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Keywords:

  • antibody engineering;
  • domain association;
  • contact analysis;
  • amino acid usage;
  • diversification strategy

Abstract

The antibody-binding site is formed as a result of the association between VH and VL domains. Several studies have shown that this association plays an important role in the mechanism of antigen–antibody interaction (Stanfield et al. Structure 1: 83–93, 1993). Considering this, we propose that variations in the VH–VL association are part of the diversification strategy of the antibody repertoires. Previously, a model of association for VH–VL domains based on geometrical characteristics of the packing at the interface was developed by Chothia et al. (J. Mol. Biol. 186: 61–663, 1985). This model includes a common association form for antibodies and a three-layer structure for the interface. In the present work, a complementary model is introduced to account for the general geometrical restrictions of the VH–VL interface, and particular arrangements related to the chemical properties or the side-chain orientations of participating residues. Groups of residues assume common side-chain orientations, which are apparently related to particular functions of different interface zones. Analyses of amino acid usage and network are in agreement with the side-chain orientation patterns. Based on these observations, a three-zone model has evolved to illuminate geometrical and functional restrictions acting over the VH–VL interface. Additionally, this study has revealed the asymmetrical relationships between VH and VL residues important for the association of the two domains. Copyright © 2003 John Wiley & Sons, Ltd.