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Molecular recognition of Fc‐specific ligands binding onto the consensus binding site of IgG: insights from molecular simulation
Author(s) -
Tong HongFei,
Lin DongQiang,
Zhang QiLei,
Wang RongZhu,
Yao ShanJing
Publication year - 2014
Publication title -
journal of molecular recognition
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.401
H-Index - 79
eISSN - 1099-1352
pISSN - 0952-3499
DOI - 10.1002/jmr.2373
Subject(s) - chemistry , ligand (biochemistry) , binding site , alanine scanning , tryptophan , molecular recognition , alanine , stereochemistry , molecular model , tyrosine , computational biology , biochemistry , molecule , receptor , biology , amino acid , mutagenesis , gene , organic chemistry , mutation
Immunoglobulin G (IgG) plays an important role in clinical diagnosis and therapeutics. Meanwhile, the consensus binding site (CBS) on the Fc domain of IgG is responsible for ligand recognition, especially for Fc‐specific ligands. In this study, molecular simulation methods were used to investigate molecular interactions between the CBS of the Fc domain and seven natural Fc‐specific ligands. The analysis on the binding energy of the Fc–ligand complex indicated that hydrophobic interactions provide the main driving force for the Fc–ligand binding processes. The hot spots on the ligands and Fc were identified with the computational alanine scanning approach. It was found that the residues of tryptophan and tyrosine on the ligands have significant contributions for the Fc–ligand binding, while Met252, Ile253, Asn434, His435, and Tyr436 are the key residues of Fc. Moreover, two binding modes based on tryptophan or tyrosine were summarized and constructed according to the pairwise interaction analysis. Guidelines for the rational design of CBS‐specific ligands with high affinity and specificity were proposed. Copyright © 2014 John Wiley & Sons, Ltd.