Targeted conformational search with map-restrained self-guided Langevin dynamics: Application to flexible fitting into electron microscopic density maps

被引：42

作者：

Wu, Xiongwu ^{[1
]}

Subramaniam, Sriram ^{[2
]}

Case, David A. ^{[3
,4
]}

Wu, Katherine W. ^{[5
]}

Brooks, Bernard R. ^{[1
]}

机构：

[1] NHLBI, Lab Computat Biol, NIH, Bethesda, MD 20892 USA

[2] NCI, Cell Biol Lab, NIH, Bethesda, MD 20892 USA

[3] Rutgers State Univ, BioMaPS Inst, Piscataway, NJ 08854 USA

[4] Rutgers State Univ, Dept Chem & Chem Biol, Piscataway, NJ 08854 USA

[5] Thomas Jefferson High Sch Sci & Technol, Alexandria, VA 22312 USA

来源：

JOURNAL OF STRUCTURAL BIOLOGY | 2013年 / 183卷 / 03期

关键词：

Self-guided Langevin dynamics; Targeted conformational search; Electron microscopy; Flexible fitting; Map-restraint; GROUP-II CHAPERONIN; LOW-RESOLUTION MAPS; CRYOELECTRON MICROSCOPY; MOLECULAR-DYNAMICS; ATOMIC STRUCTURES; PROTEIN STRUCTURES; CRYO-EM; ENERGY; MODEL; STATE;

D O I：

10.1016/j.jsb.2013.07.006

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：

We present a map-restrained self-guided Langevin dynamics (MapSGLD) simulation method for efficient targeted conformational search. The targeted conformational search represents simulations under restraints defined by experimental observations and/or by user specified structural requirements. Through map-restraints, this method provides an efficient way to maintain substructures and to set structure targets during conformational searching. With an enhanced conformational searching ability of self-guided Langevin dynamics, this approach is suitable for simulating large-scale conformational changes, such as the formation of macromolecular assemblies and transitions between different conformational states. Using several examples, we illustrate the application of this method in flexible fitting of atomic structures into density maps derived from cryo-electron microscopy. (C) 2013 The Authors. Published by Elsevier Inc. All rights reserved.

引用

页码：429 / 440

页数：12