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.

Top Publications

  1. Li Y, Migueles S, Welcher B, Svehla K, Phogat A, Louder M, et al. Broad HIV-1 neutralization mediated by CD4-binding site antibodies. Nat Med. 2007;13:1032-4 pubmed
    ..Novel antibodies to the CD4-binding site are elicited in some HIV-1-infected individuals, and new approaches to present this conserved region of gp120 to the immune system may result in improved vaccine immunogens. ..
  2. Ponomarenko J, Bourne P. Antibody-protein interactions: benchmark datasets and prediction tools evaluation. BMC Struct Biol. 2007;7:64 pubmed
    The ability to predict antibody binding sites (aka antigenic determinants or B-cell epitopes) for a given protein is a precursor to new vaccine design and diagnostics...
  3. Lee M, Lloyd P, Zhang X, Schallhorn J, Sugimoto K, Leach A, et al. Shapes of antibody binding sites: qualitative and quantitative analyses based on a geomorphic classification scheme. J Org Chem. 2006;71:5082-92 pubmed
    The topography of antibody binding sites has been classified into five types that evoke familiar geomorphic features of the Earth...
  4. Stoll P, Bassler N, Hagemeyer C, Eisenhardt S, Chen Y, Schmidt R, et al. Targeting ligand-induced binding sites on GPIIb/IIIa via single-chain antibody allows effective anticoagulation without bleeding time prolongation. Arterioscler Thromb Vasc Biol. 2007;27:1206-12 pubmed
    ..The novel clot-targeting approach of anticoagulants via single-chain antibody directed against a LIBS-epitope on GPIIb/IIIa promises effective anticoagulation with reduced bleeding risk. ..
  5. Sivasubramanian A, Sircar A, Chaudhury S, Gray J. Toward high-resolution homology modeling of antibody Fv regions and application to antibody-antigen docking. Proteins. 2009;74:497-514 pubmed publisher
    ..This first large-scale antibody-antigen docking study using homology models reveals the level of "functional accuracy" of these structural models toward protein engineering applications. ..
  6. Dey B, Pancera M, Svehla K, Shu Y, Xiang S, Vainshtein J, et al. Characterization of human immunodeficiency virus type 1 monomeric and trimeric gp120 glycoproteins stabilized in the CD4-bound state: antigenicity, biophysics, and immunogenicity. J Virol. 2007;81:5579-93 pubmed
    ..Together, the results suggest that conformational stabilization may improve the ability of gp120 to elicit neutralizing antibodies. ..
  7. Calarese D, Lee H, Huang C, Best M, Astronomo R, Stanfield R, et al. Dissection of the carbohydrate specificity of the broadly neutralizing anti-HIV-1 antibody 2G12. Proc Natl Acad Sci U S A. 2005;102:13372-7 pubmed
    ..These results have important consequences for the design of immunogens to elicit 2G12-like neutralizing antibodies as a component of an HIV vaccine. ..
  8. Nybakken G, Oliphant T, Johnson S, Burke S, Diamond M, Fremont D. Structural basis of West Nile virus neutralization by a therapeutic antibody. Nature. 2005;437:764-9 pubmed publisher
    ..Collectively, our results suggest that a vaccine strategy targeting the dominant DIII epitope may elicit safe and effective immune responses against flaviviral diseases...
  9. Haas P, de Haas C, Kleibeuker W, Poppelier M, Van Kessel K, Kruijtzer J, et al. N-terminal residues of the chemotaxis inhibitory protein of Staphylococcus aureus are essential for blocking formylated peptide receptor but not C5a receptor. J Immunol. 2004;173:5704-11 pubmed
    ..4 +/- 7.7 nM) could be an important new tool to further stimulate the fundamental research on the mechanisms underlying the FPR and its role in disease processes. ..

More Information


  1. 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. ..
  2. 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. ..
  3. 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. ..
  4. 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. ..
  5. 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...
  6. 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. ..
  7. 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...
  8. 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. ..
  9. 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. ..
  10. 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. ..
  11. 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. ..
  12. 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. ..
  13. 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. ..
  14. 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. ..
  15. 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...
  16. 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. ..
  17. 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...
  18. 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. ..
  19. 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. ..
  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. ..
  21. 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. ..
  22. 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
  23. 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. ..
  24. 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. ..
  25. 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. ..
  26. 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
  27. 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. ..
  28. Gniadecki R. Desmoglein autoimmunity in the pathogenesis of pemphigus. Autoimmunity. 2006;39:541-7 pubmed
  29. 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. ..
  30. 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
  31. 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. ..
  32. Throsby M, Geuijen C, Goudsmit J, Bakker A, Korimbocus J, Kramer R, et al. Isolation and characterization of human monoclonal antibodies from individuals infected with West Nile Virus. J Virol. 2006;80:6982-92 pubmed publisher
  33. 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. ..
  34. 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. ..
  35. 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. ..
  36. 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. ..
  37. 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
  38. 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. ..
  39. 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. ..
  40. 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. ..
  41. 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. ..
  42. 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. ..
  43. 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
  44. 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. ..
  45. 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. ..
  46. 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. ..
  47. 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. ..
  48. S Lidke D, Nagy P, J Arndt Jovin D. In vivo imaging using quantum-dot-conjugated probes. Curr Protoc Cell Biol. 2007;Chapter 25:Unit 25.1 pubmed publisher
  49. 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. ..
  50. 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. ..
  51. Kulshrestha P, Sukumar N, Murray J, Giese R, Wood T. Computational prediction of antibody binding sites on tetracycline antibiotics: electrostatic potentials and average local ionization energies on molecular surfaces. J Phys Chem A. 2009;113:756-66 pubmed publisher
  52. 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. ..
  53. 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. ..