32P, 35S or 125I) and particles (e.g., gold). In the context of the present disclosure, “particles” refer to particles, such as metal particles, suitable for labeling of molecules. Further, the affinity ligands may also be labeled with fluorescent semiconductor nanocrystals (quantum dots). Quantum dots have superior quantum yield and are more photostable compared to organic fluorophores and are therefore more easily detected (Chan et al. (2002) Curr Opi Biotech. 13: 40-46). The different types of labels can be conjugated to an organic target or a secondary affinity ligand using various chemistries, e.g., the amine reaction or the thiol reaction. However, other reactive groups than amines and thiols can be used, e.g., aldehydes, carboxylic acids and glutamine.
If the detection and/or quantification involves exposure to a second organic target or secondary affinity ligand, the affinity medium is washed once again with buffers to remove unbound secondary affinity ligands. As an example, the secondary affinity ligand may be an antibody or a fragment or a derivative thereof. Thereafter, organic targets may be detected and/or quantified with conventional methods. The binding properties for a secondary affinity ligand may vary, but those skilled in the art should be able to determine operative and optimal assay conditions for each determination by routine experimentation.
The detection, localization and/or quantification of a labeled molecule may involve visualizing techniques, such as light microscopy or immunofluoresence microscopy. Other methods may involve the detection via flow cytometry or luminometry. The method of visualization of labels may include, but is not restricted to, fluorometric, luminometric and/or enzymatic techniques. Fluorescence is detected and/or quantified by exposing fluorescent labels to light of a specific wavelength and thereafter detecting and/or quantifying the emitted light in a specific wavelength region. The presence of a luminescently tagged molecule may be detected and/or quantified by luminescence developed during a chemical reaction. Detection of an enzymatic reaction is due to a color shift in the sample arising from chemical reaction. Those of skill in the art are aware that a variety of different protocols can be modified in order for proper detection and/or quantification.
One available method for detection and/or quantification of the organic target is by linking it or the secondary affinity ligand to an enzyme that can then later be detected and/or quantified in an enzyme immunoassay (such as an EIA or ELISA). Such techniques are well established, and their realization does not present any undue difficulties to the skilled person. In such methods, the biological sample is brought into contact with a protein structure according to the invention which binds to the organic target, which is then detected and/or quantified with an enzymatically labeled secondary affinity ligand. Following this, an appropriate substrate is brought to react in appropriate buffers with the enzymatic label to produce a chemical moiety, which for example is detected and/or quantified using a spectrophotometer, fluorometer, luminometer or by visual means.
The organic target or the secondary affinity ligands can be labeled with radioisotopes to enable detection and/or quantification. Non-limiting examples of appropriate radiolabels in the present disclosure are 3H, 14C, 32P, 35S or 125I. The specific activity of the labeled affinity ligand is dependent upon the half-life of the radiolabel, isotopic purity, and how the label has been incorporated into the affinity ligand. Affinity ligands are preferably labeled using well-known techniques (Wensel T G and Meares C F (1983) in: Radioimmunoimaging and Radioimmunotherapy (Burchiel S W and Rhodes B A eds.) Elsevier, New York, pp 185-196). A thus radiolabeled affinity ligand can be used to visualize the organic target by detection of radioactivity. Radionuclear scanning can be performed with e.g. a gamma camera, magnetic resonance spectroscopy, emission tomography, gamma/beta counters, scintillation counters and radiographies.
Thus, the sample may be applied to the protein structure for detection, separation and/or quantification of the organic target. This procedure enables not only detection of the organic target, but may in addition show the distribution and relative level of expression thereof. Optionally, the organic target may be released from the affinity medium and collected. Thus, the use may comprise affinity purification on an affinity medium onto which the organic target has been immobilized. The protein structure may for example be arranged in a column or in well plates (such as 96 well plates), or on magnetic beads, agarose beads or sepharose beads. Further, the use may comprise use of the protein structures on a soluble matrix, for example using a dextran matrix, or use in a surface plasmon resonance instrument, such as a BiacoreTM instrument, wherein the analysis may for example comprise monitoring the affinity for the immobilized organic target or a number of potential affinity ligands.
The protein structures according to the invention can be washed and regenerated with various cleaning agents, including acid, base and chaotropic agents. Particularly useful cleaning agents include NaOH, such as 0.1, 0.5 or 1 M NaOH, and urea, such as 6-8 M urea, Since the protein structures according to the invention are surprisingly resistant to chemical treatment and/or sterilizing heat treatment, the methods according to the invention involving use of the protein structures may comprise a final step of regenerating the protein structure. The methods preferably comprise a final step of regenerating the affinity medium by chemical treatment and/or sterilizing heat treatment. It is preferred that the chemical treatment comprises treatment with NaOH, such as 0.1, 0.5 or 1 M NaOH, and/or urea, such as 6-8 M urea,
Fusion proteins according to the invention can be also be allowed to bind to an organic target in solution, i.e. prior to allowing the fusion protein to polymerize and form a protein structure, such as a film, a foam or a fibre. Both the spidroin-derived moieties (e.g. REP-CT) as such and the corresponding fusion proteins incorporating a B moiety polymerise into solid structures even in the presence of contaminating proteins, without appreciable incorporation of contaminants into the material, and the functional (B) moieties retain their expected binding properties. It is therefore contemplated that the binding properties of the B moiety can be used to capture compounds or cells from the surrounding solution and incorporate the captured compounds or cells into or on a protein structure according to the invention.
Thus, in another preferred method according to the invention, the fusion protein in the affinity medium is present in solution when contacting the affinity medium with the sample to achieve binding between the affinity medium and the organic target. The complex of fusion protein bound to the organic target is then allowed to form a fusion protein structure according to the invention.
This method may be particularly useful when the purpose is to “fish out” specific molecules or cells from a solution, e.g. to obtain target molecules from the media in large scale eukaryotic cell production systems when the target proteins are secreted. Since the binding of target molecules and formation of solid structures by the spidroin-derived moieties can take place at physiological conditions and since the spidroin-derived moieties are cytocompatible, the method can be applied repeatedly to an ongoing production process.
The protein structure according to the invention is also useful in separation, immobilization and/or cultivation of cells. A particularly useful protein structure in this respect is a film, a fiber or a foam, see e.g. Example 14 and 23. The film is advantageous in that it adheres to solid structures, e.g. the plastics in microtiter plates. This property of the film facilitates washing and regeneration procedures and is very useful for separation purposes.
The present invention thus provides a cell scaffold material for cultivation of cells having an organic target that is present on the cell surface. The cell scaffold material is comprising a protein structure according to the invention. In certain embodiments, the cell scaffold material is consisting of the protein structure according to the invention.
It has been found by the present inventors that a cell scaffold material comprising a polymer comprising, and optionally consisting of, the fusion protein according to the invention provides a beneficial environment for the cultivation of cells, and preferably eukaryotic cells, in a variety of different settings. Furthermore, this environment enables the establishment of cultures of cells that are otherwise very difficult, very costly or even impossible to culture in a laboratory, and for the establishment of cell-containing materials useful for tissue engineering and/or transplantation.
The invention also provides a combination of cells, preferably eukaryotic cells, and the cell scaffold material according to the invention. Such a combination according to the invention may be presented in a variety of different formats, and tailored to suit the needs of a specific situation. It is contemplated, for example, that the inventive combination may be useful as a cell-containing implant for the replacement of cells in damaged or diseased tissue.
The cell scaffold material can be utilized to capture cells either directly or indirectly. In direct capture, the B moiety is capable of selective interaction with an organic target that is present on the cell surface. Alternatively, the B moiety is capable of selective interaction with and is bound to an intermediate organic target, and that intermediate organic target is capable of selective interaction with an organic target that is present on the cell surface. Thus, in indirect capture, the cell scaffold material is further comprising an intermediate organic target, and the B moiety is capable of selective interaction with and is bound to said intermediate organic target. The intermediate organic target, in turn, is capable of selective interaction with the organic target that is present on the cell surface.
In one embodiment of the cell scaffold materials as disclosed herein, the fusion protein is further comprises an oligopeptide cell-binding motif. In connection with the cultivation of certain cells in certain situations, the presence of oligopeptide cell-binding motifs has been observed to improve or maintain cell viability, and the inclusion of such a motif into the cell scaffold material as a part of the spider silk protein is thought to provide additional benefits. The cell-binding motif is an oligopeptide coupled to the rest of the fusion protein via at least one peptide bond. For example, it may be coupled to the N-terminal or the C-terminal of the rest of the fusion protein, or at any position within the amino acid sequence of the rest of the spider silk protein. With regard to the selection of oligopeptidic cell-binding motifs, the skilled person is aware of several alternatives. Said oligopeptide may for example comprise an amino acid sequence selected from the group consisting of RGD, IKVAV, YIGSR, EPDIM and NKDIL. RGD, IKVAV and YIGSR are general cell-binding motifs, whereas EPDIM and NKDIL are known as keratinocyte-specific motifs that may be particularly useful in the context of cultivation of keratinocytes. Other useful cell-binding motifs include GRKRK from tropoelastin, KYGAASIKVAVSADR (laminin derived), NGEPRGDTYRAY (from bone sialoprotein), PQVTRGDVFTMP (from vitronectin), and AVTGRGDSPASS (from fibronectin). The coupling of an oligopeptide cell-binding motif to the rest of the spider silk protein is readily accomplished by the skilled person using standard genetic engineering or chemical coupling techniques. Thus, in some embodiments, the cell-binding motif is introduced via genetic engineering, i.e. forming part of a genetic fusion between a nucleic acid encoding a fusion protein and the cell-binding motif. As an additional beneficial characteristic of such embodiments, the cell-binding motif will be present in a 1:1 ratio to the monomers of fusion protein in the polymer making up the cell scaffold material.
The polymer in the cell scaffold material used in the methods or combination described herein may adopt a variety of physical forms, and use of a specific physical form may offer additional advantages in different specific situations. For example, in an embodiment of the methods or combination, said cell scaffold material is in a physical form selected from the group consisting of film, foam, fiber and fiber-mesh.
The present invention accordingly provides a method for immobilization of cells. A sample e.g. a biological sample such as blood, comprising cells of interest is provided. The biological sample may be an earlier obtained sample. If using an earlier obtained sample in a method, no steps of the method are practiced on the human or animal body.
The sample is applied to a cell scaffold material according to the invention under suitable conditions to allow selective interaction between the cell scaffold material and an organic target that is present on the surface of the cells of interest. The cells are allowed to immobilize to said cell scaffold material by binding between the organic target on the cell surface and said cell scaffold material. Non-bound sample is removed under suitable conditions to maintain selective binding between the cell scaffold material and the organic target. This method results in cells exhibiting the organic target being immobilized to the cell scaffold material, and specifically to the protein structure, according to the invention.
As set out above, the cell scaffold material can be utilized to capture cells either directly or indirectly. In direct capture, the B moiety is capable of selective interaction with an organic target that is present on the cell surface. Alternatively, the B moiety is capable of selective interaction with and is bound to an intermediate organic target, and that intermediate organic target is capable of selective interaction with an organic target that is present on the cell surface. Thus, in indirect capture, the cell scaffold material is further comprising an intermediate organic target, and the B moiety is capable of selective interaction with and is bound to said intermediate organic target. The intermediate organic target, in turn, is capable of selective interaction with the organic target that is present on the cell surface.
Regardless of capture method, the captured cells may be released from the fusion protein by cleavage of the fusion protein to release the moiety involved in cell capture from the cell scaffold material. As mentioned hereinabove, the fusion protein may include a cleavage site in its amino acid sequence, which allows for cleavage and removal of the relevant moiety, typically the B moiety or a cell-binding motif. Various cleavage sites are known to the person skilled in the art, e.g. cleavage sites for chemical agents, such as CNBr after Met residues and hydroxylamine between Asn-Gly residues, cleavage sites for proteases, such as thrombin or protease 3C, and self-splicing sequences, such as intein self-splicing sequences.
The present invention also provides a method for cultivation of cells. Cells of interest are immobilized to the cell scaffold material using the method disclosed hereinabove. The combination of the cell scaffold material and the immobilized cells are maintained under conditions suitable for cell culture.
In the context of the present invention, the terms “cultivation” of cells, “cell culture” etc are to be interpreted broadly, such that they encompass for example situations in which cells divide and/or proliferate, situations in which cells are maintained in a differentiated state with retention of at least one functional characteristic exhibited by the cell type when present in its natural environment, and situations in which stem cells are maintained in an undifferentiated state.
The present invention will in the following be further illustrated by the following non-limiting examples.
EXAMPLES
Example 1
Cloning, Expression and Fiber Formation of an IgG-Binding Fusion Protein
To prove the fusion protein concept, a Rep4CT protein (a REP moiety with 4 internal repeats and a CT moiety) was produced in fusion with the Z protein domain (a B moiety). The Z domain is an engineered version of the immunoglobulin G (IgG) binding domain B of staphylococcal protein A, and is a 58 amino acid long triple-helix motif that binds the fragment crystallisable (Fc) region of IgG. Our aim was to investigate whether it is possible to produce structures, such as fibers, films and membranes, from a fusion protein consisting of the Z domain fused to Rep4CT (denoted His6ZQGRep4CT, SEQ ID NO: 14) and still retain the IgG-binding ability of domain Z, as well as the structure forming properties of Rep4CT. In order to do so a fusion protein consisting of the Z domain N-terminally to Rep4CT was cloned.
Cloning
A gene encoding the His6ZQGRep4CT fusion protein (SEQ ID NOS: 14-15) was constructed as follows. Primers were designed in order to generate PCR fragments of domain Z from a vector containing such a Z sequence. Also, the primers contained a recognition site for Protease 3C cleavage (LEALFQGP, denoted QG) between Z and Rep4CT. The resulting PCR products were then treated with the restriction endonucleases NdeI and EcoRI, as was the target vector (denoted pT7His6TrxHis6QGRep4CT, harbouring a kanamycin resistance gene). Upon restriction cleavage of the target vector, the TrxHis6QG part was cleaved off. Cleaved PCR fragments and target vector were joined together with the aid of a T4 DNA Ligase, whereupon the resulting, correctly ligated vector (pT7His6ZQGRep4CT) was transformed into chemocompetent Escherichia coli (E. coli) BL21 (DE3) cells that were allowed to grow onto agar plates supplemented with kanamycin (70 μg/ml). Colonies were thereafter picked and PCR screened for correct insert and subsequently also sequenced to confirm the DNA sequence inserted of ZQG into the target vector.
Production
E. coli BL21 (DE3) cells possessing the pT7His6ZQGRep4CT vector were grown in Luria-Bertani medium (6 liter in total) supplemented with kanamycin (70 μg/ml) to an OD600 value of 1-1.5 in 30° C., followed by induction of His6ZQGRep4CT expression with 300 μM IPTG (isopropyl β-D-1-thiogalactopyranoside) and further incubation in 20° C. for approximately 2 h. Next, the cells were harvested by a 20 min centrifugation at 4 700 rpm, and the resulting cell pellets were dissolved in 20 mM Tris (pH 8.0).
Purification
Cell pellets dissolved in 20 mM Tris (pH 8.0) were supplemented with lysozyme and DNase I in order to lyse the bacterial cells, whereupon the cell lysates were recovered after 15 000 rpm of centrifugation for 30 min. Next, the recovered cell lysates were divided and loaded onto a total of four Chelating Sepharose Fast Flow Zn2+ columns, keeping the His6ZQGRep4CT protein bound to the column matrix via the His6 tag. After washing, bound proteins were eluted with 20 mM Tris/300 mM imidazole (pH 8.0). The pooled eluate fractions contained 27 mg of His6ZQGRep4CT protein according to an A280 measurement. Next, the pooled eluate liquid was divided into two equal halves (13.5 mg of His6ZQGRep4CT in each), where the first half was dialysed against 5 liters of 20 mM Tris (pH 8.0) over night, concentrated to 1.07 mg/ml and finally allowed to form fibers. FIG. 3 shows a macroscopic His6ZQGRep4CT fiber. The formation of fibers from this fusion protein (SEQ ID NO: 14) illustrates that the Z domain (B moiety) does not interfere with the fiber forming properties of Rep4CT (REP and CT moieties). The amount of His6ZQGRep4CT protein prior to cleavage with Protease 3C was 10 mg after dialysis and concentration (FIG. 4).
The second half of the eluate pool was cleaved with 1.34 mg of Protease 3C, supplemented with 1 mM dithiothreitol (DTT), separating His6Z from Rep4CT. The cleavage was performed over night under dialysis against 20 mM Tris (pH 8.0), after which the protein solution was allowed to pass a Ni-NTA Agarose column, and the flow through fraction, containing Rep4CT, was collected, concentrated to 0.79 mg/ml and allowed to form fibers. The final amount of Rep4CT after cleavage was 6 mg (FIG. 4).
FIG. 4 shows an SDS-PAGE gel from the purification of the fusion protein His6ZQGRep4CT (SEQ ID NO: 14) and its subsequent Protease 3C cleavage product Rep4CT (residues 81-339 of SEQ ID NO: 14). The gel was loaded in the following order:
(1) Spectra Multicolor Broad Range Protein Ladder, Fermentas
(2) Cell lysate
(3) Flow through from cell lysate loaded onto a Chelating Sepharose Fast Flow Zn2+ column
(4) Eluate pool of His6ZQGRep4CT from a Chelating Sepharose Fast Flow Zn2+ column
(5) His6ZQGRep4CT cleaved with Protease 3C
(6) Flow through of cleaved His6ZQGRep4CT loaded onto a Ni-NTA Agarose column
(7) Regeneration of the Ni-NTA Agarose column with 5 ml of 20 mM Tris/500 mM imidazole (pH 8.0).
The molecular weights of His6ZQGRep3CT, His6Z, Rep4CT and Protease 3C are 32 kDa, 9 kDa, 23 kDa and 30 kDa, respectively.
The fact that macroscopic fibers of His6ZQGRep4CT (SEQ ID NO: 14) could be obtained although Rep4CT has been fused to another protein, i.e. the 58 amino acid long Z domain with binding affinity for IgG, demonstrates that Rep4CT still retains its fiber forming properties despite fused to the Z domain (residues 13-70 of SEQ ID NO: 14). Moreover, the Z domain of the fusion protein seems to confer good solubility to His6ZQGRep4CT.
Example 2
Binding of Biotinylated IgG to Fusion Protein Fibers
To further prove the fusion protein concept, it was studied whether the B moiety in a fusion protein structure retains its capacity of selective interaction with an organic target. In this study, the ability of the Z domain (B moiety) in fibers of the fusion protein His6ZQGRep4CT (SEQ ID NO: 14) to bind IgG was assessed. A solution of biotinylated rabbit IgG was incubated with His6ZQGRep4CT fibers, after which the same fibers were incubated in a solution with streptavidin-functionalized beads, and the fibers were subsequently visualized in a light microscope. The choice of using IgG made in rabbit falls back on the fact that IgG from rabbit bind with strong affinity to the Z domain.
An approximately 50 mm long His6ZQGRep4CT fiber, prepared as described in Example 1, was immersed in a binding solution containing 50 μl of 1×PBS/0.5% bovine serum albumin and 10 μl of 0.5 mg/ml biotinylated IgG produced in rabbit (anti-rat IgG (H+L), mouse adsorbed, Vector Laboratories, Inc.), and incubated for 75 min in room temperature with light shaking. The supernatant was discarded, and the fiber was washed three times in 60 μl 1×PBS/0.07% Tween 20. Next, the fiber was immersed in a solution containing 40 μl of 1×PBS/0.5% bovine serum albumin and 20 μl of 10 mg/ml Dynabeads M-280 Streptavidin (Dynal AS), and again incubated for 75 min in room temperature with light shaking. The supernatant was discarded and the fiber washed three times in 60 μl 1×PBS/0.07% Tween 20.
To get an indication of nonspecific binding of Dynabeads to the fiber, another His6ZQGRep4CT fiber was immersed in only a Dynabeads solution, as described above, without the preceding incubation with biotinylated IgG. The same procedure as described above for His6ZQGRep4CT was performed with fibers of Rep4CT type, and all fibers were visualized in a USB microscope with a fixed 500× magnification.
FIG. 5 is a visualization of His6ZQGRep4CT and Rep4CT fibers after binding of biotinylated rabbit IgG, followed by streptavidin-functionalised Dynabeads. Panels (A, B) show two representative pictures of the His6ZQGRep4CT fiber, taken at different positions along the fiber, that first was incubated with biotinylated IgG (produced in rabbit), followed by incubation with Dynabeads M-280 Streptavidin (Ø 2.8 μm). Panels (C, D) show two representative pictures of another His6ZQGRep4CT fiber that was only immersed in a Dynabeads M-280 Streptavidin solution, without the preceding incubation with IgG. The corresponding pictures of Rep4CT fibers are shown in panels (E, F) and (G, H), respectively. All pictures were taken at a fixed 500× magnification with a USB microscope and the Dynabeads appears in the pictures as dark grey dots.
In FIG. 5, it seems like the Dynabeads are almost only seen in panels A and B, both these pictures showing a His6ZQGRep4CT fiber subjected to biotinylated IgG, followed by streptavidin-functionalised Dynabeads. This result implies that a considerable fraction of the Z domains in the fusion protein have retained their IgG-binding ability in His6ZQGRep4CT after fiber formation.
Example 3
Binding of Pure and Serum IgG to Fusion Protein Fibers and Films
To further explore the capacity of the B moiety in a fusion protein structure of selective interaction with an organic target, the ability of domain Z in the fusion protein His6ZQGRep4CT (SEQ ID NO: 14) to bind IgG was studied. Fibers and films of this fusion protein were used for binding of purified IgG and IgG from serum, followed by elution and subsequent analysis on SDS-PAGE, where IgG under non-reducing conditions appears as a  ̃146 kDa band. Serum is the remaining fluid phase after blood clotting, and the two main constituents of serum are albumin and IgG. In rabbit serum, for example, the concentration of IgG is 5-10 mg/ml and that of albumin even higher. Purified IgG and serum were both of rabbit source.
Films of His6ZQGRep4CT were prepared by air-drying 100 μl of protein solution (0.96 mg/ml) over night at room temperature at the bottom of individual wells of a 24-well tissue culture plate. The casted films were then stored at +4° C. for 18 days, either immersed in 20 mM Tris (pH 8.0), denoted “T films”, or without immersed in any liquid, denoted “A films”. FIG. 6 shows part of a casted His6ZQGRep4CT film made at the bottom of a well from a hydrophilic, 24-well tissue culture plate. To capture the picture, an inverted light microscope at 2× magnification was used. Fibers of the fusion protein were prepared as described in Example 1 and stored at +4° C. in 20 mM Tris (pH 8.0) until used.
Two parallel experiment setups were conducted. In the first setup, triplicates of T films, A films and fibers made of His6ZQGRep4CT were immersed in 500 μl of 50 μg/ml purified rabbit IgG (purified from pooled rabbit sera, Vector Laboratories, Inc.) for 1 h at room temperature with mild shaking. In the other setup, triplicates of the same type of His6ZQGRep4CT films and fibers were instead immersed in 500 μl of a five times dilution of heat-inactivated, centrifuged rabbit serum (National Veterinary Institute, Uppsala, Sweden), also for 1 h at room temperature with mild shaking. The supernatant was discarded from all fibers and films, followed by washing three times in 500 μl 20 mM Tris (pH 8.0). Bound IgG, from purified IgG or from serum, was eluted by 30 min of incubation in 500 μl of 0.5 M acetic acid/1 M urea/100 mM NaCl (pH 2.7). The same procedure as described above for His6ZQGRep4CT fibers and A films was also conducted for films and fibers of His6TrxHis6QGRep4CT and Rep4CT as controls. Eluted fractions were analysed with SDS-PAGE under non-reducing conditions (FIG. 7-9).
FIG. 7 shows a non-reducing SDS-PAGE gel. Eluted fractions were loaded in lanes as follows:
(1-3) His6TrxHis6QGRep4CT, A film, incubated with rabbit IgG
(4-6) His6TrxHis6QGRep4CT, A film, incubated with rabbit serum
(7-8) His6TrxHis6QGRep4CT, fiber, incubated with rabbit IgG
(9) Spectra Multicolor Broad Range Protein Ladder, Fermentas
(10-11) His6TrxHis6QGRep4CT, fiber, incubated with rabbit serum
(12-14) His6ZQGRep4CT, T film, incubated with rabbit IgG
(15-17) His6ZQGRep4CT, T film, incubated with rabbit serum.
FIG. 8 shows another non-reducing SDS-PAGE gel. Eluted fractions were loaded according to:
(1-3) His6ZQGRep4CT, A film, incubated with rabbit IgG
(4-6) His6ZQGRep4CT, A film, incubated with rabbit serum
(7-9) His6ZQGRep4CT, fiber, incubated with rabbit IgG
(10) Spectra Multicolor Broad Range Protein Ladder, Fermentas
(11-13) His6ZQGRep4CT, fiber, incubated with rabbit serum
(14-16) Rep4CT, A film, incubated with rabbit IgG.
FIG. 9 shows a further non-reducing SDS-PAGE gel. Eluted fractions were loaded according to:
(1-3) Rep4CT, A film, incubated with rabbit serum
(4-6) Rep4CT, fiber, incubated with rabbit IgG
(7) Spectra Multicolor Broad Range Protein Ladder, Fermentas
(8-10) Rep4CT, fiber, incubated with rabbit serum
(11) Purified rabbit IgG (50 μg/ml), used in incubation
(12) Rabbit serum (1:50 dilution), used in incubation.
The results in FIG. 7-9 show that all types of His6ZQGRep4CT matrices, i.e. films (both A and T type) and fibers have the ability to bind IgG (either purified or from serum) via the Z domain. Moreover, the His6ZQGRep4CT matrices exposed to rabbit serum do not seem to bind anything else of the serum fraction but IgG. Matrices of the other two protein variants used (i.e. His6TrxHis6QGRep4CT and Rep4CT) do not seem to bind anything at all, except from fibers of Rep4CT exposed to serum, and that show weak bands within the IgG ( ̃146 kDa) and albumin ( ̃70 kDa) region. This approach to evaluate the IgG-binding ability of the Z domain within the fusion protein His6ZQGRep4CT (SEQ ID NO: 14) is a strong indication that the Z domain is active in both fiber and film versions of the fusion protein. No other fraction of rabbit serum than IgG is observed to bind to His6ZQGRep4CT.
Example 4
Binding Reproducibility of Pure and Serum IgG to Fusion Protein Fibers and Films
To explore the reproducibility of the IgG binding to films and fibers of the fusion protein His6ZQGRep4CT (SEQ ID NO: 14), the experiments in Example 3 were performed again. The same fibers and films of His6ZQGRep4CT, His6TrxHis6QGRep4CT and Rep4CT that were used in Example 3 were used again. All fiber and film materials had been immersed for 70 days in 20 mM Tris (pH 8.0) at +4° C. after the previous experiments had been performed. The experiments were carried out as described in Example 3. Eluted fractions were analysed with SDS-PAGE under non-reducing conditions (FIGS. 10-12).
FIG. 10 shows a non-reducing SDS-PAGE gel. Eluted fractions were loaded according to:
(1-3) His6TrxHis6QGRep4CT, A film, incubated with rabbit IgG
(4-6) His6TrxHis6QGRep4CT, A film, incubated with rabbit serum
(7-8) His6TrxHis6QGRep4CT, fiber, incubated with rabbit IgG
(9) Spectra Multicolor Broad Range Protein Ladder, Fermentas
(10-11) His6TrxHis6QGRep4CT, fiber, incubated with rabbit serum
(12-14) His6ZQGRep4CT, T film, incubated with rabbit IgG
(15-17) His6ZQGRep4CT, T film, incubated with rabbit serum.
FIG. 11 shows another non-reducing SDS-PAGE gel. Eluted fractions were loaded according to:
(1-3) His6ZQGRep4CT, A film, incubated with rabbit IgG
(4-6) His6ZQGRep4CT, A film, incubated with rabbit serum
(7-9) His6ZQGRep4CT, fiber, incubated with rabbit IgG
(10) Spectra Multicolor Broad Range Protein Ladder, Fermentas
(11-13) His6ZQGRep4CT, fiber, incubated with rabbit serum
(14-16) Rep4CT, A film, incubated with rabbit IgG.
FIG. 12 shows a non-reducing SDS-PAGE gel. Eluted fractions were loaded according to:
(1-3) Rep4CT, type A film, incubated with rabbit serum
(4-6) Rep4CT, fiber, incubated with rabbit IgG
(7) Spectra Multicolor Broad Range Protein Ladder, Fermentas
(8-10) Rep4CT, fiber, incubated with rabbit serum
(11) Empty well
(12) Purified rabbit IgG (50 μg/ml), used in incubation
(13) Rabbit serum (1:50 dilution), used in incubation.
The IgG binding patterns for all three protein matrices (i.e. His6ZQGRep4CT, His6TrxHis6QGRep4CT and Rep4CT) corresponds to what was observed in Example 3, although rather weak bands corresponding to albumin ( ̃70 kDa) is seen for His6ZQGRep4CT fibers incubated with rabbit serum. This initial IgG-binding reproducibility study, show that both fibers and films of His6ZQGRep4CT can be used at least twice for binding and elution of purified and serum IgG. A further study of reproducibility is reported in Example 19.
Example 5
IgG Binding to Fusion Protein Matrices and to a Commercial Protein a Matrix
The IgG-binding capacity of His6ZQGRep4CT fusion protein structures was evaluated by comparison with a commercially available protein A matrix (Protein A Sepharose CL-4B, GE Healthcare). Fibers and films of His6ZQGRep4CT (SEQ ID NO: 14) were prepared inside spin columns. The protein A matrix was also added to spin columns in such a way that the total number of protein A molecules attached to the matrix was equal to the total number of Z molecules within His6ZQGRep4CT films. Binding of purified IgG and IgG from serum to films and fibers of His6ZQGRep4CT, as well as to the protein A matrix was allowed to occur, followed by elution and subsequent analysis on SDS-PAGE.
Films of His6ZQGRep4CT were prepared by air-drying 100 μl of protein solution (1.05 mg/ml) for three days at room temperature at the bottom of the polyethylene frit inside spin columns (SigmaPrepTM Spin Columns, Sigma), giving a total of 3×10−9 mole of His6ZQGRep4CT per film. Also, fibers of His6ZQGRep4CT were placed onto frits inside the same type of spin columns.
The same procedure was carried out for films and fibers of Rep4CT, where the films contained a total of 4×10−9 mole of Rep4CT per film. For the commercial protein A matrix, a drained matrix volume corresponding to 3×10−9 mole of protein A was transferred to the frit per spin column, whereupon the matrix was washed with 1×500 μl plus 2×150 μl of deionized water by centrifugation of the spin columns at 400 rcf for 1.5 min.
Two parallel experiment setups were conducted for fibers and films of His6ZQGRep4CT and Rep4CT, as well as with the protein A matrix. In the first setup, duplicates of all three different matrices were immersed in 500 μl of 50 μg/ml purified rabbit IgG (IgG purified from rabbit serum, Sigma) for 1 h at room temperature. In the other setup, duplicates of the same three types of matrices were instead immersed in 500 μl of a five times dilution of centrifuged rabbit serum (Normal rabbit serum, Invitrogen), also for 1 h at room temperature.
The supernatant was discarded from all fibers and films by simple pipetting and for the protein A matrix by centrifugation (400 rcf, 1.5 min), followed by washing three times in 500 μl 20 mM Tris (pH 8.0). Bound IgG, from purified IgG or from serum, was eluted by 30 min of incubation in 500 μl of 0.5 M acetic acid/1 M urea/100 mM NaCl (pH 2.7). Eluted fractions were analysed on SDS-PAGE under non-reducing conditions (FIGS. 13-15), and are denoted as coming from run 1. Immediately after the elution, all matrices were washed with 3×500 μl 20 mM Tris (pH 8.0), after which the just described experiment was repeated once more to evaluate the reproducibility of IgG binding. Eluted fractions from the repeated experiment are denoted as coming from run 2. Note: Under non-reducing SDS-PAGE conditions, the molecular weight of IgG is around 146 kDa.
FIG. 13 shows a non-reducing SDS-PAGE gel of eluted fractions from run 1, loaded according to:
(1) Purified rabbit IgG (50 μg/ml), used in incubation
(2) Rabbit serum (1:50 dilution), used in incubation
(3-4) His6ZQGRep4CT, film, incubated with rabbit IgG
(5-6) His6ZQGRep4CT, film, incubated with rabbit serum
(7-8) Rep4CT, film, incubated with rabbit IgG
(9) Spectra Multicolor Broad Range Protein Ladder, Fermentas
(10-11) Rep4CT, film, incubated with rabbit serum
(12-13) Protein A Sepharose CL-4B matrix, incubated with rabbit IgG
(14-15) Protein A Sepharose CL-4B matrix, incubated with rabbit serum
(16-17) His6ZQGRep4CT, fiber, incubated with rabbit IgG.
FIG. 14. shows a non-reducing SDS-PAGE gel of eluted fractions coming from both run 1 and run 2, loaded according to:
(1-2) His6ZQGRep4CT, fiber, incubated with rabbit serum, run 1
(3-4) Duplicates of Rep4CT, fiber, incubated with rabbit IgG, run 1
(5-6) Duplicates of Rep4CT, fiber, incubated with rabbit serum, run 1
(7) Spectra Multicolor Broad Range Protein Ladder, Fermentas
(8) Purified rabbit IgG (50 μg/ml), used in incubation
(9) Rabbit serum (1:50 dilution), used in incubation
(10-11) His6ZQGRep4CT, film, incubated with rabbit IgG, run 2
(12-13) His6ZQGRep4CT, film, incubated with rabbit serum, run 2
(14-15) Rep4CT, film, incubated with rabbit IgG, run 2
(16-17) Rep4CT, film, incubated with rabbit serum, run 2.
FIG. 15 shows a non-reducing SDS-PAGE gel of eluted fractions, all coming from run 2 and loaded according to:
(1-2) Protein A Sepharose CL-4B matrix, incubated with rabbit IgG
(3-4) Protein A Sepharose CL-4B matrix, incubated with rabbit serum
(5-6) His6ZQGRep4CT, fiber, incubated with rabbit IgG
(7) Spectra Multicolor Broad Range Protein Ladder, Fermentas
(8-9) His6ZQGRep4CT, fiber, incubated with rabbit serum
(10-11) Rep4CT, fiber, incubated with rabbit IgG
(12-13) Rep4CT, fiber, incubated with rabbit serum.
The results in FIG. 13-15 show that the matrices selectively bind IgG from serum. The IgG-binding capacity of all types of His6ZQGRep4CT matrices, i.e. films and fibers, is in the same range as the commercial protein A matrix. Similarly to the commercial protein A matrix, the fusion protein structures can be regenerated with maintained binding capacity.
Example 6
Cleaning-in-Place (CIP) of Fusion Protein Matrices and a Commercial Protein a Matrix
To evaluate whether precipitated or denatured substances remain attached to protein structures made of His6ZQGRep4CT (SEQ ID NO: 14) and Rep4CT and to a commercial protein A matrix (Protein A Sepharose CL-4B, GE Healthcare) after elution, a cleaning-in-place (CIP) with 8 M urea was carried out for all the matrices exposed to rabbit serum used in the experiments in Examples 4-5.
Fibers and films made of His6ZQGRep4CT and Rep4CT from Example 4 and Example 5, and a commercial Protein A matrix from Example 5, all previously exposed to rabbit serum, were immersed in 200 μl of 8 M urea at room temperature for 20 min, prior to supernatant removal, and subsequent analysis of urea fractions on SDS-PAGE under non-reducing conditions (FIG. 16-17).
FIG. 16 shows a non-reducing SDS-PAGE gel from cleaning-in-place with 8 M urea of matrices subjected twice to rabbit serum. The gel was loaded according to:
(1) Rabbit serum (1:50 dilution)
(2) Empty well
(3-5) His6ZQGRep4CT, T film, from Example 4
(6-8) His6ZQGRep4CT, A film, from Example 4
(9) Spectra Multicolor Broad Range Protein Ladder, Fermentas
(10-12) His6ZQGRep4CT, fiber, from Example 4
(13-15) Rep4CT, A film, from Example 4
(16) Rep4CT, fiber, from Example 4
(17) Empty well.
FIG. 17 shows a second non-reducing SDS-PAGE gel from cleaning-in-place with 8 M urea of matrices subjected twice to rabbit serum. The gel was loaded according to:
(1) Rabbit serum (1:50 dilution)
(2) Empty well
(3-4) Rep4CT, fiber, from Example 4
(5-6) His6ZQGRep4CT, film, from Example 5
(7) Rep4CT, film, from Example 5
(8) Spectra Multicolor Broad Range Protein Ladder, Fermentas
(9) Rep4CT, film, from Example 5
(10-11) His6ZQGRep4CT, fiber, from Example 5
(12-13) Rep4CT, fiber, from Example 5
(14-15) Protein A Sepharose CL-4B matrix, from Example 5
(16-17) Empty wells.
The results in FIG. 16-17 indicate that only low amounts of precipitated or denatured substances remain attached to the fusion protein structures after elution and cleaning. In particular, only low amounts of precipitated or denatured substances, in the same range as for the commercial protein A matrix, remain attached to films of the His6ZQGRep4CT fusion protein.
Example 7
Cloning, Expression and Fiber Formation of an Albumin-Binding Fusion Protein
To further prove the fusion protein concept, Rep4CT was produced in fusion with the albumin binding domain (Abd) from streptococcal protein G. Abd is a 5-kDa triple-helix motif that binds albumin. In order to do so a fusion protein consisting of the Abd domain N-terminally to Rep4CT (denoted His6AbdQGRep4CT) was cloned (SEQ ID NOS: 16-17).
Cloning
Primers were designed in order to generate PCR fragments of Abd from a vector containing such a sequence. Also, the primers contained a Protease 3C cleavage site, denoted QG, between Abd and Rep4CT. The resulting PCR products were then treated with the restriction endonucleases NdeI and EcoRI, as was the target vector, denoted pT7His6TrxHis6QGRep4CT (harbouring a kanamycin resistance gene). Upon restriction cleavage of the target vector, the TrxHis6QG part was cleaved off. Cleaved PCR fragments and target vector were joined together with the aid of a T4 DNA Ligase, whereupon the resulting, correctly ligated vector (pT7His6AbdQGRep4CT) was transformed into chemocompetent E. coli BL21 (DE3) cells that were allowed to grow onto agar plates supplemented with kanamycin. Colonies were thereafter picked and PCR screened for correct insert and subsequently also sequenced.
Production
E. coli BL21 (DE3) cells possessing the pT7His6AbdQGRep4CT vector were grown in Luria-Bertani medium (6 liters in total) supplemented with kanamycin to an OD600 of 1-1.5 in 30° C., followed by induction of His6AbdQGRep4CT expression with IPTG and further incubation in 20° C. for approximately 2 h. Next, the cells were harvested by centrifugation, and the resulting cell pellet was dissolved in 20 mM Tris (pH 8.0).
Purification
Cell pellets dissolved in 20 mM Tris (pH 8.0) were supplemented with lysozyme and DNase I in order to completely lyse the bacterial cells, whereupon the supernatants were recovered after 15 000 rpm of centrifugation. Next, the recovered supernatants were loaded onto a Ni IMAC column or a Chelating Sepharose Fast Flow ZN column, keeping the His6AbdQGRep4CT protein bound to the matrix via the His6 tag. After washing, bound proteins were eluted with 20 mM Tris/300 mM imidazole (pH 8.0). The pooled eluate fractions, containing His6AbdQGRep4CT (SEQ ID NO: 16) was dialyzed against 5 liters of 20 mM Tris (pH 8.0), concentrated, and a final amount of 4 mg protein was obtained.
Fiber and Film Formation
From the purified, soluble Abd-Rep4CT protein, both fibers and films were successfully made at a protein concentration of 0.87 mg/ml
The fact that macroscopic fibers and films of Abd-Rep4CT were obtained although Rep4CT had been fused to another protein, namely the albumin binding domain (Abd), demonstrates that Rep4CT retains its fiber forming properties despite fused to the Abd domain. Next, the aim was to reveal whether the Abd domain had retained its albumin-binding ability when fused to Rep4CT, see Examples 24 and 25.
Example 8
Cloning, Expression and Fiber Formation of an IgG-Binding Fusion Protein
To further prove the fusion protein concept, Rep4CT was produced in fusion with the IgG binding domain C2 from streptococcal protein G. C2 contains 55 amino acids, and the structure is constituted of two β-hairpins that are associated to form a four stranded mixed antiparallel/parallel β-sheet with a single α-helix lying across one face of the sheet. In order to do so a fusion protein consisting of the C2 domain N-terminally to Rep4CT (denoted His6C2QGRep4CT) was cloned (SEQ ID NOS: 18-19).
Cloning
Primers were designed in order to generate PCR fragments of C2 from a vector containing such a sequence. Also, the primers contained a Protease 3C cleavage site, denoted QG, between C2 and Rep4CT. The resulting PCR products were then treated with the restriction endonucleases NdeI and EcoRI, as was the target vector, denoted pT7His6TrxHis6QGRep4CT (harbouring a kanamycin resistance gene). Upon restriction cleavage of the target vector, the TrxHis6QG part was cleaved off. Cleaved PCR fragments and target vector were joined together with the aid of a T4 DNA Ligase, whereupon the resulting, correctly ligated vector (pT7His6C2QGRep4CT) was transformed into chemocompetent E. coli BL21 (DE3) cells that were allowed to grow onto agar plates supplemented with kanamycin. Colonies were thereafter picked and PCR screened for correct insert and subsequently also sequenced.
Production
E. coli BL21 (DE3) cells possessing the pT7His6C2QGRep4CT vector were grown in Luria-Bertani medium (6 liters in total) supplemented with kanamycin to an OD600 of 1-1.5 in 30° C., followed by induction of His6C2QGRep4CT expression with IPTG and further incubation in 20° C. for approximately 2 h. Next, the cells were harvested by centrifugation and the resulting cell pellet dissolved in 20 mM Tris (pH 8.0).
Purification
Cell pellets dissolved in 20 mM Tris (pH 8.0) were supplemented with lysozyme and DNase I in order to completely lyse the bacterial cells, whereupon the supernatants were recovered after 15 000 rpm of centrifugation. Next, the recovered supernatants were loaded onto a Ni IMAC column, keeping the His6C2QGRep4CT protein bound to the matrix via the His6 tag. After washing, bound proteins were eluted with 20 mM Tris/300 mM imidazole (pH 8.0). The pooled eluate fractions, containing His6C2QGRep4CT was dialyzed against 5 liters of 20 mM Tris (pH 8.0), concentrated, and a final amount of 6 mg protein was obtained.
Fiber and Film Formation
From the purified, soluble C2-Rep4CT protein, both fibers and films were successfully made at a protein concentration of 0.87 mg/ml. The fact that macroscopic fibers and films of C2-Rep4CT was obtained although Rep4CT had been fused to another protein, namely the IgG binding domain C2, demonstrates that Rep4CT retains its fiber forming properties despite being fused to the C2 domain. Next, the aim was to reveal whether the C2 domain had retained its IgG-binding ability when fused to Rep4CT, see Examples 26 and 27.
Example 9
Cloning, Expression and Formation of Films and Fibers of a Biotin-Binding Fusion Protein
Streptavidin is a tetramer of four identical monomers with one binding site per monomer. It shows high affinity towards biotin (vitamin H), reaching a dissociation constant of Kd ̃10−15 M, making this an essentially irreversible binding event. Streptavidin also shows a high stability in presence of proteases, at elevated temperatures and in denaturing agents, and at extreme pH values (Wilchek, M. et al., Anal. Biochem. 171: 1-32 (1988)). Thus, this interaction is attractive in many applications including protein labeling, separation and targeting. In practice, biotinylation is nowadays easily facilitated utilizing biotinylated linker molecules that also houses one out of several reactive organic molecules that attacks and bridge the biotin to different biological molecules, e.g. proteins and DNA. However the production of high density functional surfaces coated with Streptavidin has proven difficult to achieve, see e.g. Table 4. To reduce the binding strengths in applications where reversibility in binding is essential (e.g. during purification) and to be able to successfully express soluble protein in E. coli, a monomeric variant of streptavidin has been developed, M4 (Wu. S.-C. et al., Protein Expres. Purif. 46, 268-273 (2006)). Compared to the monomers of the wild type tetramer streptavidin, M4 has four amino acid substitutions (V55T, T76R, L109T and V125R), which keep M4 in an active monomeric form.
M4 was N- or C-terminally fused to Rep4CT (SEQ ID NOS: 20-21) by recombinant techniques. The resulting proteins and genes encoding them were named M4Rep4CT (SEQ ID NOS: 22-23), modM4Rep4CT (SEQ ID NOS: 24-25) and Rep4CTM4 (SEQ ID NOS: 26-27), respectively. The difference between M4Rep4CT and modM4Rep4CT is the substitution of a Gly to Arg-Ala-Arg in the linker region between M4 and Rep4CT. All proteins were expressed fused to a His6-Trx-His6 tag that was cleaved off and removed during purification.
Production and purification of all proteins were performed essentially as described in Stark, M. et al., Biomacromolecules 8, 1695-1701 (2007) and Hedhammar M. et al., Biochemistry 47, 3407-3417 (2008). The protein concentration of Rep4CTM4, M4Rep4CT and modM4Rep4CT was measured at 280 nm using a molar extinction coefficient of 53860 M−1 cm−1. The purified protein sample was subjected to reducing SDS-PAGE, and protein purity was determined after staining of the gel with Coomassie Brilliant Blue R-250. The theoretical molecular weights of all the purified proteins and other relevant physical properties are listed in Table 3.







TABLE 3







Physical parameters of the expressed proteins













Amino
Molecular
Molar extinction



SEQ 
acids
weight*
coefficient*


Protein
ID NO
(#)
(g/mol)
(M−1 cm−1)





Rep4CT
20
263
23053
11920


Rep4CTM4
26
428
40157
53860


M4Rep4CT
22
427
40100
53860


modM4Rep4CT
24
429
40427
53860





*Theoretical values






From each of the Rep4CTM4, M4Rep4CT and modM4Rep4CT fusion proteins, both film and fibers were formed. These results confirm that Rep4CT retains its ability to self assemble into solid structures although fused to M4. This also confirms that it is possible to obtain fibers and films of proteins where M4 is fused to Rep4CT using linkers of different lengths.
Example 10
Binding of a Biotin-Containing Target to Fusion Protein Fibers and Films
(A) Binding of Biotinylated Atto-565 to Rep4CTM4 Films.
Rep4CTM4 (SEQ ID NO: 26) and Rep4CT (SEQ ID NO. 20, control) were allowed to form films by drying 25 μl of protein solution in room temperature in the bottom of wells in clear or black 96 well microtiter plates. The plates were stored at room temperature for one to two weeks before use. The wells were incubated with 100 μl 1% BSA in PBS (pH 7.4) for >1 hour at room temperature in order to avoid non-specific binding. Background values were obtained by measuring fluorescence intensity in the wells with films of the respective protein, Rep4CT or Rep4CTM4, in 50 μl phosphate buffered saline (PBS) prior to addition of biotinylated Atto-565. The wells were further incubated with 50 μl of an 80 μM solution of biotinylated Atto-565 (Sigma Aldrich, Germany) dissolved in 1% BSA in PBS (pH 7.4). The mixture was allowed to stand in room temperature between two to three hours before washing twice with PBS containing 0.05% Tween-20 (PBS-T) and once with PBS. The resulting fluorescence intensity was recorded after adding 50 μl of PBS into the wells in a Tecan Infinite M200 microplate reader (λex=565 nm, λem=590 nm).
A dilution series was prepared in PBS, and 50 μl of samples of different concentrations of biotinylated Atto-565 was added to wells with the respective films, in triplicates, whereafter the resulting fluorescence intensity from the wells was recorded.
In FIG. 18, the fluorescence intensities from protein films after soaking with biotinylated Atto-565 and washing are observed in 2× magnification using a Nicon Eclipse Ti—S fluorescence microscope (λex=509-550 nm and λem=570-614 nm). The difference in fluorescence intensity between Rep4CTM4 films (panel A) and Rep4CT films (panel B) after addition of biotinylated Atto-565 is evident.
In order to establish the total amount of biotinylated Atto-565 binding to the Rep4CTM4 films, fluorescence intensity was recorded using a dilution series of known amounts of biotinylated Atto-565. In this way, the fluorescence intensities from samples with known amounts (in moles) biotinylated Atto-565 (in triplicates, in wells with Rep4CTM4) were used to obtain a standard curve. The resulting fluorescence intensity values corresponding to background value (Rep4CTM4 films without biotinylated Atto-565) and data points correlating to three concentrations of biotinylated Atto-565 added to the wells are shown in the graph in FIG. 19. The table below the graph in FIG. 19 show the values obtained from a linear regression to the fluorescence intensity values, with standard deviations from measurement in n=3 wells with the same biotinylated Atto-565 concentration.
Starting from the fluorescence intensity values resulting from binding experiments of biotinylated Atto-565 to films of Rep4CTM4 (FIG. 20), these values were used to calculate the amount of moles of biotinylated Atto-565 that correspond to the obtained fluorescence intensity. The resulting fluorescence values are plotted in FIG. 20, with panels A and B displaying values before (−) and after (+) addition of biotinylated Atto-565 to wells with films of Rep4CT (A) and Rep4CTM4 (B). Panel C shows a comparison of the resulting fluorescence intensities after addition of biotinylated Atto-565 to films of Rep4CT or Rep4CTM4. There was no significant (ns) difference between before and after values for the Rep4CT films (panel A). Significant differences between before and after addition of biotinylated Atto-565 values with Rep4CTM4 (panel B; P<0.01), and between proteins (panel C; P<0.0001), were confirmed by statistical tests. The bars in FIG. 20 indicate standard deviation between fluorescence intensity values of n=10 films.
The biotinylated fluorophore/surface area ratio obtained from the binding experiments was calculated. To surface areas of approximately 28 mm2, 2.1 μmol biotinylated Atto-565 was bound to the Rep4CTM4 films. This results in a bound biotin/surface area of 0.073 μmol/mm2 (Table 5).
(B) Binding of Biotinylated Horse Radish Peroxidase (HRP) to Rep4CTM4 Films
Due to its relatively high stability and the production of chromogenic products in the conversion of a non-chromogenic substrate and peroxide, HRP is commonly used coupled to a secondary antibody or a binder molecule (e.g. biotin) in applications such as ELISAs, Western blots and immunohisto-chemistry. In order to establish the total amount of biotinylated HRP binding to films made of Rep4CTM4 (SEQ ID NO: 26) and Rep4CT (SEQ ID NO: 20; control), biotinylated HRP was allowed to bind to each respective film. The rate of product formation was recorded at 570 nm using known amounts of substrates. The molar extinction coefficient for the product, resorufin, was obtained from the manufacturer (Invitrogen), stated to be 54000 cm−1M−1.
Protein solutions (25 μl) of Rep4CTM4 and Rep4CT were allowed to completely dry in the bottom of wells in clear 96 well microtiter plates, thus forming films. The wells were incubated with 100 μl of 1% BSA in PBS (pH 7.4) for >1 hour before incubation with 50 μl of a 0.3 mg/ml biotinylated HRP (Invitrogen, Camarillo, Calif.) in 1% BSA in PBS (pH 7.4) for >1 hour. The wells were subsequently washed twice with PBS-T and once with PBS. Reactions were initiated by addition of 50 μl of a 50 μM Amplex red solution (Invitrogen) with 2 mM hydrogen peroxide dissolved in 0.2% BSA, 28 mM NaCl, 0.54 mM KCl, 0.3 mM KH2PO4, 42 mM Na2HPO4 (pH 7.4) at room temperature. Kinetic measurements were conducted on a Tecan Infinite M200 microplate reader.
Known amounts of biotinylated HRP (free in solution) were used to establish which amount of HRP that resulted in the same rate of product formation as in measurements with biotinylated HRP on the films. The resulting reaction velocities in catalysis by biotinylated HRP free in solution (pH 7.4) of 50 μM Amplex red and 2 mM hydrogen peroxide to the product, resorufin, are shown in the graph in FIG. 21. Data points correlates to triplicate measurements with the same concentration of biotinylated HRP. The table below the graph in FIG. 21 shows the value obtained from a linear regression to the data. The bars in the graph in FIG. 21 indicate standard deviations from measurements in n=3 wells with the same concentration of biotinylated HRP. The resulting standard curve and slope in FIG. 21 was used for calculation of the amount of biotinylated HRP that was bound to the fusion protein films.
The reaction velocities in catalysis of 50 μM Amplex red and 2 mM H2O2 in wells where films of the fusion protein and control were incubated with biotinylated HRP is shown in FIG. 22. The reaction velocities in FIGS. 21 and 22 are expressed as the formation of resorufin in μM per minute, calculated using the extinction coefficient provided by Invitrogen (54 000 cm−1M−1). Bars indicate standard deviation for reactions measured in n=8 wells. FIG. 22 shows a significant difference in rate of product formation (and hence also bound biotinylated HRP) between wells coated with Rep4CTM4 and the controls, Rep4CT-coated wells. It was determined that 0.2 μmol HRP/mm2 was bound to the Rep4CTM4 films, (Table 5).
(C) Comparison with Commercial Products
The production of high density functional surfaces coated with Streptavidin has proven difficult to achieve. The biotin binding capacities of commercially available plates are listed in Table 4.







TABLE 4







Biotin binding capacities of commercially available plates














Coat
Biotin/coat




Biotina
areab
area


Company
Plate
(pmol)
(mm2)
(pmol/mm2)





Nunc/Thermo
Passively
13
150
0.087


scientific
Coated






plates





Pierce/Thermo
HBCc
0.78d-125
 90
0.008-1.4


scientific






Pierce/Thermo
Standard 
 5
 90
0.055


scientific
Capacity





Grenier 
c-bottom
20
210
0.096


bio-one






R&D systems
EvenCoat
  7e
150
0.047


Sigma screen/
S6940 
300 
150
2.0 


Sigma Aldrich
(HBCc)





aBiotin-binding capacity as stated by manufacturer


bCalculated based on coat volume as stated by manufacturer


cHBC = high binding capacity.


dThe limits were calculated based on stated detection range of a 8 kDa biotinylated molecule.


eCalculation based on stated binding of biotinylted antibodies using a MW = 120 kDa.






The biotinylated fluorophore/surface area ratio obtained from the binding experiments with biotinylated Atto-565 in Example 10 A and biotinylated HRP in Example 10 B are summarized in Table 5. The densities of the two different biotinylated molecules on films of Rep4CTM4 (SEQ ID NO: 26) are 0.073-0.2 μmol/mm2.







TABLE 5







Biotin binding capacities of films of M4 fusion protein














Bio-
Sur-
Biotinylated
Bio-


Biotin-

tinylated
face
molecule/
tinylated


ylated
Rep4CTM4
molecule
area
surface area
Rep4CTM4


product
(nmol)
(pmol)
(mm2)
(pmol/mm2)
(%)





Atto-
0.082
2.1
28
0.073
2.6


565







HRP
0.082
5.1
28
0.2 
6.2









The results in Tables 4-5 indicate that films made of fusion proteins with a M4 moiety provide a biotin binding density in the same ranges as for commercial alternatives, regardless of whether the biotin is coupled to a small (fluorophore) or large (protein) molecule.
Statistics
GraphPad Prism 4.0 (GraphPad Software, San Diego, Calif.) was used for statistical analysis of data. In Example 10 A, a non-parametric paired Wilcoxon test was used in the comparison between fluorescence values before and after addition of biotinylated Atto-565 to films formed from either Rep4CT or Rep4CTM4. Further, a non-parametric, unpaired Mann Whitney U test was used to compare fluorescence intensity in wells after incubation of biotinylated Atto-565 using Rep4CT or Rep4CTM4 film, and also to compare the [resorufin]/min values obtained from measurements on films incubated with biotinylated HRP in Example 10 B. P-values<0.05 were considered significant.
Example 11
Binding of a Biotionylated Antibody and a Secondary Antibody to Fusion Protein Fibers and Films
Film and fibers of Rep4CT (SEQ ID NO: 20, control) and modM4Rep4CT (SEQ ID NO: 24) are tested for binding capacity to a biotinylated antibody of rabbit origin. The films are formed in 8×1 or 12×1 well strips (wells in equal size to the 96 well microplate formats).
After preincubation of the films and fibers with 1% BSA in PBS (pH 7.4), the biotinylated antibody (rabbit) is incubated with the protein structures (film/fiber) for >1 h, followed by addition of a secondary anti-rabbit antibody, radioactively labeled with 125I. The films and fibers are washed. Detection of the gamma radiation is carried out on individual films or individual fibers in a gamma counter. A dilution series of known amounts of 125I-labeled antibody is prepared, and radiation is measured to obtain a standard curve from which the amount of bound biotinylated antibody to the fusion protein films and fibers can be calculated.
Example 12
Preparation of a Pure Film of Fusion Protein
Films were casted using 25 μl of RepCT4M4 (SEQ ID NO: 26) at a concentration of 10-20 μM. 100 μl of PBS (pH 7.4) was allowed to incubate in wells with film for one hour. This solution was removed, and 50 μl hexafluoroisopropanol (HFIP) was added to break the film and solubilize the protein. To additional films, the same amount of HFIP was added without prior washing with PBS. The HFIP was allowed to work on the four films for 3.5 h, and the resulting clear HFIP solution was transferred into Eppendorf tubes containing 50 μl of 20% SDS. The water in the tubes was evaporated, and the remaining content was dissolved in 60 μl 10 mM Tris-HCl (pH 8.0) and subjected to reducing SDS-PAGE.
The results are shown in FIG. 23. Lane 1 corresponds to the proteins in the SpectraTM Multicolor Broad Range Protein Ladder (Fermentas). Numbers correspond to protein sizes. Lane 2 corresponds to purified Rep4CTM4 films that were not soaked with PBS before adding the HFIP. Lane 3 corresponds to a Rep4CTM4 film which has been soaked in PBS for one hour before removing this solution and thereafter adding HFIP.
Although some proteins are co-purified with the Rep4CTM4 protein (lane 2, FIG. 23), incubation with 100 μl PBS for one hour dissolves contaminating proteins leaving a film consisting only of Rep4CTM4 proteins, as judged by reducing SDS-PAGE (lane 3, FIG. 23). Thus, most contaminating proteins are removed by the polymerization process as such, and any remaining impurities in proteins structures made of fusion proteins can easily be removed by gentle washing with aqueous buffers.
Example 13
Capture of Organic Targets in Solution
A ZRep4CT protein solution ( ̃1 mg/ml) is added to a sample consisting of serum, whereby the IgG molecules in the sample are allowed to bind to the Z moiety of the fusion protein in solution. The mixture is subjected to a hydrophobic/hydrophilic interface which causes the Rep4CT part of the fusion protein/Ig G complex to form a film or a foam, leaving other serum proteins in solution and capturing the IgG on a solid structure.
Alternatively, the mixture is allowed to dry on a solid support, forming a film with immobilized IgG. This film is washed with a buffer, e.g. PBS, to dissolve and remove contaminating proteins.
Alternatively, fibers are formed by providing a hydrophobic-hydrophilic interface and subjecting the mixture to shear forces. The Rep4CT part of the fusion protein/IgG complex polymerises into macroscopic fibers, leaving other proteins in the solution.
The solid structures formed (films, foams or fibers) may be collected, and the IgG can be recovered in a suitable elution buffer (e.g. by lowering the pH to 2.7). Eluted proteins are identified on SDS-PAGE. See also Example 22.
Example 14
Fusion Protein Scaffolds for Cell Capture
(A) In Vivo Studies of Non Adherent Cells in the Anterior Chamber of the Eye
ZRep4CT fibers/films/foams are allowed to incubate with IgG against CD45 or CD34. Leucocytes are captured to ZRep4CT scaffolds with IgG against CD45 and mast cells are captured on ZRep4CT scaffolds with IgG against CD34. The cells are allowed to immobilize onto the scaffold. The cells and the fusion protein scaffolds are transplanted into the anterior chamber of the eye of a naked mice. The cells are inspected in vivo through the eye window.
(B) In Vitro Studies of Non-Adherent Cells
Mast cells and leucocytes are grown on ZRep4CT scaffolds with IgG against CD34 and CD45 respectively, and then monitored in vitro. Some cells are non adherent in a phase during development, e.g. neural stem cells that can grow in clusters. In the neural clusters the cells stay in a non-differentiated form. Neural stem cells are grown in clusters on ZRep4CT scaffolds with IgG against a cell receptor on the neural stem cells.
(C) Selection of Specific Cells
A ZRep4CT scaffold (film/foam/fiber) is used for selection of cells through specific antibodies. Mast cells are selected in a two step procedure. Step 1: Binding of cells onto a ZRep4CT scaffolds with IgG against CD34. Step 2: Selection of mast cells on ZRep4CT scaffolds with IgG against the C-kit receptor.
(D) Protein Production in Eukaryotic Cells Grown on ZRep4CT
Many cells used for protein production are derived from non-adherent cell lines. However, large scale production is in many ways facilitated when adherent cells are used, as the physical separation is facilitated. By the use of a ZRep4CT scaffold with IgG against a cell receptor, growth of non-adherent cells can be done in adherent way.
Example 15
Investigation of the Influence of Urea Treatment on IgG Binding to Z-Rep4CT
The effect of urea treatment of Z-Rep4CT films and fibers on IgG binding was here evaluated. Films and fibers of Z-Rep4CT were treated with urea prior to binding of IgG from rabbit serum. Bound IgG was eluted and analyzed by SDS-PAGE.
Fibers and films of Z-Rep4CT, which in Example 6 were observed to bind IgG from rabbit serum and were treated with 8 M urea (200 μl 8 M urea, 20 min, room temperature), were incubated with 500 μl rabbit serum (1:5 dilution) for 1 h at room temperature. Films and fibers of Rep4CT (SEQ ID NO: 20) were used as control material, and were treated in the same way. After washing three times with 600 μl PBS, bound IgG was eluted in 500 μl by lowering the pH to approximately 2.7 with elution buffer (0.5 M acetic acid, 1 M urea, 100 mM NaCl), after which the eluted fractions were analyzed by non-reducing SDS-PAGE (not shown).
It was concluded from the gel that films and fibers of Z-Rep4CT retain their binding capacity for IgG after treatment with 8 M urea. Control films and fibers of Rep4CT did not show any IgG binding.
Example 16
Investigation of the Influence of NaOH Treatment on IgG Binding to Z-Rep4CT
To further evaluate durability to cleaning conditions, the effect of NaOH treatment of Z-Rep4CT (SEQ ID NO: 14) films and fibers on IgG binding was evaluated. Fibers and films of Z-Rep4CT from Example 4 and 5, which in Example 6 were observed to bind IgG from rabbit serum and were treated with 8 M urea (200 μl 8 M urea, 20 min, room temperature), were now further treated with 1 M NaOH (500 μl 1 M NaOH, 20 min, room temperature). Films and fibers of Rep4CT (SEQ ID NO: 20) were used as control material, and were treated in the same way. After NaOH treatment, the films and fibers were incubated with 500 μl rabbit serum (1:5 dilution) for 1 h at room temperature. After washing three times with 600 μl PBS, bound IgG was eluted in 500 μl by lowering the pH to approximately 2.7 with elution buffer (i.e. 0.5 M acetic acid, 1 M urea, 100 mM NaCl), after which the eluted fractions were analyzed by non-reducing SDS-PAGE (not shown).
It was concluded from the gel that films and fibers of Z-Rep4CT retain their binding capacity for IgG after treatment with 1 M NaOH. Control films and fibers of Rep4CT did not show any IgG binding.
Example 17
Quantification of IgG-HRP Binding to Z-Rep4CT Films
(A) IgG-HRP Binding to Z-Rep4CT Films
In order to quantify the IgG binding to Z-Rep4CT, horseradish peroxidase (HRP) conjugated IgG (IgG-HRP) was bound to Z-Rep4CT films.
Films of Z-Rep4CT (SEQ ID NO: 14) and Rep4CT (control, SEQ ID NO: 20) at different concentrations (0.011-890 pmoles) were casted in 96-well plates). The films were blocked with 100 μl 1% BSA for 1 h at room temperature. The films were then incubated for 1 h at room temperature in 50 μl IgG-HRP (i.e. 34 pmole IgG-HRP, rabbit source IgG), and the films were washed twice with 100 μl 0.05% Tween, followed by a final wash with 100 μl of PBS. To measure bound IgG-HRP to films, 50 μl of 50 μM Amplex Red/2 mM H2O2 was added to one film at a time, followed by monitoring of the absorbance at 570 nm for three minutes at a Tecan Plate Reader. A dilution series of soluble IgG-HRP (0.05-0.5 pmole) was also measured in the same type of plate as for the films, by blocking the wells with 100 μl 1% bovine serum albumin (BSA) for 1 h, prior to addition of 20 μl soluble IgG-HRP, 20 μl 125 μM Amplex Red and 10 μl 9.79 mM H2O2. Triplicate measurements were performed for the films and the dilution series.
A linear regression fit was made using Tecan software for each individual measurement, corresponding to the linear region of the absorbance at 570 nm (Abs570/min) versus time raw data plot. The slope corresponds to the HRP conversion rate of colorless substrate to colored product, and is proportional to the number of bound IgG-HRP molecules.
For each individual triplicate, a mean value and a standard deviation of the amount of bound IgG-HRP (pmole) was calculated. FIG. 24 A shows the amount of IgG-HRP bound to Z-Rep4CT and Rep4CT films of different protein concentrations, and FIG. 24 B shows the fractions of Z-Rep4CT and Rep4CT molecules in films of different protein concentrations that have bound IgG-HRP.
For films containing 1.1 pmole of protein and more, Z-Rep4CT films bind significantly more IgG-HRP than the corresponding Rep4CT control films. The fraction of Z-Rep4CT molecules in these films that have bound IgG-HRP is approximately  ̃7% or less.
(B) IgG-HRP Binding to Z-Rep4CT Films after NaOH Treatment
To investigate the effect of NaOH treatment on IgG binding to Z-Rep4CT films, IgG-HRP was bound to NaOH treated films and the amount of bound IgG-HRP detected.
Films of Z-Rep4CT (SEQ ID NO: 14; 1.1-890 pmole) and Rep4CT (SEQ ID NO: 20, 108 pmole) with bound IgG-HRP from Example 17 (A) were incubated in 100 μl of elution buffer (pH 2.7) for 1 h at room temperature in order to remove the bound IgG-HRP. Next, the films were incubated in 100 μl of 1 M NaOH for 20-30 min at room temperature, followed by washing twice in 150 μl PBS. The wells containing the films were then blocked with 1% BSA, incubated with IgG-HRP (34 pmole) and washed three times, prior to addition of 50 μM Amplex Red/2 mM H2O2 and subsequent monitoring of the absorbance at 570 nm as set out above in (A). For each individual triplicate, a mean value and a standard deviation of the amount of bound IgG-HRP (pmole) was calculated.
FIG. 25 A shows the amount of IgG-HRP bound to Z-Rep4CT and Rep4CT films of different protein concentrations, and FIG. 25 B shows the fractions of Z-Rep4CT and Rep4CT molecules in films of different protein concentrations that have bound IgG-HRP. FIG. 26 visualizes the amounts of bound IgG-HRP, before and after NaOH treatment, to Z-Rep4CT and Rep4CT films.
The 108 pmole Z-Rep4CT films show significantly more binding than the corresponding Rep4CT films, and the amount of Z-Rep4CT binding of IgG-HRP to NaOH treated films show a trend to increase as the amount of protein in the film increases. It seems that the amount of bound IgG-HRP to Z-Rep4CT films is reduced approximately 2-4-fold by the harsh 1 M NaOH treatment compared to untreated films.
Example 18
Quantification of IgG-Fluorophore Binding to Z-Rep4CT Films
Binding of IgG conjugated to a fluorophore was performed to Z-Rep4CT and Rep4CT films containing different amounts of protein.
Films of Z-Rep4CT (SEQ ID NO: 14) and Rep4CT (control, SEQ ID NO: 20) at different concentrations (0.011-890 pmoles) were prepared and blocked as set out in Example 17. The films were then incubated for 1 h at room temperature in 50 μl IgG-fluorophore (100 pmole IgG-fluorophore, rabbit source IgG, fluorophore: Alexa Fluor 633), after which the films were washed two times with 100 μl 0.05% Tween, followed by a final wash with 100 μl of PBS. Before fluorescence measurements, 100 μl PBS was added to each film.
A dilution series of soluble IgG-fluorophore (0-1 pmole) was also measured in the same type of plate as for the films, by blocking the wells with 100 μl 1% bovine serum albumin (BSA) for 1 h, prior to addition of 100 μl soluble IgG-fluorophore. The fluorescence was measured as triplicates for films and the dilution series on a Tecan Plate Reader instrument (excitation: 632 nm, emission: 660 nm, Gain: 200).
For each individual triplicate, a mean value and a standard deviation of the amount of bound IgG-fluorophore (pmole) were calculated (FIG. 27 A) for films with 0.011-55 pmole protein. The fraction of Z-Rep4CT and Rep4CT molecules binding IgG-fluorophore was also calculated (FIG. 27 B).
It can be concluded that there is significantly more binding of IgG-Alexa Fluor 633 to Z-Rep4CT films than to the corresponding Rep4CT control films. No significant difference in IgG-fluorophore binding between 0.011-11 pmole Z-Rep4CT films is observed, and this does not seem to be due to autofluorescence of Z-Rep4CT films alone at this wavelength (data not shown). The IgG-fluorophore binding to Z-Rep4CT films containing more than 55 pmole of protein could not be calculated in any reliable way, because the fluorescence signals from those were outside the calibration curve.
By comparing the amounts of bound IgG-fluorophore by Z-Rep4CT films with the corresponding binding of IgG-HRP in Example 17, Z-Rep4CT seems to bind more IgG-fluorophore than IgG-HRP (e.g.  ̃4- and  ̃6-fold difference for 55 and 1.1 pmole films, respectively), which may be due to the difference in size between the fluorophore and HRP. Furthermore, the fraction of Z-Rep4CT molecules binding IgG-fluorophore also seems to have increased compared to those of IgG-HRP binding.
Example 19
Binding of IgG from Human Blood Plasma to Z-Rep4CT Films
In this experiment, three films of Z-Rep4CT (SEQ ID NO: 14) were prepared as set out in Example 3. All films had been stored, after they were casted, for eight months in +4° C. without being immersed in any liquid during storage. Each Z-Rep4CT film was incubated with 500 μl of human blood plasma (1:5 dilution) for 1 h at room temperature. After washing three times with 600 μl PBS, bound IgG was eluted in 500 μl by lowering the pH to approximately 2.7 with elution buffer (0.5 M acetic acid, 1 M urea, 100 mM NaCl), after which the eluted fractions were analyzed by non-reducing SDS-PAGE (not shown). Films of Rep4CT (SEQ ID NO: 20) were used as control material, and were treated in the same way.
It is evident from the gel that IgG ( ̃146 kDa) appears in the eluted fractions from Z-Rep4CT films, indicating that films of Z-Rep4CT have retained the ability to bind IgG from human blood plasma after eight months of storage in +4° C., without being immersed in any liquid. The control films of Rep4CT do not show any IgG in the eluted fractions. These findings extend the observations of experimental reproducibility reported in Example 4 when using the structures according to the invention, and also show that the protein structures can bind human IgG.
Example 20
Binding of IgG from Human Blood Plasma to an Autoclaved Z-Rep4CT Fiber
The ability of Z-Rep4CT to bind IgG after sterilization by autoclave treatment was investigated. After autoclave treatment of a Z-Rep4CT fiber, the fiber was allowed to bind IgG from human blood plasma. The IgG binding of the autoclaved fiber was compared to that of a non-autoclaved fiber.
Two approximately equally sized Z-Rep4CT (SEQ ID NO: 14) fibers were transferred to two tubes containing 20 mM Tris (pH 8). One of the fibers was then autoclaved for 20 min at 121° C. Two Rep4CT (SEQ ID NO: 20) fibers were used as control material, and were treated in the same way.
The fibers were incubated with 500 μl of human blood plasma (1:5 dilution) for 1 h at room temperature. After washing three times with 600 μl PBS, bound IgG was eluted in 500 μl by lowering the pH to approximately 2.7 with elution buffer (0.5 M acetic acid, 1 M urea, 100 mM NaCl), after which the eluted fractions were analyzed by non-reducing SDS-PAGE (FIG. 28).
The gel shown in FIG. 28 was loaded according to:
(1) Human blood plasma (1:5), 1.4 μl loaded
(2) Z-Rep4CT, non-autoclaved fiber, 14 μl loaded
(3) Z-Rep4CT, autoclaved fiber, 14 μl loaded
(4) Rep4CT, non-autoclaved fiber, 14 μl loaded
(5) Rep4CT, autoclaved fiber, 14 μl loaded
(6) Molecular weight marker.
Both the non-autoclaved and the autoclaved Z-Rep4CT fiber show a clear IgG band around 146 kDa. There is no obvious difference in the strength of these IgG bands, suggesting that autoclave treatment has little effect on IgG binding ability. Neither non-autoclaved nor autoclaved fibers of Rep4CT show any IgG in the eluted fractions. All fibers show an additional, much weaker, albumin band ( ̃50-60 kDa).
Example 21
Protease 3C Cleavage of Z-Rep4CT Fibers
The Z-Rep4CT protein (full protein architecture being His6-Z-LEALFQGP-Rep4CT; SEQ ID NO: 14) contains a Protease 3C recognition site (LEALFQGP, Protease 3C cleaving between the amino acids Q and G) between the Z domain and the Rep4CT segment.
An arbitrary sized Z-Rep4CT fiber was transferred to an Eppendorf tube, and protease cleavage was started by adding 9.6 μg of Protease 3C and 0.35 μl of 1 M DTT (dithiothreitol) to a total volume of 350 μl. The cleavage was allowed to proceed for 24 h at +4° C., after which a sample for SDS-PAGE was withdrawn from the cleavage supernatant. The cleavage was then allowed to proceed for another 24 h (+4° C.) when a second sample for SDS-PAGE was withdrawn from the cleavage supernatant. The two withdrawn samples were then analysed by SDS-PAGE (FIG. 29).
The gel shown in FIG. 29 was loaded according to:
(1), molecular weight marker
(2), supernatant of the Z-Rep4CT fiber cleaved with Protease 3C for 24 h
(3), supernatant of the Z-Rep4CT fiber cleaved with Protease 3C for 48 h.
It can be seen from FIG. 29 that both supernatants after cleavage of a Z-Rep4CT fiber with Protease 3C contained two distinct bands. The first band, slightly below 35 kDa, corresponds to Protease 3C ( ̃31 kDa), while the second band is situated just above 10 kDa. Since cleavage of Z-Rep4CT by Protease 3C would generate two oligopeptide segments corresponding to (i) His6-Z-LEALFQ ( ̃9 kDa) and (ii) GP-Rep4CT ( ̃23 kDa), it is concluded that the second band corresponds to the cleaved-off HZ fragment (9 kDa). It is therefore concluded that the Protease 3C cleavage site is available for cleavage in Z-Rep4CT fibers and therefore, the HZ part can be removed.
Example 22
Fiber Formation of Soluble Z-Rep4CT in the Presence of IgG
When mixing soluble Z-Rep4CT with IgG, the kinetics of IgG binding to the Z domains should be faster than the formation of Z-Rep4CT fibers. The possibility to form fibers even if most of the Z domains are occupied with IgG was studied.
Fiber Formation in the Presence of IgG
Purification of Z-Rep4CT (SEQ ID NO: 14) was carried out in the same way as stated earlier, and the purified protein solution was concentrated to 2.2 mg/ml. Fiber formation was carried out at four different conditions, all in a total fiber forming volume of 3 ml containing 71 nmole of soluble Z-Rep4CT protein. The first condition involved only Z-Rep4CT; the second condition was Z-Rep4CT mixed with purified rabbit IgG (8 times excess of Z-Rep4CT compared to IgG); the third condition was Z-Rep4CT mixed with rabbit serum ( ̃1.5 times excess of serum IgG compared to Z-Rep4CT); and the fourth condition was Z-Rep4CT mixed with rabbit serum ( ̃7 times excess of Z-Rep4CT compared to serum IgG). Fiber formation was allowed to proceed for three days in room temperature.
After three days of fiber formation, fibers had formed for conditions 1, 2 and 4. In addition to a formed fiber for condition 4, a considerable amount of Z-Rep4CT protein aggregates had also formed. For condition 3, no fiber or aggregates were visible at all.
One conclusion from this might be that fiber formation is impaired if the presence of lots of other biomolecules, as can be the case in condition 3, shield individual Rep4CT molecules from interacting with each other. Another aspect of this can be that if too much of IgG is present, as can be the case in condition 3, many of the Z domains in Z-Rep4CT may have bound IgG, and a large fraction of Z-Rep4CT with bound IgG may prevent fiber formation.
Removal of Bound IgG from Z-Rep4CT Fibers
Fibers made at conditions 1, 2 and 4, together with the aggregates from condition 4 were recovered and washed in 20 mM Tris (pH 8). Next, all fibers and the aggregates were divided into two equal halves, one half for elution of bound IgG by lowering the pH and the other half for cleavage with Protease 3C.
A first group of fibers and aggregates were transferred to Eppendorf tubes and 144 μl of elution buffer (0.5 M acetic acid, 1 M urea, 100 mM NaCl), pH 2.7, was added to each tube. Elution of IgG was allowed to proceed for 30 min at room temperature, after which the elution supernatants were recovered and analyzed by SDS-PAGE (FIG. 30).
To a second group of fibers and aggregates, 144 μl of Protease 3C (i.e. 110 μg Protease 3C), containing DTT, was added. The Protease 3C cleavage was allowed to proceed over night at +4° C., after which the cleavage supernatants were recovered and analyzed by SDS-PAGE (FIG. 30).
FIG. 30 displays a non-reducing SDS-PAGE gel of IgG removed from Z-Rep4CT fibers and aggregates formed by mixing soluble Z-Rep4CT with IgG. The gel was loaded according to:
(1) Purified, soluble Z-Rep4CT (2.2 mg/ml)
(2) Low pH elution of a Z-Rep4CT fiber (condition 1)
(3) Low pH elution of a Z-Rep4CT fiber (condition 2)
(4) Low pH elution of a Z-Rep4CT fiber (condition 4)
(5) Low pH elution of Z-Rep4CT aggregates (condition 4)
(6) Molecular weight marker
(7) Protease 3C cleavage of a Z-Rep4CT fiber (condition 1)
(8) Protease 3C cleavage of a Z-Rep4CT fiber (condition 2)
(9) Protease 3C cleavage of a Z-Rep4CT fiber (condition 4)
(10) Protease 3C cleavage of Z-Rep4CT aggregates (condition 4).
[Note: The molecular weight of His6Z, Protease 3C and rabbit IgG is 9, 30 and  ̃146 kDa, respectively.]
It is evident form FIG. 30 that IgG is recovered from all tested fibers and aggregates regardless of under what conditions they were formed. See also Example 13.
Example 23
Capture of Lymphocytes to Z-Rep4CT Using Antibody Binding
Using Z-Rep4CT matrices, e.g. fibers and films, to bind the Fc part of IgG, opens for the possibility for further binding of something that the captured IgGs are specifically directed to. One appealing thought would be to isolate a certain cell type from a biological sample containing many different cell types, using the captured IgG on the Z-Rep4CT matrix as a cell affinity ligand. To test this cell capture approach, Z-Rep4CT fibers and films were allowed to bind IgGs that are specifically directed to the CD3 molecule on the cell surface of human T lymphocytes. The captured cells were analyzed by fluorescence microscopy,
Protein expression and purification of Z-Rep4CT (SEQ ID NO: 14) were carried out as described earlier. The purified protein was concentrated to  ̃1 mg/ml, after which fibers and films were made according to previously stated procedures (films were made in 24-well tissue culture plates). In addition, Rep4CT (SEQ ID NO: 20) control fibers and films were prepared in the same way from a  ̃1 mg/ml protein solution.
To capture IgG directed towards the CD3 molecule of human lymphocytes onto the matrices, the fibers and films were immersed in 150 μl of a 1:20 dilution of fluorophore conjugated anti-human CD3 IgG (mouse monoclonal IgG2a to the human CD3 antigen, labeling: Alexa Fluor 488) for 1 h at room temperature. The fibers and films were washed three times with 300 μl of PBS (pH 7.4), after which they were analyzed for IgG binding with an inverted Nikon Eclipse Ti fluorescence microscope (excitation at 455-490 nm, detection at 500-540 nm). Both fiber and film of Z-Rep4CT bound the Alexa Fluor 488 conjugated IgG antibody, thus confirming the ability of the Z domain in Z-Rep4CT to bind IgG. Z-Rep4CT matrices not exposed to IgG do not show any fluorescence signal in this selected region, and control fibers and films of Rep4CT do not show any fluorescence even if exposed to IgG.
Mononuclear cells (i.e. lymphocytes and monocytes) were separated from freshly collected human peripheral blood by gradient centrifugation at room temperature (30 min, 400×g) in Ficoll-Paque density gradient separation medium. The mononuclear cell fraction was recovered after centrifugation followed by two washes in PBS, whereafter the cells were resuspended in 20 ml of RPMI/10% FCS medium. Monocyte depletion was achieved by transferring the cell suspension to a T-75 tissue culture flask, followed by incubation 90 min at 37° C. After monocyte depletion, cells in suspension were recovered and the total number of lymphocytes was counted to 11×106.
In order to bind lymphocytes to Z-Rep4CT (SEQ ID NO: 14) matrices, lymphocytes (1 ml,  ̃0.37×106 cells/ml) were applied to fibers and films, followed by incubation for 30 min at +4° C. (with gentle wobbling). Next, fibers and films were washed three times with 3 ml of PBS/2% FCS (pH 7.4). Bound cells were fixated in 2% PFA (ParaFormAldehyde) for 15 min at +4° C. Cell nuclei were stained by immersing fibers and films with bound cells in 200 μl of DAPI (1 μg/ml) staining solution for 5 min at room temperature prior to washing three times with 300 μl PBS. PBS at a volume of 300 μl was added to each fiber and film before fluorescence microscopy analysis using an inverted Nikon Eclipse Ti instrument (excitation at 380-395 nm, detection at 415-475 nm).
The pictures of Z-Rep4CT fibers (not shown) show a few bound lymphocyte cells for the fiber that has not been exposed to anti-human CD3 IgG antibodies, whereas the fiber that has been exposed to IgG seem to have bound more lymphocytes. In the case of Z-Rep4CT films, stained cells are clearly visible for the film exposed to IgG, but also for the film not exposed to IgG. However, also for the films, it seems like the film exposed to anti-human CD3 IgG prior to cell binding has more cells bound than the corresponding film not exposed to IgG before cell binding. Moreover, control fibers and films of Rep4CT (SEQ ID NO: 20) do not show any lymphocyte binding at all.
In this experiment, it has been shown by fluorescence microscopy that fibers and films of Z-Rep4CT, in contrast to those of Rep4CT, have the ability to bind a fluorescently labeled IgG antibody, namely mouse anti-human CD3 IgG. Furthermore, both Z-Rep4CT fibers and films have the ability to bind lymphocytes, regardless of possessing the IgG antibody specifically recognizing human T lymphocytes or not. This could imply that the Z domain itself has some affinity for human lymphocytes. However, the number of bound cells to Z-Rep4CT matrices seems to be slightly increased when coated with IgG prior to cell binding. To be able to know if the bound cells are lymphocytes of T type, it is necessary to apply a second antibody also directed to the human CD3 molecule, in order to distinguish T lymphocytes from other types of lymphocytes (e.g. B lymphocytes and NK cells).
Example 24
Binding of Albumin from Human Plasma to Abd-Rep4CT Films
To evaluate the accessibility of the Abd domain (residues 13-58 in SEQ ID NO: 16) in the films, and the ability of Abd-Rep4CT films to bind albumin, human blood plasma was used as albumin source. Bound albumin was eluted and analyzed by SDS-PAGE.
Six films of Abd-Rep4CT (SEQ ID NO: 16) prepared in Example 7 were incubated with 500 μl of human blood plasma (1:5 dilution) for 1 h at room temperature. After washing three times with 600 μl PBS, bound albumin was eluted in 500 μl by lowering the pH to approximately 2.7 with elution buffer (0.5 M acetic acid, 1 M urea, 100 mM NaCl), after which the eluted fractions were analyzed by non-reducing SDS-PAGE (FIG. 31). Films of Rep4CT (SEQ ID NO: 20), also prepared in Example 7, were used as control material, and were treated in the same way.
The gel shown in FIG. 31 was loaded according to:
(1) Human blood plasma (1:50), 0.7 μl loaded
(2-7) Hexaplicate of Abd-Rep4CT, film, 14 μl loaded
(8) Empty well incubated with human blood plasma, 14 μl loaded
(9) Molecular weight marker
(10-12) Triplicates of Rep4CT, film, 14 μl loaded.
All six films of Abd-Rep4CT have bound albumin from human blood plasma (lanes 2-7). As only a single albumin band ( ̃60 kDa) appears in the eluted fraction of these Abd-Rep4CT films, they seem to not bind anything unspecifically from the human blood plasma. Films of Rep4CT do not show any albumin in the eluted fractions (lanes 10-12).
To investigate the stability of the films, the albumin binding ability of Abd-Rep4CT films that had been used once before (see above), and had been stored 29 days in PBS (+4° C.) was tested again. The six films of Abd-Rep4CT were incubated with 500 μl of human blood plasma (1:5 dilution) for 1 h at room temperature. After washing three times with 600 μl PBS, bound albumin was eluted in 500 μl by lowering the pH to approximately 2.7 with elution buffer (0.5 M acetic acid, 1 M urea, 100 mM NaCl), after which the eluted fractions were analyzed by non-reducing SDS-PAGE (not shown). Films of Rep4CT were used as control material, and were treated in the same way.
All six films of Abd-Rep4CT retained the ability to bind albumin from human blood plasma after storage for 29 days in PBS. Films of Rep4CT did not show any albumin in the eluted fractions.
Example 25
Cleaning of Abd-Rep4CT Films
(A) Urea Treatment of Abd-Rep4CT Films
Films of Abd-Rep4CT (SEQ ID NO: 16) (six films in total, previously used in Example 24) were incubated with 500 μl of 8 M urea for 20 min in room temperature, after which they were washed three times in 600 μl PBS. Next, the films were incubated in 500 μl of human blood plasma (1:5 dilution) for 1 h at room temperature. After washing three times with 600 μl PBS, bound albumin was eluted in 500 μl by lowering the pH to approximately 2.7 with elution buffer (i.e. 0.5 M acetic acid, 1 M urea, 100 mM NaCl), after which the eluted fractions were analyzed by non-reducing SDS-PAGE (not shown). All six films of Abd-Rep4CT can still bind albumin from human blood plasma after treatment with 8 M urea.
(B) NaOH Treatment of Abd-Rep4CT Fibers and Films
A fiber of Abd-Rep4CT (SEQ ID NO: 16) was first incubated in 500 μl of human blood plasma (1:5 dilution) for 1 h at room temperature. After washing three times with 600 μl PBS, bound albumin was eluted in 500 μl by lowering the pH to approximately 2.7 with elution buffer (0.5 M acetic acid, 1 M urea, 100 mM NaCl), after which the eluted fraction was analyzed by non-reducing SDS-PAGE. The same procedure was carried out for a Rep4CT (SEQ ID NO: 20) control fiber.
For treatment with NaOH, triplicates of three sets of Abd-Rep4CT (SEQ ID NO: 16) films were used: (i) films previously treated with 8 M urea (see (A) above) that are treated with 1 M NaOH, followed by albumin binding; (ii) previously unused films that are treated with 1 M NaOH, followed by albumin binding; and (iii) previously unused films that are only analyzed for albumin binding. The Abd-Rep4CT fibers used above for albumin binding are treated with 1 M NaOH, followed by albumin binding again.
For treatment with NaOH, the Abd-Rep4CT fiber and films [film sets (i) and (ii)] were incubated with 500 μl of 1 M NaOH for  ̃20 min in room temperature, after which they were washed three times in 600 μl PBS. Next, the fiber and all three sets of films were incubated in 500 μl of human blood plasma (1:5 dilution) for 1 h at room temperature. After washing three times with 600 μl PBS, bound albumin was eluted in 500 μl by lowering the pH to approximately 2.7 with elution buffer (0.5 M acetic acid, 1 M urea, 100 mM NaCl), after which the eluted fractions were analyzed by non-reducing SDS-PAGE (FIG. 32).
The gel in FIG. 32 was loaded according to:
(1) Human blood plasma (1:5), 1.4 μl loaded
(2-3, 5) Triplicate of Abd-Rep4CT film, treated with 8 M urea and 1 M NaOH before albumin binding, 14 μl loaded
(4) Molecular weight marker
(6-8) Triplicate of Abd-Rep4CT film, untreated before albumin binding, 14 μl loaded
(9-11) Triplicate of Abd-Rep4CT film, treated with 1 M NaOH before albumin binding, 14 μl loaded
(12) Abd-Rep4CT fiber, untreated before albumin binding, 14 μl loaded
(13) Abd-Rep4CT fiber, treated with 1 M NaOH before albumin binding, 14 μl loaded
(14) Rep4CT fiber, untreated before albumin binding, 14 μl loaded.
The Abd-Rep4CT fiber clearly binds albumin ( ̃60 kDa) both before and after treatment with 1 M NaOH (lane 12 and 13, respectively), whereas the corresponding untreated Rep4CT fiber does not show any albumin binding (lane 14). All Abd-Rep4CT films show albumin binding with no obvious difference in band strength between the untreated films and the films treated with 1 M NaOH before albumin binding (lanes 6-8 and 9-11, respectively). However, the films treated with both 8 M urea and 1 M NaOH before albumin binding show a decrease in the strength of the eluted albumin bands (lanes 2, 3 and 5) compared to the other two sets of films.
Example 26
Binding of Rabbit and Mouse IgG to C2-Re 4CT Films and Fibers
The accessibility of the C2 domain (residues 13-67 in SEQ ID NO: 18) in C2-Rep4CT fibers and films was analysed as follows. Two films and one fiber of C2-Rep4CT (SEQ ID NO: 18) were incubated with 500 μl rabbit serum (1:5 dilution), while another two films and one fiber of C2-Rep4CT (SEQ ID NO: 18) were incubated with 500 μl of  ̃50 μg/ml mouse IgG1 (monoclonal anti-rabbit immunoglobulins, mouse IgG1 isotype, mouse ascites fluid) for 1 h at room temperature. After washing three times with 600 μl PBS, bound IgG was eluted in 500 μl by lowering the pH to approximately 2.7 with elution buffer (0.5 M acetic acid, 1 M urea, 100 mM NaCl), after which the eluted fractions were analyzed by non-reducing SDS-PAGE (FIG. 33). Films and fibers of Rep4CT (SEQ ID NO: 20) were used as control material, and were treated in the same way.
The gel of FIG. 33 was loaded according to:
(1) Mouse ascites fluid (isotype IgG1)
(2) Rabbit serum (1:50)
(3-4) Duplicates of C2-Rep4CT, film, mouse IgG1 
(5, 7) Duplicates of C2-Rep4CT, film, rabbit serum
(6) Molecular weight marker
(8) C2-Rep4CT, fiber, mouse IgG1 
(9) C2-Rep4CT, fiber, rabbit serum
(10-11) Duplicates of Rep4CT, film, mouse IgG1 
(12) Rep4CT, film, rabbit serum
(13) Rep4CT, fiber, rabbit serum
(14) Rep4CT, fiber, mouse IgG1 
[Note: Rabbit IgG is  ̃146 kDa and mouse IgG is  ̃160 kDa under non-reducing SDS-PAGE conditions.]
Binding of mouse IgG1 from ascites fluid to C2-Rep4CT films did not give any detectable IgG band in the eluted fractions on SDS-PAGE (lanes 3-4), but the C2-Rep4CT fiber seems to have bound mouse IgG1 (lane 8, mouse IgG is  ̃160 kDa). However, both films (lanes 5 and 7) and the fiber (lane 9) of C2-Rep4CT show binding of IgG from rabbit serum. As the source of mouse IgG1 is here in the form of an ascites fluid, it may be the case that something in this fluid is somehow disturbing the binding between C2 and IgG1 in the film. Control films and fibers of Rep4CT did not show any IgG in the eluted fractions (lanes 10-14).
Example 27
Binding of IgG from Human Blood Plasma to C2-Rep4CT Films
To further investigate the ability of C2-Rep4CT to bind IgG, two films of each of C2-Rep4CT (SEQ ID NO: 18), Z-Rep4CT (SEQ ID NO: 14) and Rep4CT (SEQ ID NO: 20) were incubated with 500 μl of human blood plasma (1:5 dilution) for 1 h at room temperature. After washing three times with 600 μl PBS, bound IgG was eluted in 500 μl by lowering the pH to approximately 2.7 with elution buffer (0.5 M acetic acid, 1 M urea, 100 mM NaCl), after which the eluted fractions were analyzed by non-reducing SDS-PAGE (FIG. 34).
The gel in FIG. 34 was loaded according to:
(1) Human blood plasma (1:5), 1.4 μl loaded
(2) Molecular weight marker
(3-4) Duplicates of C2-Rep4CT, film, 14 μl loaded
(5-6) Duplicates of Z-Rep4CT, film, 14 μl loaded
(7-8) Duplicates of Rep4CT, film, 14 μl loaded.
In FIG. 34, it can be seen that Z-Rep4CT films have clearly bound IgG from human blood plasma (lanes 5-6). The C2-Rep4CT films also show weaker IgG bands in the eluted fractions (lanes 3-4). The control films of Rep4CT show no binding of IgG from human blood plasma (lanes 7-8).
Example 28
Comparison of Secondary Structure in Z-Rep4CT and Rep4CT Fibers and Films Using ATR-FTIR
The secondary structure of the Z domain is α-helical in its active conformation, while the secondary structure of Rep4CT fibers is predominantly of β-sheet type. If the Z domains in Z-Rep4CT fibers and films are correctly folded, one would expect a higher α-helical content in those matrices compared to in Rep4CT fibers and films. In order to investigate the difference in secondary structure, fibers and films of Z-Rep4CT and Rep4CT were analyzed by the spectroscopic method Attenuated Total Reflectance Fourier Transform InfraRed spectroscopy (ATR-FTIR), by which it is possible to distinguish α-helical (band position: 1648-1657 cm−1) from β-sheet structure (band positions: 1623-1641, 1674-1695 cm−1).
One film of Z-Rep4CT (SEQ ID NO: 14) and one of Rep4CT (SEQ ID NO: 20) were made by allowing 15 μl of protein solution to air-dry in room temperature over night. Fibers were made for Z-Rep4CT and Rep4CT and thereafter air-dried for  ̃30 min in room temperature under tension. ATR-FTIR was then recorded using a platinum ATR unit from Bruker. The IR spectra for both fiber and film (not shown) show that Z-Rep4CT has a higher α-helical content than Rep4CT, which indicates the presence of a correctly folded Z domain. This is in line with maintained functionality of the Z domain in Z-Rep4CT structures according to the invention, see e.g. Examples 2-5, 17-19 and 22-23.

## Claims

1. A protein structure capable of selective interaction with an organic target, wherein said protein structure is a polymer comprising as a repeating structural unit a recombinant fusion protein that is capable of selective interaction with the organic target and comprising the moieties B, REP and CT, and optionally NT, wherein:
B is a non-spidroin moiety of more than 30 amino acid residues, which provides the capacity of selective interaction with the organic target,
wherein the B moiety is selected from the group consisting of the Z domain of staphylococcal protein A, staphylococcal protein A and the E, D, A, B and C domains thereof; streptococcal protein G, the albumin-binding domain thereof and the C1, C2 and C3 domains thereof; streptavidin and monomeric streptavidin (M4); GA modules from Finegoldia magna; and variants thereof wherein the B moiety is capable of selective interaction with the organic target;
REP is a moiety of from 70 to 300 amino acid residues and is derived from the repetitive fragment of a spider silk protein,
wherein the REP moiety is selected from the group of L(AG)nL, L(AG)nAL, L(GA)nL, L(GA)nGL, wherein
n is an integer from 2 to 10;
each individual A segment is an amino acid sequence of from 8 to 18 amino acid residues, wherein from 0 to 3 of the amino acid residues are not Ala, and the remaining amino acid residues are Ala;
each individual G segment is an amino acid sequence of from 12 to 30 amino acid residues, wherein at least 40% of the amino acid residues are Gly; and
each individual L segment is a linker amino acid sequence of from 0 to 20 amino acid residues;
CT is a moiety of from 70 to 120 amino acid residues and is derived from the C-terminal fragment of a spider silk protein, wherein the CT moiety has at least 50% identity to SEQ ID NO: 9 or at least 80% identity to SEQ ID NO: 7; and
NT, when optionally present, is a moiety of from 100 to 160 amino acid residues and is derived from the N-terminal fragment of a spider silk protein; wherein the NT moiety has at least 50% identity to SEQ ID NO: 8 or at least 80% identity to SEQ ID NO: 6.

2. The protein structure according to claim 1, wherein the B moiety is selected from the group consisting of the Z domain derived from staphylococcal protein A, and variants thereof wherein the B moiety is capable of selective interaction with the organic target.

3. The protein structure according to claim 1, wherein the B moiety is selected from the group consisting of staphylococcal protein A, the E, D, A, B and C domains thereof, and variants thereof wherein the B moiety is capable of selective interaction with the organic target.

4. The protein structure according to claim 1, wherein the B moiety is selected from the group consisting of streptococcal protein G, the albumin-binding domain thereof, the C1, C2 and C3 domains thereof and variants thereof wherein the B moiety is capable of selective interaction with the organic target.

5. The protein structure according to claim 1, wherein the B moiety is selected from the group consisting of streptavidin, monomeric streptavidin (M4) and variants thereof wherein the B moiety is capable of selective interaction with the organic target.

6. The protein structure according to claim 1, wherein the B moiety is selected from the group consisting of GA modules from Finegoldia magna and protein fragments having at least 70% identity to GA modules from Finegoldia magna.

7. The protein structure according to claim 1, wherein said recombinant fusion protein is selected from the group of proteins defined by the formulas:


Bx-REP-By-CT-Bz and Bx-CT-By-REP-Bz,

wherein x, y and z are integers from 0 to 5;
and x+y+z≧1.

8. The protein structure according to claim 7, wherein said recombinant fusion protein is selected from the group of proteins defined by the formulas By-REP-CT, By-CT-REP, REP-CT-BE and CT-REP-BE;
wherein x and z are integers from 1 to 5.

9. The protein structure according to claim 8, wherein said recombinant fusion protein is selected from the group of proteins defined by the formulas B-REP-CT, B-CT-REP, REP-CT-B and CT-REP-B.

10. The protein structure according to claim 1, wherein said protein structure has a size of at least 0.1 μm in at least two dimensions.

11. The protein structure according to claim 1, wherein said protein structure is in a physical form selected from the group consisting of fiber, film, foam, net, mesh, sphere and capsule.

12. The protein structure according to claim 1, wherein the CT moiety has at least 90% identity to SEQ ID NO:7.

13. The protein structure according to claim 12, wherein the CT moiety is SEQ ID NO:7.

14. A method for providing a protein structure capable of selective interaction with an organic target, wherein said protein structure is a polymer comprising as a repeating structural unit a recombinant fusion protein that is capable of selective interaction with the organic target and comprising moieties B, REP CT, and optionally NT, wherein the polymer comprises more than 100 fusion protein structural units, and wherein:
B is a non-spidroin moiety of more than 30 amino acid residues, which provides the capacity of selective interaction with the organic target,
wherein the B moiety is selected from the group consisting of the Z domain of staphylococcal protein A, staphylococcal protein A and the E, D, A, B and C domains thereof; streptococcal protein G, the albumin-binding domain thereof and the C1, C2 and C3 domains thereof; streptavidin and monomeric streptavidin (M4); GA modules from Finegoldia magna; and variants thereof wherein the B moiety is capable of selective interaction with the organic target;
REP is a moiety of from 70 to 300 amino acid residues and is derived from the repetitive fragment of a spider silk protein,
wherein the REP moiety is selected from the group of L(AG)nL, L(AG)nAL, L(GA)nL, L(GA)nGL, wherein
n is an integer from 2 to 10;
each individual A segment is an amino acid sequence of from 8 to 18 amino acid residues, wherein from 0 to 3 of the amino acid residues are not Ala, and the remaining amino acid residues are Ala;
each individual G segment is an amino acid sequence of from 12 to 30 amino acid residues, wherein at least 40% of the amino acid residues are Gly; and
each individual L segment is a linker amino acid sequence of from 0 to 20 amino acid residues;
CT is a moiety of from 70 to 120 amino acid residues and is derived from the C-terminal fragment of a spider silk protein, wherein the CT moiety has at least 50% identity to SEQ ID NO: 9 or at least 80% identity to SEQ ID NO: 7; and
NT, when optionally present, is a moiety of from 100 to 160 amino acid residues and is derived from the N-terminal fragment of a spider silk protein; wherein the NT moiety has at least 50% identity to SEQ ID NO: 8 or at least 80% identity to SEQ ID NO: 6,

said method comprising the steps of:
(a) providing said recombinant fusion protein; and
(b) subjecting the fusion protein to conditions to achieve formation of a polymer comprising the recombinant fusion protein.

15. An affinity medium for immobilization of an organic target, said affinity medium comprising a fusion protein that is capable of selective interaction with the organic target and comprising the moieties B, REP, CT, and optionally NT, wherein:
B is a non-spidroin moiety of more than 30 amino acid residues, which provides the capacity of selective interaction with the organic target,
wherein the B moiety is selected from the group consisting of the Z domain of staphylococcal protein A, staphylococcal protein A and the E, D, A, B and C domains thereof; streptococcal protein G, the albumin-binding domain thereof and the C1, C2 and C3 domains thereof; streptavidin and monomeric streptavidin (M4); GA modules from Finegoldia magna; and variants thereof wherein the B moiety is capable of selective interaction with the organic target;
REP is a moiety of from 70 to 300 amino acid residues and is derived from the repetitive fragment of a spider silk protein,
wherein the REP moiety is selected from the group of L(AG)nL, L(AG)nAL, L(GA)nL, L(GA)nGL, wherein
n is an integer from 2 to 10;
each individual A segment is an amino acid sequence of from 8 to 18 amino acid residues, wherein from 0 to 3 of the amino acid residues are not Ala, and the remaining amino acid residues are Ala;
each individual G segment is an amino acid sequence of from 12 to 30 amino acid residues, wherein at least 40% of the amino acid residues are Gly; and
each individual L segment is a linker amino acid sequence of from 0 to 20 amino acid residues;
CT is a moiety of from 70 to 120 amino acid residues and is derived from the C-terminal fragment of a spider silk protein, wherein the CT moiety has at least 50% identity to SEQ ID NO: 9 or at least 80% identity to SEQ ID NO: 7; and
NT, when optionally present, is a moiety of from 100 to 160 amino acid residues and is derived from the N-terminal fragment of a spider silk protein; wherein the NT moiety has at least 50% identity to SEQ ID NO: 8 or at least 80% identity to SEQ ID NO: 6.

16. A cell scaffold material for cultivation of cells having an organic target that is present on the cell surface, said cell scaffold material comprising the protein structure according to claim 1, wherein said cell scaffold material is further comprising an intermediate organic target, wherein the B moiety is capable of selective interaction with and is bound to said intermediate organic target, and wherein said intermediate organic target is capable of selective interaction with the organic target that is present on the cell surface.

17. A method for separation of an organic target from a sample, comprising the steps of:
providing a sample containing the organic target;
providing the affinity medium according to claim 15, wherein said affinity medium is capable of selective interaction with the organic target;
contacting said affinity medium with said sample under suitable conditions to achieve binding between the affinity medium and the organic target; and
removing non-bound sample.

18. A method for immobilization of cells, comprising
providing a sample comprising cells of interest;
applying said sample to the cell scaffold material according to claim 16, wherein said cell scaffold material is capable of selective interaction with an organic target that is present on the cell surface; and
allowing said cells to immobilize to said cell scaffold material by binding between the organic target on the cell surface and said cell scaffold material.

19. A method for cultivation of cells, comprising
immobilizing cells of interest to a cell scaffold material according to the method of claim 18; and
maintaining said cell scaffold material having cells applied thereto under conditions suitable for cell culture.