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Research Article: Quantitative Sequence–Kinetics Relationship in Antigen–Antiboby Interaction Kinetics Based on a Set of Descriptors
Author(s) -
RongKai Xie,
HaiXia Long,
XiaoMing Cheng,
YuanQiang Wang,
Yong Lin,
Ying Yang,
Bo Zhu,
ZhiHua Lin
Publication year - 2010
Publication title -
chemical biology and drug design
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.59
H-Index - 77
eISSN - 1747-0285
pISSN - 1747-0277
DOI - 10.1111/j.1747-0285.2010.01022.x
Subject(s) - kinetics , peptide , chemistry , residue (chemistry) , quantitative structure–activity relationship , partial least squares regression , principal component analysis , sequence (biology) , dissociation (chemistry) , computational biology , stereochemistry , biological system , biochemistry , biology , mathematics , physics , statistics , quantum mechanics
The interaction between recombinant Fab57P and the coat protein of tobacco mosaic virus was studied using quantitative structure–activity relationship (QSAR) method. The development of quantitative multivariate model has shown to be a promising approach for unraveling protein–protein interactions by designed mutations in peptide sequence. This approach makes it possible to stereo‐chemically determine which residue properties contribute most to the interaction. A set of side‐chain descriptors was proposed and applied in structural characterization of three positions (positions 142, 145 and 146) in the peptide antigen. Quantitative sequence–kinetics relationship (QSKR) models describing the dissociation rates (log k d ) were developed successfully using orthogonal signal correction–partial least squares method. The results showed that peptides will have high log k d values when the amino acids in position 142 and 145 have high net charge index, and when residue 145 has high hydrophobicity and residue 146 has low hydrophobicity.