bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using a neural network to identify potential HLA‐DR1 binding sites within proteins
Authors: Bisset Leslie R , Fierz Walter 
Published: May 2005

AbstractThe presentation by antigen‐presenting cells of immunodominant peptide segments in association with major histocompatibility complex (MHC) encoded proteins is fundamental to the efficacy of a specific immune response. One approach used to identify immunodominant segments within proteins has involved the development of predictive algorithms which utilize amino acid sequence data to identify structural characteristics or motifs associated within vivoantigenicity. The parallel‐computing technique termed ‘neural networking’ has recently been shown to be remarkably efficient at addressing the problem of pattern recognition and can be applied to predict protein secondary structure attributes directly from amino acid sequence data. In order to examine the potential of a neural network to generalize peptide structural feature related to binding within class II MHC‐encoded proteins, we have trained a neural network to determine whether or not any given amino acid of a protein is part of a peptide segment capable of binding to HLA‐DR1. We report that a neural network trained on a data base consisting of peptide segments known to bind to HLA‐DR1 is able to generalize features relating to HLA‐DR1‐binding capacity (r= 0.17 andp= 0.0001).
Kinetic measurements of molecular interactions by spectrofluorometry
Authors: Voss Edward W. 
Published: May 2005

AbstractThe kinetics of antibody–antigen interactions are reviewed in terms of general trends observed in both polyclonal and monoclonal antibody populations. Anti‐fluorescein antibodies are featured in the review as model proteins to explore fluorescence‐based kinetic measurements. Since the fluorescence of the fluorescein ligand is significantly quenched upon interaction with both polyclonal and monoclonal anti‐fluorescein antibodies, the quenching parameter can be advantageously employed in measuring the rates of association (k1) and dissociation (k2). The near diffusion‐limited k1 rates and the prolonged k2 rates are discussed in terms of antibody affinity and mechanisms involved in ligand binding. Specific prolongation effects of reagents, such as anti‐metatype antibodies, on the dissociation rate are discussed in terms of antibody dynamics and conformational substates.
Peptide vaccines incorporating a ‘promiscuous’ T‐cell epitope bypass certain haplotype restricted immune responses and provide broad spectrum immunogenicity
Authors: Kaumaya Pravin T. P. , Kobs‐Conrad Susan , Seo Young Hoon , Lee Hyosil , Vanbuskirk Anne M. , Feng Ningguo , Sheridan John F. , Stevens Vernon 
Published: May 2005

AbstractAn ideal peptide vaccine should contain both B‐ and T‐cell epitopes. Recognition of antigen by B cells is highly dependent on the three‐dimensional conformation of the antigen whereas T cells recognize antigen only after it has been processed to release a peptide fragment which is bound to the major histocompatibility complex (MHC) class II molecule. However, T cells provide ‘help’ to B cells displaying the same processed, MHC‐restricted from of the antigen, demonstrating that the T‐cell response to a protein antigen is under genetic control. Thus, strategies for co‐inclusion of T cell ‘helper’ epitopes with the B‐cell determinant elicit immune responses that are in most cases genetically restricted to only one or a few alleles of the MHC with limited activity across divergent MHC class II haplotypes. This genetically restricted T cell stimulatory activity of peptides is a serious obstacle and consequently such constructs would be of limited practical value as a vaccine targeted to a majority of an outbred population. In the study described here, we have engineered tow peptides to encompass the sequences from the universally immunogenic tetanus toxoid (TT) epitope and the contraceptive vaccine candidate lactate dehydrogenase C4 (LDH‐C4). We demonstrate the feasibility of using ‘promiscuous’ T‐Cell epitopes colinearly constructed with a defined B‐cell epitope to induce high titer antipeptide IgG antibodies specific for native protein antigen LDH‐C4 in several inbred strains of mice, outbred mice and rabbits. There appears to be a strong correlation between the capacity for the hybrid peptides to be stimulatory for the corresponding T cells in C57BL/6 (H‐2b) and C3H/HeJ (H‐2k) mice and their ability to be immunogenic. This correlation, however, appears to break down in H‐2d strains of mice since no antibodies were detected in BALB/c and barely detectable levels of antibodies in B10.D2 although activated T cells were detectable. Conversely, high titers of antipeptide antibodies are elicited in some strains (B10.BR) (H‐2k); C57BL/10 (H‐2k) without detectable IL‐2 responses. Finally, we show that a determinant which was previously restricted to H‐2k can be rendered immunogenic in H‐2b with the ‘promiscuous’ TT epitope. Thus, certain haplotype‐restricted immune responses can be bypassed, setting forth the ground work for the design of a universal vaccine by broadening the effective response in a larger number of individuals typically of the genetically diverse outbred human population.
Strong immunogenicity of a multicomponent peptide vaccine developed with the branched lysine oligopeptide method for human immunodeficiency virus infection
Authors: Okuda Kenji , Kaneko Tamiko , Yamakawa Tadashi , Tanaka Shunichi , Shigematsu Takashi , Yamamoto Akihiro , Hamajima Kenji , Nakajima Kiichiro , Kawamoto Susumu , Phanuphak Praphan 
Published: May 2005

AbstractWe synthesized one V3 peptide each from HTLV‐IIIB, Thai A and Thai B, conjugating then to the T cell epitope of the env region, and we also synthesized a p17 protein peptide of the gag region (HGP‐30). These peptide were then coupled to 8‐lysine copolymers using N‐succinimidyl maleimido carboxylate (Mr = ca 60 000). We designated this the branched lysine oligopeptide method. The large peptide complexes constructed from these four macromolecular peptide were used with aluminium hydroxide or complete Freund's adjuvant to immunize mice and rabbits four times. ELISA assay with aluminium hydroxide or complete Freund's adjuvant to immunize mice and rabbits four times. ELISA assay showed high titres of anti‐peptide antibodies to each V3loop peptide and the HGP‐30 peptide. Strong inhibition of CD4+ dependent cell fusion was obtained with these antisera when IIIb, Thai A and Thai B strains of human immunodeficiency virus (HIV) were used. Strong anti‐fusion inhibition was also observed with two other HIV strains. In addition, an increase of the anti‐HIV effect was observed when we used sera obtained by multicomponent vaccine immunization. The same kind of inhibition was also observed in p24 assay systems using these immunized antisera. Activation of IL‐2 production in lymphocytes was observed in p24 assay systems using these immunized antisera. Activation of IL‐2 production in lymphocytes was observed in mice immunized with this vaccine. These results suggest that immunization with macromolecular peptide complexes can result in strong immunogenicity towards HIV‐1.
Enzymology in vivo using NMR and molecular genetics
Authors: Brindle Kevin M. , Fulton Alexandra M. , Williams Simon‐Peter 
Published: May 2005

AbstractModels of metabolic flux regulation are frequently based on an extrapolation of the kinetic properties of enzymes measured in vitro to the intact cell. Such an extrapolation assumes a detailed knowledge of the intracellular environment of these enzymes in terms of their free substates and effectors concentrations and possible interaction with other cellular macromolecules, which may modify their kinetic properties. These is a considerable incentive, therefore, to study the properties of enzymes directly in vivo. We have been using non‐invasive NMR techniques, in conjunction with molecular genetic manipulation of enzyme levels, to study the kinetic properties of individual enzymes in vivo. We have also developed a novel strategy which has allowed us to monitor, by NMR, the ligand binding properties and mobilities of enzymes in the intact cell. This technique may also allow us to measured the diffusion coefficients of these proteins in the cell. These studies should give new insight into the properties of enzymes in vivo
Glycolytic enzyme–tubulin interactions: Role of tubulin carboxy terminals
Authors: Volkar K. Warren , Knull Harvey R. 
Published: May 2005

AbstractTubulin and microtubules were modified with the protease, subtilisin. The modification reduced the length of α‐or β‐tubulin by cleaving a peptide fragment from the C‐terminals. Generation of α′β′‐tubulin, which is cleaved at both the α‐ and β‐subunit terminals, and αβ′‐tubulin, which is cleaved at the β′‐subunit C‐terminal, have already been reported. In this work an isotype, α′β‐tubulin, was produced. The three modified tubulin isotypes were compared for their ability to interact with glycolytic enzymes. Cleavage of α led to a poorer interaction when tested via affinity chromatography. Tubulin also inhibits the activity of aldolase and glyceraldehyde 3‐phosphate dehydrogenase. When the α‐subunit C‐terminal was intact, inhibition was greatest. These results imply that the C‐terminal of the tubulin α‐subunit is subunit is responsible for interactions with glycolytic enzymes.
Evidence for (PNA)2/DNA triplex structure upon binding of PNA to dsDNA by strand displacement
Authors: Nielsen Peter E. , Egholm Michael , Buchardt Ole 
Published: May 2005

AbstractThe binding of PNA (peptide nucleic acid) T2CT2CT4‐LysNH2 to the double‐stranded DNA target 5′ ‐A2GA2GA4 was studied by KMnO4 and dimethylsulfate (DMS) probing. It is found that upon sequence‐specific strand displacement binding of the PNA to the dsDNA target concomitant protection of the N‐7 of guanines within the target takes place. It is furthermore shown that the binding of this PNA is more efficient at pH 5.5 that at pH 6.5 and very inefficient at pH 7.5. These results clearly indicate that C+G Hoogsteen base pairing is present and important for binding and that the strand displacement complex therefore involves a PNA·DNA‐PNA triplex.
Separate regulation of a membrane protein, gp130, present in receptor complex specific for interleukin‐6 and other functionally related cytokines
Authors: Falus András , Biró Judit , Rákász Éva , Brunner Thomas , Bischoff Stephan 
Published: May 2005

AbstractIn addition to specific ligand binding elements, receptor assembly for interleukin(IL)‐6, oncostatin‐M, leukaemia inhibitory factor, ciliary neurotrophic factor and IL‐11 includes and additional unit, gp130. This molecule is a transmembrane glycoprotein of 130 kDa. In this paper, reviewing molecular, biochemical and functional data on gp130, we describe the dissimilar action of IL‐3 on the expression of the binding unit of the IL‐6 receptor and that of gp130. According to FACS studies, resting basophils express only IL‐6 receptors and no gp130 molecules on the plasma membranes. After incubation with IL‐3, the surface appearance and de novo transcription of gp130 was shown by FACS and mRNA polymerase chain reaction analysis.
(Patho)physiologic pathways to drug targeting: Artificial viral envelopes
Authors: Schreier Hans , Ausborn Michael , Günther Susanne , Weissig Volkmar , Chander Ramesh 
Published: May 2005

AbstractThe goal of this study was to exploit molecular recognition of cell surface receptors by viral surface glycoproteins as a means for the selective intracellular delivery of macromolecules. To accomplish this, artificial viral envelopes (AVE) resembling the human immunodeficiency virus‐1 (HIV‐1) were designed as a model system. Recombinant HIV‐1 surface glycoprotein gp160 (HIV‐1 rgp 160) was inserted in the artificial envelope by a two‐step detergent dialysis process. The artificial HIV‐1 envelope recognized the CD4 cell surface receptor. FITC‐dextran and ricin A were employed as model macromolecules as they cannot passively diffuse across cell membranes. Selective transfer of FITC‐dextran encapsulated in HIV‐1 rgp160 AVE into a CD4‐positive cell line (REX‐1B) versus a CD4‐negative cell line (KG‐1) was demonstrated. Ricin A at concentrations as low as 2 ng/ml arrested cell growth of CD4‐positive MOLT‐4 cells, whereas 8ng/ml ricin A in solution had no effect on cell growth. The arrest of cell growth was reverted in the presence of excess anti‐gp120 monoclonal antibody. Naked enveloped (without HIV‐1 rgp 160 inserted) were alsofound to interact with cells and transfer material, although less efficiently and in a non‐specific manner. Viral mimicry using AVE may be a means for targeted intracellular delivery of peptides, proteins, enzymes, toxins, oligodeoxynucleotides, gene constructs, and other non‐diffusive, labile or toxic macromolecules.
Segregation of normal and pathological human red blood cells, lymphocytes and fibroblasts by immobilized metal‐ion affinity partitioning
Authors: Nanak E. , Vijayalakshmi M. A. , Chadha K. C. 
Published: May 2005

AbstractImmobilized metal‐ion affinity partitioning (IMAP) is shown to be useful as a preliminary screening test and for the separation of different cell populations based upon recognition of the differences in the proteins on cell surfaces. The feasibility of using IMAP to segregate a spectrum of normal human cells (red blood cells, lymphocytes and fibroblasts) from their counterpart pathological cells has been demonstrated.A clear segregation between normal and sickle‐cell anemia red blood cells (RBC), or malaria (Plasmodium vivax) infected RBCs was obtained. Further, the partition differences were found to depend on the nature and the concentration of metal used.Cells form breast cancer and those from the lugn adenocarcinoma showed differences in their partition pattern as compared to normal fibroblasts when PEG–IDA–M(II) was added to the phase system. Maximum differences between the three cell populations were observed in the presence of 10% PEG‐IDA‐Ni(II).Normal lymphocytes and Burkitt's lymphoma cells (Raji nad Namalwa cell lines) were shown to partition differently in the presence of PEG–IDA–M(II) in the phase system. Normal lymphocytes could be distinguished from the Burkitt's lymphoma cell lines in all three phases (top, interface and bottom), in the presence of 10% PEG–IDA–Ni(II) in the system.These differences in the partition behavior could mainly be attributed to the density, surface exposure and micro‐environment of histidine residues of cell membrane‐associated proteins. These data, along with those obtained for normal and pathological human cells show that IMAP could be a simple and versatile tool for the segregation and study of cells.
Detection and side‐chain specificity of IgE antibodies to flucloxicillin in allergic subjects
Authors: Baldo Brain A. , Pham Nghia H. , Weiner John 
Published: May 2005

AbstractUnlike studies on the antigenicity of penicillins in laboratory animals, limited information is available on the allergenicity of penicillins in man, especially with regard to fine structural allergenic differences between the many different penicillins. Inconsistent with the earlier conclusions of others, our studies suggest that side‐chain structures to flucloxacillin‐reactive IgE antibodies. Quantitative hapten inhibition studies revealed potent inhibition by flucloxacillin and three structurally related penicillins: oxacillin, cloxacillin and dicloxacillin. Analysis of the results showed that the side‐chain group of flucloxacillin, 3‐2(‐chloro‐6‐fluorophenyl)‐5‐methyl‐4‐isoxazolyl, is recognized by some antibodies and that the 5‐methyl‐3‐phenyl‐4‐isoxazolyl group, with or without halogen substituents, accounts for the reactivity of other antibodies and for the cross‐reactions seen with some other penicillins. Since it is the side‐chain group that distinguishes the many different types of penicillin, and since IgE antibodies in many of the allergic reactions recognize the side‐chain groups, it is becoming clear that specific assays are required for the detection of IgE antibodies to each of the different penicillins.
Changes in kinetic properties of oxytocin receptors in longitudinal muscle membranes of rat uterus during gestation
Authors: Kaneko Yuji , Kawarabayashi Tatsuhiko , Sugimori Hajime , Tsukamoto Takuji 
Published: May 2005

AbstractReceptors of oxytocin were found to occur in the membrane fraction obtained from longitudinal muscle of pregnant rat uterus. The affinity of the membrane receptor for oxytocin increased through an increase in the association rate and a decrease in the dissociation rate during gestation. The membrane oxytocin receptor concentrations rose almost three‐fold from Day 15 to Day 21. A transition of oxytocin receptors from a single class of independent sites to site–site interacted multiple binding sites, which most likely exhibit positive cooperativity during the last seven days of gestation, was observed. These results suggest that changes in the dynamics of uterine oxytocin receptors also play an important role in the onset of labor.
Kinetic analysis of the interaction between protein a domain variants and human Fc using plasmon resonance detection
Authors: Jendeberg Lena , Persson Björn , Andersson Roland , Karlsson Robert , Uhlén Mathias , Nilsson Björn 
Published: May 2005

AbstractA real time biospecific interaction analysis (BIA) was performed to study the specific interaction between the Fc portion of human immunoglobulin G1 (Fc1) and a one domain analogue (designated Z) of staphylococcal protein A, in monovalent (Z) and divalent (ZZ) forms, and five different single amino acid substituted Z variants (L17D, N28A, F30A, I31A, K35A). Experimental BIA data were used to calculate association rate constants (Kon), dissociation rate constants (koff). The divalent form (ZZ) showed a higher affinity for Fc1 mainly because of a slower off rate. Out of the five mutant Z protein, four (L17D, N28A, I31A, K35A) four had the major effect to Fc1 compared to the parent Z molecule. Surprisingly, two (L17D, I31A) of these four had the major effect of a decreased binding energy as a lowered kon while the other two (N28A, K35A) mutant proteins showed an increased koff as the major kinetic difference from Z in their binding to Fc1. For five of the six different Z variants, as well as for the ZZ molecule, calculated kaff and calculated differences in binding free energies relative to the parent Z molecule (ΔΔG), are in good agreement with the corresponding values obtained in a competitive displacement assay using radioactively labeled Z as a tracer (Cedergren et al., (1993) Prot. Eng. 6, 441‐448). However, the I31A variant, with a measured kon that was more than three orders of magnitude lower than that of Z in the BIA assay, showed a significant weaker affinity to FcI when calculated from BIA data compared ot the competitive displacement assay. The discrepancy between these two methods for Z(I31A) is discussed as well as possible explanations for the unexpected large effect of lowered kon for two of the mutant Z proteins.
Structural requirements for and consequences of an antiviral porphyrin binding to the V3 loop of the human immunodeficiency virus (HIV‐1) envelope glycoprotein gp120
Authors: Neurath A. Robert , Strick Nathan , Debnath Asim K. 
Published: May 2005

AbstractSeveral porphyrin derivatives were reported to have anti‐HIV‐1 activity. Among them, meso‐teta(4‐carboxyphenyl)porphine (MYCPP) and other carboxyphenyl derivatives were the most potent inhibitors (EC50 < 0.7 μM). MTCPP bound to the HIV‐1 enveloope glycoprotein gp120 and to full‐length V3 loop peptides corresponding to several HIV‐1 isolates but not to other peptides from gp120+gp41. However, it remained possible that MTCPP bound to HIV‐1 envelop glycoprotein gp120 and to full‐length V3 loop peptides corresponding to several HIV‐1 isolates but not to other peptides from gp120+gp41. However, it remained possible that MTCPP bound to regions on gp120 which cannot be mimicked by peptides. Further characterization of the binding domain for MTCPP is important for understanding the antiviral activity of porphyrins and for the design of anit‐HIV‐1 drugs interfering with functions of the virus envelope. Results presented here show that: (i) deletion of the V3 loop from the gp120 sequence resulted in drastically diminished MTCPP binding, suggesting that the V3 loop is the dominant if not the only target site on gp120; (ii) this site was only partially mimicked by full‐length V3 loop peptides; (iii) MTCPP binding to the gp120 V3 loop elicited allosteric effects resulting in decreased accessibility of the CD4 receptor binding site; (iv) the binding site for MTCPP lies within the central portion of the V3 loop (KSIHIGPGRAFY for the HIV‐1 subtype B consensus sequence) and does not involve directly the GPG apex of the loop. These results may help in designing antiviral compounds with improved activity.
Gene transfer of lacZ into avian neural tube and neural crest cells by retroviral infection of grafted embryonic tissues
Authors: Stocker K. M. , Brown A. M. C. , Ciment G. 
Published: May 2005

AbstractWe describe here a new method for transferring genes into cells of the neural tube and neural crest of early avian embryos in vivo. Using the marker gene lacZ as an example, we infected dissected neural tubes from Hamburger‐Hamilton stage 12–13 quail embryos with a replication‐defective retrovirus carrying lacZ during a 2 hr period of exposure to the virus in culture. Infected neural tubes were then grafted into uninfected host chicken embryos in ovo and, after continued development for several days, the chimeric embryos were processed for β‐galactosidase histochemistry to identify the progeny of infected cells. We show that virus‐infected neural tubes grafted isotopically into the trunk region of host embryos gave rise to cells of both the spinal cord and neural crest. Infected neural crest cells localized within dorsal root ganglia, sympathetic ganglia, peripheral nerves, and within the skin, where they were likely to give rise to melanocytes. These data are consistent with those using other cell marking techniques applied to the neural crest, indicating that retrovirus infection in culture, grafting, and β‐galactosidase expression has a neutral effect on neural crest cell migration and localization. These results indicate the heterospecific grafting of early avian tissues infected with retroviruses carrying foreign genes may be an effective strategy for testing the biological role of various gene products during development. © 1993 Wiley‐Liss, Inc.
Korrosionsstudien an Leichtmetallen
Authors: Fink Frederick W. 
Published: May 2005

AbstractDurch sorgfältige Auslese der Verwendungsmöglichkeiten und Entwicklung der Korrosionsfestigkeit für spezielle Anwendungsarten können Magnesium, Aluminium und Titan für viele Industriezweige von erhöhtem Nutzen sein.
Über die Beeinflussung der Oxydationsgeschwindigkeit des Eisens durch Behandlung mit Lithiumoxyddampf
Authors: Brauns Erwin , Rahmel Alfred 
Published: May 2005

AbstractEs werden Versuche beschrieben, durch Einbau von Fremdionen mit abweichender Wertigkeit die Konzentration der Gitterfehlstellen des FeO zu verringern und dadurch die Oxydationsgeschwindigkeit des Eisens bei höheren Temperaturen herabzusetzen. Hierzu wird im Hochvakuum auf kleine Eisenblechproben Li2O aufgedampft. Die Proben werden an‐schließend in Luft von 1 at oxydiert.Unter geeigneten Versuchsbedingungen läßt sich bei bestimmter Li2O‐Konzentration und 850°C eine zeitweise Erniedrigung der Oxydationsgeschwindigkeit erreichen. Die Wirkung geht jedoch nach wenigen Stunden verloren, da durch das Wachsen der Oxydschicht eine „Verdünnung”︁ des Li2O eintritt. Die „wirksame”︁ Li2O‐Konzentration wird zu 1,5 bis 2,5 Gew‐% abgeschätzt. Größere Li2O‐Konzentrationen erhöhen die Oxydationsgeschwindigkeit, geringere sind wirkungslos. Weiterhin muß durch geeignete, „Vorbehandlung”︁ erreicht werden, daß das Li2O überwiegend in die FeO‐Phase des aus drei Oxydphasen (FeO, Fe3O4, Fe2O3) bestehenden Zunders gelangt.Bei Temperaturen um 600°C konnte kein Einfluß der Li2O ‐Bedampfung auf die Oxydationsgeschwindigkeit beobachtet werden.