Genomes and Genes
antibody binding sites
Summary: Local surface sites on antibodies which react with antigen determinant sites on antigens (EPITOPES.) They are formed from parts of the variable regions of FAB FRAGMENTS.
- Emberson L, Trivett A, Blower P, Nicholls P. Expression of an anti-CD33 single-chain antibody by Pichia pastoris. J Immunol Methods. 2005;305:135-51 pubmed..Flow cytometry and Biacore analysis demonstrated binding to target antigen CD33 on the surface of human leukaemic cell line HL-60, and to recombinant soluble CD33 respectively. ..
- Potgieter T, Cukan M, Drummond J, Houston Cummings N, Jiang Y, Li F, et al. Production of monoclonal antibodies by glycoengineered Pichia pastoris. J Biotechnol. 2009;139:318-25 pubmed publisher..This paper provides proof of concept that glycoengineered yeast can be used to produce functional full-length monoclonal antibodies at commercially viable productivities. ..
- Chahal F, Entwistle J, Glover N, MacDonald G. A targeted proteomic approach for the identification of tumor-associated membrane antigens using the ProteomeLab PF-2D in tandem with mass spectrometry. Biochem Biophys Res Commun. 2006;348:1055-62 pubmed..This approach has been validated in the identification of ErB2/HER-2 and was subsequently used to identify CD44E as the cognate antigen for VB1-008, one of our fully human, tumor-specific, monoclonal antibodies. ..
- Jiang S, Wang J, Xu R, Liu Y, Wang X, Cao J, et al. Alternate arrangement of PpL B3 domain and SpA D domain creates synergistic double-site binding to VH3 and Vkappa regions of fab. DNA Cell Biol. 2008;27:423-31 pubmed publisher..The demonstration of this novel binding property would promote to achieve the designed hybrid IBPs for useful immunological applications. ..
- Chan S, Ong T, Gao Y, Tiong Y, Wang D, Chew F, et al. Nuclear magnetic resonance structure and IgE epitopes of Blo t 5, a major dust mite allergen. J Immunol. 2008;181:2586-96 pubmed..Findings in this study further stressed the importance of surface-charged residues on IgE binding and have implications in the cross-reactivity and use of Blo t 5 mutants as a hypoallergen for immunotherapy...
- Sakakura M, Takahashi H, Shimba N, Fujii I, Shimada I. Structural basis of the transition-state stabilization in antibody-catalyzed hydrolysis. J Mol Biol. 2007;367:133-47 pubmed..The present NMR studies have enabled us to visualize the concept of transition-state stabilization in enzymatic catalysis, in which the transition-state contacts are better than those of the substrate. ..
- Sompuram S, Vani K, Hafer L, Bogen S. Antibodies immunoreactive with formalin-fixed tissue antigens recognize linear protein epitopes. Am J Clin Pathol. 2006;125:82-90 pubmed..synthesized corresponding peptides derived from the GenBank database sequence that contain the predicted antibody binding sites. Our data indicate that all 9 antibodies bind to linear epitopes, ie, composed of contiguous amino acids...
- Papp K, Szekeres Z, Erdei A, Prechl J. Two-dimensional immune profiles improve antigen microarray-based characterization of humoral immunity. Proteomics. 2008;8:2840-8 pubmed publisher..Our data suggest that 2-D immune profiling could enrich the data obtained from proteomic scale serum profiling studies. ..
- Atassi M, Dolimbek B, Steward L, Aoki K. Molecular bases of protective immune responses against botulinum neurotoxin A--how antitoxin antibodies block its action. Crit Rev Immunol. 2007;27:319-41 pubmed..Thus, analysis of the locations of the Ab-binding and the snp-binding regions provides a molecular rationale for the ability of protecting Abs to block BoNT/A action in vivo. ..
- Reisser Rubrecht L, Torne Celer C, Rénier W, Averseng O, Plantevin S, Quemeneur E, et al. High-affinity uranyl-specific antibodies suitable for cellular imaging. Chem Res Toxicol. 2008;21:349-57 pubmed..Our results suggest that U04S mAb epitopes mostly include the uranyl fraction and its paratopes can accommodate a wide variety of chelating groups. ..
- Zein H, Teixeira da Silva J, Miyatake K. Structure-function analysis and molecular modeling of DNase catalytic antibodies. Immunol Lett. 2010;129:13-22 pubmed publisher..This study demonstrates the potential usefulness of the protein DNA surrogate in the investigation of the origin of anti-DNA antibodies' hydrolyzing activities. ..
- Jones M, Seldon T, Smede M, Linville A, Chin D, Barnard R, et al. A method for rapid, ligation-independent reformatting of recombinant monoclonal antibodies. J Immunol Methods. 2010;354:85-90 pubmed publisher..The effectiveness of this method was demonstrated by the creation of a functional, fully human anti-human CD83 monoclonal antibody. ..
- Nag A, Monine M, Blinov M, Goldstein B. A detailed mathematical model predicts that serial engagement of IgE-Fc epsilon RI complexes can enhance Syk activation in mast cells. J Immunol. 2010;185:3268-76 pubmed publisher..Serial engagement rapidly returns receptors that have dissociated from aggregates to new aggregates before the receptors have fully returned to their basal state. ..
- Xu H, Zhao X, Lu J, Williams D. Relationship between the structural conformation of monoclonal antibody layers and antigen binding capacity. Biomacromolecules. 2007;8:2422-8 pubmed..The results have shown that within the flat-on orientation adopted by the adsorbed antibody, steric hindrance is the main constraint on binding, restricting the access of the antigen to active sites within the antibody layer. ..
- Akerstr m S, Tan Y, Mirazimi A. Amino acids 15-28 in the ectodomain of SARS coronavirus 3a protein induces neutralizing antibodies. FEBS Lett. 2006;580:3799-803 pubmed publisher..Interestingly, only the anti-3a N-terminal antibody can inhibit SARS-CoV propagation in Vero E6 culture although the binding affinity of the anti-3a N-terminal antibody was lower than the anti-3a C-terminal antibody...
- Geng S, Feng J, Li Y, Sun Y, Gu X, Huang Y, et al. Binding activity difference of anti-CD20 scFv-Fc fusion protein derived from variable domain exchange. Cell Mol Immunol. 2006;3:439-43 pubmed..The study highlights the potential relationship between the antibody binding activity and their 3-D conformation, which appears to be worthwhile in providing direction for future antibody design of recombinant antibody. ..
- Neeli I, Richardson M, Khan S, Nicolo D, Monestier M, Radic M. Divergent members of a single autoreactive B cell clone retain specificity for apoptotic blebs. Mol Immunol. 2007;44:1914-21 pubmed..Conversely, selection of autoreactive B cells for binding to apoptotic cells leads to clonal expansion, antibody diversification, and the development of linked sets of anti-nuclear autoantibodies...
- Zhang Y, Wu X, Zhao Y, Bao E, Wang Q, Zhang W, et al. [Analysis of monoclonal antibody binding sites in ovine prion protein]. Sheng Wu Gong Cheng Xue Bao. 2009;25:348-53 pubmed..The binding sites of 4C6, 5F11 and 7F11 were further confirmed to be in 149 aa-158 aa. This conclusion may contribute to the research for pathogenesis and diagnostic method of scrapie and bovine transmissible spongiform encephalopathy. ..
- Viertlboeck B, Schmitt R, Hanczaruk M, Crooijmans R, Groenen M, Göbel T. A novel activating chicken IgY FcR is related to leukocyte receptor complex (LRC) genes but is located on a chromosomal region distinct from the LRC and FcR gene clusters. J Immunol. 2009;182:1533-40 pubmed..Surprisingly, ggFcR is not encoded in the leukocyte receptor complex, but it is located as a single isolated gene at the extremity of chicken chromosome 20. ..
- Chi S, Wahl M, Mowery Y, Shan S, Mukhopadhyay S, Hilderbrand S, et al. Angiostatin-like activity of a monoclonal antibody to the catalytic subunit of F1F0 ATP synthase. Cancer Res. 2007;67:4716-24 pubmed..Thus, MAb3D5AB1 shows angiostatin-like properties superior to angiostatin and may be exploited in cancer chemotherapy. ..
- Moffett S, Mélançon D, DeCrescenzo G, St Pierre C, Deschênes F, Saragovi H, et al. Preparation and characterization of new anti-PSMA monoclonal antibodies with potential clinical use. Hybridoma (Larchmt). 2007;26:363-72 pubmed..These MAbs have potential clinical value in the development of diagnostic and therapeutic applications for prostate cancer. ..
- Gray E, Moore P, Pantophlet R, Morris L. N-linked glycan modifications in gp120 of human immunodeficiency virus type 1 subtype C render partial sensitivity to 2G12 antibody neutralization. J Virol. 2007;81:10769-76 pubmed
- Král V, Mader P, Collard R, Fabry M, Horejsi M, Rezacova P, et al. Stabilization of antibody structure upon association to a human carbonic anhydrase IX epitope studied by X-ray crystallography, microcalorimetry, and molecular dynamics simulations. Proteins. 2008;71:1275-87 pubmed..Theoretical arguments presented in this work indicate that two adjacent arginine residues (ArgH50 and ArgH52) are responsible for the observed proton transfer. ..
- Atassi M. Immune recognition of BoNTs A and B: how anti-toxin antibodies that bind to the heavy chain obstruct toxin action. Toxicon. 2009;54:600-13 pubmed publisher..On BoNT/B, Ab-binding regions overlapped with the sites that bind to mouse and rat synaptotagmin II or to ganglioside, thereby explaining Ab blocking of BoNT/B action. ..
- Wu X, Yang Z, Li Y, Hogerkorp C, Schief W, Seaman M, et al. Rational design of envelope identifies broadly neutralizing human monoclonal antibodies to HIV-1. Science. 2010;329:856-61 pubmed publisher..Exceptionally broad HIV-1 neutralization can be achieved with individual antibodies targeted to the functionally conserved CD4bs of glycoprotein 120, an important insight for future HIV-1 vaccine design. ..
- Xin H, Cutler J. Hybridoma passage in vitro may result in reduced ability of antimannan antibody to protect against disseminated candidiasis. Infect Immun. 2006;74:4310-21 pubmed
- Wang J, Zhang A, Li R, Jin M. [Prokaryotic expression of recombinant Streptococcus suis IgG binding protein and its binding activity with IgG]. Sheng Wu Gong Cheng Xue Bao. 2009;25:509-13 pubmed..But the SPG from different serotypes of S. suis showed no great differences in their binding activities with IgG from the same host species. ..
- Gniadecki R. Desmoglein autoimmunity in the pathogenesis of pemphigus. Autoimmunity. 2006;39:541-7 pubmed
- Ponomarenko J, Bui H, Li W, Fusseder N, Bourne P, Sette A, et al. ElliPro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics. 2008;9:514 pubmed publisher..As ElliPro is based on the geometrical properties of protein structure and does not require training, it might be more generally applied for predicting different types of protein-protein interactions. ..
- Bernstein H, Plasterer M, Schiff S, Kitchen C, Kitchen S, Zack J. CD4 expression on activated NK cells: ligation of CD4 induces cytokine expression and cell migration. J Immunol. 2006;177:3669-76 pubmed
- Luo J, Taylor P, Losen M, De Baets M, Shelton G, Lindstrom J. Main immunogenic region structure promotes binding of conformation-dependent myasthenia gravis autoantibodies, nicotinic acetylcholine receptor conformation maturation, and agonist sensitivity. J Neurosci. 2009;29:13898-908 pubmed publisher..This reveals a structural and functional, as well as antigenic, significance of the MIR. ..
- Krasnorutskii M, Buneva V, Nevinsky G. Antibodies against pancreatic ribonuclease A hydrolyze RNA and DNA. Int Immunol. 2008;20:1031-40 pubmed publisher..Our data suggest that a fraction of abzymes (or catalytically active antibodies) from AI patients hydrolyzing both DNA and RNA may be antibodies against RNase or its complexes with other proteins. ..
- Beck Z, Karasavvas N, Matyas G, Alving C. Membrane-specific antibodies induced by liposomes can simultaneously bind to HIV-1 protein, peptide, and membrane lipid epitopes. J Drug Target. 2008;16:535-42 pubmed publisher..These membrane-specific antibodies have unique binding characteristics. ..
- Inomo A, Sugi T, Fujita Y, Matsubayashi H, Izumi S, Mikami M. The antigenic binding sites of autoantibodies to factor XII in patients with recurrent pregnancy losses. Thromb Haemost. 2008;99:316-23 pubmed publisher..5%) recognized amino acids 1-30, the amino-terminal heavy chain region that is known as factor XII binding site to platelet glycoprotein Ibalpha. ..
- Beyer T, Lohse S, Berger S, Peipp M, Valerius T, Dechant M. Serum-free production and purification of chimeric IgA antibodies. J Immunol Methods. 2009;346:26-37 pubmed publisher..In conclusion, the described methodology may assist in the development of recombinant IgA antibodies for therapeutic applications. ..
- Tanfous N, Essafi M, Larguech B, Barbouche R, Fathallah D. Characterization of a novel monoclonal antibody with restricted specificity to the free beta 2 integrin alpha M CD11b subunit. Hybridoma (Larchmt). 2007;26:373-9 pubmed
- Siva A, Kirkland R, Lin B, Maruyama T, McWhirter J, Yantiri Wernimont F, et al. Selection of anti-cancer antibodies from combinatorial libraries by whole-cell panning and stringent subtraction with human blood cells. J Immunol Methods. 2008;330:109-19 pubmed..Compared with traditional cell panning, this method considerably increased the selectivity of antibodies to tumor-associated antigens. ..
- Li J, Chen X, Huang J, Jiang S, Chen Y. Identification of critical antibody-binding sites in the HIV-1 gp41 six-helix bundle core as potential targets for HIV-1 fusion inhibitors. Immunobiology. 2009;214:51-60 pubmed publisher..These sites may serve as targets for design of small molecule HIV fusion inhibitors, e.g., organic compounds, peptides, and low molecular weight proteins. ..
- LaFond R, Molini B, Van Voorhis W, Lukehart S. Antigenic variation of TprK V regions abrogates specific antibody binding in syphilis. Infect Immun. 2006;74:6244-51 pubmed..pallidum to establish chronic infection. ..
- Fontayne A, De Maeyer B, De Maeyer M, Yamashita M, Matsushita T, Deckmyn H. Paratope and epitope mapping of the antithrombotic antibody 6B4 in complex with platelet glycoprotein Ibalpha. J Biol Chem. 2007;282:23517-24 pubmed..The experimental results were finally used to build a more accurate docking model. Taken together, this information provides guidelines for the design of new derivatized lead compounds with antithrombotic properties. ..
- Jozsi M, Strobel S, Dahse H, Liu W, Hoyer P, Oppermann M, et al. Anti factor H autoantibodies block C-terminal recognition function of factor H in hemolytic uremic syndrome. Blood. 2007;110:1516-8 pubmed..These results suggest that aHUS-associated FH autoantibodies mimic the effect of C-terminal FH mutations, as they inhibit the regulatory function of FH at cell surfaces by blocking its C-terminal recognition region. ..
- Saltini C, Pallante M, Puxeddu E, Contini S, Voorter C, Drent M, et al. M. avium binding to HLA-DR expressed alleles in silico: a model of phenotypic susceptibility to sarcoidosis. Sarcoidosis Vasc Diffuse Lung Dis. 2008;25:100-16 pubmed
- Wallmann J, Proell M, Stepanoska T, Hantusch B, Pali Schöll I, Thalhamer T, et al. A mimotope gene encoding the major IgE epitope of allergen Phl p 5 for epitope-specific immunization. Immunol Lett. 2009;122:68-75 pubmed publisher..We therefore suggest that mimotope gene vaccines are potential candidates for epitope-specific immunotherapy of type I allergy. ..
- Cossins A, Harrison S, Popplewell A, Gore M. Recombinant production of a VL single domain antibody in Escherichia coli and analysis of its interaction with peptostreptococcal protein L. Protein Expr Purif. 2007;51:253-9 pubmed..The dAb protein produced was shown by NMR and CD to be a folded beta-sheet domain. This domain is bound by PpL with a Kd of approximately 50 nM as determined by stopped-flow fluorimetry. ..
- Alaedini A, Okamoto H, Briani C, Wollenberg K, Shill H, Bushara K, et al. Immune cross-reactivity in celiac disease: anti-gliadin antibodies bind to neuronal synapsin I. J Immunol. 2007;178:6590-5 pubmed..Anti-gliadin Abs from patients with celiac disease also bound to the protein. Such cross-reactivity may provide clues into the pathogenic mechanism of the neurologic deficits that are associated with gluten sensitivity. ..
- Somers V, Govarts C, Somers K, Hupperts R, Medaer R, Stinissen P. Autoantibody profiling in multiple sclerosis reveals novel antigenic candidates. J Immunol. 2008;180:3957-63 pubmed..Autoantibody profiles against epitopes derived from MS brain tissue could serve as diagnostic markers or form the basis for the identification of a subgroup of MS patients. ..
- Fuh G. Synthetic antibodies as therapeutics. Expert Opin Biol Ther. 2007;7:73-87 pubmed..Synthetic antibody libraries complement the existing natural repertoire-based antibody libraries and hybridoma approach to maximize the potentials of antibodies as therapeutics. ..
- Nelson K, Foley J, Yager P. Concentration gradient immunoassay. 1. An immunoassay based on interdiffusion and surface binding in a microchannel. Anal Chem. 2007;79:3542-8 pubmed..This assay method is suitable for rapid quantitative detection of low molecular weight analytes for point-of-care diagnostic instrumentation. ..
- Oganesyan V, Gao C, Shirinian L, Wu H, Dall Acqua W. Structural characterization of a human Fc fragment engineered for lack of effector functions. Acta Crystallogr D Biol Crystallogr. 2008;64:700-4 pubmed publisher..Thus, the dramatic broad-ranging effects of TM on IgG binding to several effector molecules cannot be explained in terms of major structural rearrangements in this portion of the Fc. ..
- Birtalan S, Zhang Y, Fellouse F, Shao L, Schaefer G, Sidhu S. The intrinsic contributions of tyrosine, serine, glycine and arginine to the affinity and specificity of antibodies. J Mol Biol. 2008;377:1518-28 pubmed publisher..Results of such studies should illuminate the basic principles underlying natural protein-protein interactions and should aid the design of synthetic binding proteins with functions beyond the scope of natural proteins. ..