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Antibody-antigen interactions: contact analysis and binding site topography.

Abstract：

:We have analysed antigen-contacting residues and combining site shape in the antibody Fv and Fab crystal structures now available from the Protein Data Bank. Antigen-contacting propensities are presented for each antibody residue, allowing a new definition for the complementarity determining regions (CDRs) to be proposed based on observed antigen contacts. Contacts are more common at CDR residues which are located centrally within the combining site; some less central CDR residues are only contacted by large antigens. Non-contacting residues within the CDRs coincide with residues identified by Chothia and co-workers as important in defining "canonical" conformations. An objective means of classifying protein surfaces by gross topography has been developed and applied to the antibody combining site surfaces. The surfaces have been clustered into four topographic classes: concave and moderately concave (mostly hapten binders), ridged (mostly peptide binders) and planar (mostly protein binders). We have determined the topographic classes for ten pairs of complexed and uncomplexed antibody-antigen crystal structures; four change topographic class on complexation. The results will be of use in antibody engineering, antigen docking and in clinical immunology. To demonstrate one application, we show how the data can be used to locate the antigen binding pocket on antibody structures.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

MacCallum RM,Martin AC,Thornton JM

doi

10.1006/jmbi.1996.0548

subject

Has Abstract

pub_date

1996-10-11 00:00:00

pages

732-45

issue

5

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(96)90548-3

journal_volume

262

pub_type

杂志文章

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