Advanced replica-exchange sampling to study the flexibility and plasticity of peptides and proteins

被引:50
作者
Ostermeir, Katja [1 ]
Zacharias, Martin [1 ]
机构
[1] Tech Univ Munich, Phys Dept T38, D-85748 Garching, Germany
来源
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS | 2013年 / 1834卷 / 05期
关键词
Molecular dynamics simulation; Peptide and protein folding; Potential scaling; Conformational sampling; Accelerated sampling; Force field calculation; MOLECULAR-DYNAMICS SIMULATIONS; DIFFUSION EQUATION METHOD; MONTE-CARLO; EFFICIENCY; OPTIMIZATION; CONVERGENCE; THERMODYNAMICS; REFINEMENT; PREDICTION; SYSTEMS;
D O I
10.1016/j.bbapap.2012.12.016
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
Molecular dynamics (MD) simulations are ideally suited to investigate protein and peptide plasticity and flexibility simultaneously at high spatial (atomic) and high time resolution. However, the applicability is still limited by the force field accuracy and by the maximum simulation time that can be routinely achieved in current MD simulations. In order to improve the sampling the replica-exchange (REMD) methodology has become popular and is now the most widely applied advanced sampling approach. Many variants of the REMD method have been designed to reduce the computational demand or to enhance sampling along specific sets of conformational variables. An overview on recent methodological advances and discussion of specific aims and advantages of the approaches will be given. Applications in the area of free energy simulations and advanced sampling of intrinsically disordered peptides and proteins will also be discussed. This article is part of a Special Issue entitled: The emerging dynamic view of proteins: Protein plasticity in allostery, evolution and self-assembly. (C) 2013 Elsevier B.V. All rights reserved.
引用
收藏
页码:847 / 853
页数:7
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