Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction

JOURNAL OF MOLECULAR BIOLOGY

卷:380

Article

Smith, Colin A.^1,2,3,4  Kortemme, Tanja^1,2,4 

[1] Univ Calif San Francisco, Calif Inst Quatitat Biosci, San Francisco, CA 94158 USA

[2] Univ Calif San Francisco, Dept Biopharmaceut Sci, San Francisco, CA 94158 USA

[3] Univ Calif San Francisco, Dept Pharmaceut Chem, San Francisco, CA 94143 USA

[4] Univ Calif San Francisco, Grad Program Biol & Med Informat, San Francisco, CA 94158 USA

关键词: flexible backbone sampling;    backrub motion;    point mutation;    Monte Carlo;    triosephosphate isomerase loop 6;   

DOI  :  10.1016/j.jmb.2008.05.023

来源: Elsevier

【 摘 要 】

Incorporation of effective backbone sampling into protein simulation and design is an important step in increasing the accuracy of computational protein modeling. Recent analysis of high-resolution crystal structures has suggested a new model, termed backrub, to describe localized, hinge-like alternative backbone and side-chain conformations observed in the crystal lattice. The model involves internal backbone rotations about axes between C-alpha atoms. Based on this observation, we have implemented a backrub-inspired sampling method in the Rosetta structure prediction and design program. We evaluate this model of backbone flexibility using three different tests. First, we show that Rosetta backrub simulations recapitulate the correlation between backbone and side-chain conformations in the high-resolution crystal structures upon which the model was based. As a second test of backrub sampling, we show that backbone flexibility improves the accuracy of predicting point-mutant side-chain conformations over fixed backbone rotameric sampling alone. Finally, we show that backrub sampling of triosephosphate isomerase loop 6 can capture the millisecond/microsecond oscillation between the open and closed states observed in solution. Our results suggest that backrub sampling captures a sizable fraction of localized conformational changes that occur in natural proteins. Application of this simple model of backbone motions may significantly improve both protein design and atomistic simulations of localized protein flexibility. (C) 2008 Elsevier Ltd. All rights reserved.

【 授权许可】

Free