Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin

被引：157

作者：

Wlodarski, Tomasz ^{[1
,3
]}

Zagrovic, Bojan ^{[1
,2
]}

机构：

[1] Mediterranean Inst Life Sci, Lab Computat Biophys, Split 21000, Croatia

[2] Univ Split, Dept Phys, Split 2100, Croatia

[3] Univ Warsaw, Lab Bioinformat & Bioengn, Interdisciplinary Ctr Math & Computat Modeling, PL-02089 Warsaw, Poland

来源：

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA | 2009年 / 106卷 / 46期

关键词：

ubiquitin binding; protein recognition; Kolmogorov-Smirnov test; PROTEIN-PROTEIN INTERACTIONS; RESIDUAL DIPOLAR COUPLINGS; DYNAMIC ENERGY LANDSCAPE; MODEL-FREE APPROACH; MOLECULAR RECOGNITION; EQUILIBRIUM DYNAMICS; CONSERVED RESIDUES; BINDING CASCADES; FOLDING FUNNELS; ENZYME;

D O I：

10.1073/pnas.0906966106

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Noncovalent binding interactions between proteins are the central physicochemical phenomenon underlying biological signaling and functional control on the molecular level. Here, we perform an extensive structural analysis of a large set of bound and unbound ubiquitin conformers and study the level of residual induced fit after conformational selection in the binding process. We show that the region surrounding the binding site in ubiquitin undergoes conformational changes that are significantly more pronounced compared with the whole molecule on average. We demonstrate that these induced-fit structural adjustments are comparable in magnitude to conformational selection. Our final model of ubiquitin binding blends conformational selection with the subsequent induced fit and provides a quantitative measure of their respective contributions.

引用

页码：19346 / 19351

页数：6

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