期刊
BIOINFORMATICS
卷 33, 期 19, 页码 2971-2976出版社
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btx389
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资金
- National Research Foundation, Prime Minister's Office, Singapore under its BIOLOGICAL DESIGN TOOLS AND APPLICATIONS Programme (BDTA Award) [NRF2013-THE001-070]
- Agency for Science, Technology and Research (A*STAR) Joint Council Office (JCO) Career Development Award, Singapore [15302FG145]
In this study, computational methods are applied to investigate the general properties of antigen engaging residues of a paratope from a non-redundant dataset of 403 antibody-antigen complexes to dissect the contribution of hydrogen bonds, hydrophobic, van der Waals contacts and ionic interactions, as well as role of water molecules in the antigen- antibody interface. Consistent with previous reports using smaller datasets, we found that Tyr, Trp, Ser, Asn, Asp, Thr, Arg, Gly, His contribute substantially to the interactions between antibody and antigen. Furthermore, antibody-antigen interactions can be mediated by interfacial waters. However, there is no reported comprehensive analysis for a large number of structured waters that engage in higher ordered structures at the antibody- antigen interface. From our dataset, we have found the presence of interfacial waters in 242 complexes. We present evidence that suggests a compelling role of these interfacial waters in interactions of antibodies with a range of antigens differing in shape complementarity. Finally, we carry out 296 835 pairwise 3D structure comparisons of 771 structures of contact residues of antibodies with their interfacial water molecules from our dataset using CLICK method. A heuristic clustering algorithm is used to obtain unique structural similarities, and found to separate into 368 different clusters. These clusters are used to identify structural motifs of contact residues of antibodies for epitope binding.
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