Automated Prediction of Protein Association Rate Constants

Overview

Journal Structure

Publisher Cell Press

Specialties Biochemistry
Biotechnology
Cell Biology
Molecular Biology

Date 2011 Dec 14

PMID 22153497

Citations 74

Authors

Sanbo Qin

Xiaodong Pang

Huan-Xiang Zhou

Affiliations

Soon will be listed here.

Abstract

The association rate constants (k(a)) of proteins with other proteins or other macromolecular targets are a fundamental biophysical property. Observed rate constants span over ten orders of magnitude, from 1 to 10(10) M(-1)s(-1). Protein association can be rate limited either by the diffusional approach of the subunits to form a transient complex, with near-native separation and orientation but without short-range native interactions, or by the subsequent conformational rearrangement to form the native complex. Our transient-complex theory showed promise in predicting k(a) in the diffusion-limited regime. Here, we develop it into a web server called TransComp (http://pipe.sc.fsu.edu/transcomp/) and report on the server's accuracy and robustness based on applications to over 100 protein complexes. We expect this server to be a valuable tool for systems biology applications and for kinetic characterization of protein-protein and protein-nucleic acid association in general.

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