Probing the Nanosecond Dynamics of a Designed Three-Stranded Beta-Sheet with a Massively Parallel Molecular Dynamics Simulation

被引：5

作者：

Voelz, Vincent A. ^{[2
]}

Luttmann, Edgar ^{[2
]}

Bowman, Gregory R. ^{[1
]}

Pande, Vijay S. ^{[1
]}

机构：

[1] Stanford Univ, Biophys Program, Stanford, CA 94305 USA

[2] Stanford Univ, Dept Chem, Stanford, CA 94305 USA

来源：

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES | 2009年 / 10卷 / 03期

关键词：

Ultrafast folding; downhill folding; DPDP; DPDP-II; designed beta-sheet proteins; FOLDING DYNAMICS; SPEED LIMIT; COOPERATIVITY; KINETICS; TRANSITION; STABILITY; ENSEMBLE; HELICES; VARIANT; WELL;

D O I：

10.3390/ijms10031013

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Recently a temperature-jump FTIR study of a designed three-stranded sheet showing a fast relaxation time of similar to 140 +/- 20 ns was published. We performed massively parallel molecular dynamics simulations in explicit solvent to probe the structural events involved in this relaxation. While our simulations produce similar relaxation rates, the structural ensemble is broad. We observe the formation of turn structure, but only very weak interaction in the strand regions, which is consistent with the lack of strong backbone-backbone NOEs in previous structural NMR studies. These results suggest that either (PP)-P-D-P-D-II folds at time scales longer than 240 ns, or that (PP)-P-D-P-D-II is not a well-defined three-stranded beta-sheet. This work also provides an opportunity to compare the performance of several popular forcefield models against one another.

引用

页码：1013 / 1030

页数：18

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