Freddolino Lydia, Harrison Christopher B, Liu Yanxin, Schulten Klaus
Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801.
Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801.
Nat Phys. 2010 Oct 1;6(10):751-758. doi: 10.1038/nphys1713.
Experimental studies of protein folding processes are frequently hampered by the fact that only low resolution structural data can be obtained with sufficient temporal resolution. Molecular dynamics simulations offer a complementary approach, providing extremely high resolution spatial and temporal data on folding processes. The effectiveness of such simulations is currently hampered by continuing questions regarding the ability of molecular dynamics force fields to reproduce the true potential energy surfaces of proteins, and ongoing difficulties with obtaining sufficient sampling to meaningfully comment on folding mechanisms. We review recent progress in the simulation of three common model systems for protein folding, and discuss how recent advances in technology and theory are allowing protein folding simulations to address their current shortcomings.
蛋白质折叠过程的实验研究常常受到这样一个事实的阻碍，即只能以足够的时间分辨率获得低分辨率的结构数据。分子动力学模拟提供了一种互补的方法，可提供关于折叠过程的极高分辨率的空间和时间数据。目前，此类模拟的有效性受到有关分子动力学力场能否再现蛋白质真实势能面的持续质疑，以及在获得足够的采样以对折叠机制进行有意义的评论方面持续存在的困难的阻碍。我们回顾了蛋白质折叠的三种常见模型系统模拟的最新进展，并讨论了技术和理论上的最新进展如何使蛋白质折叠模拟能够克服其当前的缺点。
