时间分辨力的力分布分析。
Time-resolved force distribution analysis.
作者信息
Costescu Bogdan I, Gräter Frauke
机构信息
Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.
出版信息
BMC Biophys. 2013 May 1;6(1):5. doi: 10.1186/2046-1682-6-5.
BACKGROUND
Biomolecules or other complex macromolecules undergo conformational transitions upon exposure to an external perturbation such as ligand binding or mechanical force. To follow fluctuations in pairwise forces between atoms or residues during such conformational changes as observed in Molecular Dynamics (MD) simulations, we developed Time-Resolved Force Distribution Analysis (TRFDA).
RESULTS
The implementation focuses on computational efficiency and low-memory usage and, along with the wide range of output options, makes possible time series analysis of pairwise forces variation in long MD simulations and for large molecular systems. It also provides an exact decomposition of pairwise forces resulting from 3- and 4-body potentials and a unified treatment of pairwise forces between atoms or residues. As a proof of concept, we present a stress analysis during unfolding of ubiquitin in a force-clamp MD simulation.
CONCLUSIONS
TRFDA can be used, among others, in tracking signal propagation at atomic level, for characterizing dynamical intermolecular interactions (e.g. protein-ligand during flexible docking), in development of force fields and for following stress distribution during conformational changes.
背景
生物分子或其他复杂大分子在受到外部扰动（如配体结合或机械力）时会发生构象转变。为了追踪分子动力学（MD）模拟中观察到的此类构象变化过程中原子或残基之间成对力的波动情况，我们开发了时间分辨力分布分析（TRFDA）方法。
结果
该方法的实现着重于计算效率和低内存使用，并结合广泛的输出选项，使得对长MD模拟和大分子系统中原子对间力变化进行时间序列分析成为可能。它还能精确分解由三体和四体势产生的成对力，并对原子或残基之间的成对力进行统一处理。作为概念验证，我们展示了在力钳MD模拟中泛素展开过程的应力分析。
结论
TRFDA可用于追踪原子水平的信号传播、表征动态分子间相互作用（如柔性对接过程中的蛋白质-配体相互作用）、力场开发以及追踪构象变化过程中的应力分布等。
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