Changes in flexibility upon binding: Application of the self-consistent pair contact probability method to protein-protein interactions

被引:11
作者
Canino, LS [1 ]
Shen, TY
McCammon, JA
机构
[1] Univ Calif San Diego, Dept Phys, La Jolla, CA 92093 USA
[2] Howard Hughes Med Inst, Dept Chem & Biochem, La Jolla, CA 92093 USA
[3] Univ Calif San Diego, Dept Pharmacol, La Jolla, CA 92093 USA
关键词
D O I
10.1063/1.1517605
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
We extend the self-consistent pair contact probability method to the evaluation of the partition function for a protein complex at thermodynamic equilibrium. Specifically, we adapt the method for multichain models and introduce a parametrization for amino acid-specific pairwise interactions. This method is similar to the Gaussian network model but allows for the adjusting of the strengths of native state contacts. The method is first validated on a high resolution x-ray crystal structure of bovine Pancreatic Phospholipase A2 by comparing calculated B-factors with reported values. We then examine binding-induced changes in flexibility in protein-protein complexes, comparing computed results with those obtained from x-ray crystal structures and molecular dynamics simulations. In particular, we focus on the mouse acetylcholinesterase:fasciculin II and the human alpha-thrombin:thrombomodulin complexes. (C) 2002 American Institute of Physics.
引用
收藏
页码:9927 / 9933
页数:7
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