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Analysis of the antigen combining site: Correlations between length and sequence composition of the hypervariable loops and the nature of the antigen

Collis, A. V. J., Brouwer, A. P. and Martin, A. C. R. (2003) Analysis of the antigen combining site: Correlations between length and sequence composition of the hypervariable loops and the nature of the antigen. Journal of Molecular Biology, 325 (2). pp. 337-354. ISSN 0022-2836

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To link to this item DOI: 10.1016/s0022-2836(02)01222-6

Abstract/Summary

It has long been suggested that the overall shape of the antigen combining site (ACS) of antibodies is correlated with the nature of the antigen. For example, deep pockets are characteristic of antibodies that bind haptens, grooves indicate peptide binders, while antibodies that bind to proteins have relatively flat combining sites. In. 1996, MacCallum, Martin and Thornton used a fractal shape descriptor and showed a strong correlation of the shape of the binding region with the general nature of the antigen. However, the shape of the ACS is determined primarily by the lengths of the six complementarity-determining regions (CDRs). Here, we make a direct correlation between the lengths of the CDRs and the nature of the antigen. In addition, we show significant differences in the residue composition of the CDRs of antibodies that bind to different antigen classes. As well as helping us to understand the process of antigen recognition, autoimmune disease and cross-reactivity these results are of direct application in the design of antibody phage libraries and modification of affinity. (C) 2003 Elsevier Science Ltd. All rights reserved.

Item Type:Article
Refereed:Yes
Divisions:Faculty of Life Sciences > School of Biological Sciences
ID Code:10704
Uncontrolled Keywords:antibodies, antigen combining site, complementarity-determining, regions, sequence composition, PROTEIN DATA-BANK, DIFFERENT STRAINS, HUMAN-ANTIBODIES, FAB FRAGMENT, BINDING-SITE, IMMUNOGLOBULINS, RECOGNITION, REGIONS, CLASSIFICATION, SPECIFICITY

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