Mixed Monte Carlo/Molecular Dynamics simulations of the prion protein

被引：7

作者：

Ribeiro, Andre A. S. T. ^{[1
]}

de Alencastro, Ricardo B. ^{[1
]}

机构：

[1] Univ Fed Rio de Janeiro, Inst Quim, Ctr Technol, Ilha Fundao, BR-21941909 Rio De Janeiro, RJ, Brazil

来源：

JOURNAL OF MOLECULAR GRAPHICS & MODELLING | 2013年 / 42卷

关键词：

Monte Carlo; Molecular Dynamics; Enhanced sampling; GROMACS; Prion misfolding; MOLECULAR-DYNAMICS; FOLDING SIMULATIONS; NMR STRUCTURE; FORCE-FIELD; CONVERSION; FEATURES; DOMAIN; PH; METADYNAMICS; INSTABILITY;

D O I：

10.1016/j.jmgm.2013.02.007

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

In this paper we present the results of mixed Monte Carlo/Molecular Dynamics (MC/MD) simulations of the D178N mutant of the human prion protein. We have used the MC moves for polypeptide sampling known as Concerted Rotations with Angles (CRA) to selectively sample the region of the prion protein comprising the beta-sheet and one of the a-helices. The results indicate that the MC/MD simulations sample the phase space substantially faster than regular Molecular Dynamics simulations starting with the same initial conditions. This work further indicates the MC/MD technique as a potentially powerful simulation tool, allowing the selective sampling of a region of a physical system that is deemed important. (C) 2013 Elsevier Inc. All rights reserved.

引用

页码：1 / 6

页数：6

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