文章基本信息

标题：Equilibrium simulations of proteins using molecular fragment replacement and NMR chemical shifts
本地全文：下载
作者：Wouter Boomsma ; Pengfei Tian ; Jes Frellsen 等
期刊名称：Proceedings of the National Academy of Sciences
印刷版ISSN：0027-8424
电子版ISSN：1091-6490
出版年度：2014
卷号：111
期号：38
页码：13852-13857
DOI：10.1073/pnas.1404948111
语种：English
出版社：The National Academy of Sciences of the United States of America
摘要：SignificanceChemical shifts are the most fundamental parameters measured in nuclear magnetic resonance spectroscopy. Since these parameters are exquisitely sensitive to the local atomic environment, they can provide detailed information about the three-dimensional structures of proteins. It has recently been shown that using such information directly as input in molecular simulations based on the molecular fragment replacement strategy can help the process of protein structure determination. Here, we show how to implement this strategy to determine not only the structures of proteins but also their thermal fluctuations, thereby broadening the scope of chemical shifts in structural biology. Methods of protein structure determination based on NMR chemical shifts are becoming increasingly common. The most widely used approaches adopt the molecular fragment replacement strategy, in which structural fragments are repeatedly reassembled into different complete conformations in molecular simulations. Although these approaches are effective in generating individual structures consistent with the chemical shift data, they do not enable the sampling of the conformational space of proteins with correct statistical weights. Here, we present a method of molecular fragment replacement that makes it possible to perform equilibrium simulations of proteins, and hence to determine their free energy landscapes. This strategy is based on the encoding of the chemical shift information in a probabilistic model in Markov chain Monte Carlo simulations. First, we demonstrate that with this approach it is possible to fold proteins to their native states starting from extended structures. Second, we show that the method satisfies the detailed balance condition and hence it can be used to carry out an equilibrium sampling from the Boltzmann distribution corresponding to the force field used in the simulations. Third, by comparing the results of simulations carried out with and without chemical shift restraints we describe quantitatively the effects that these restraints have on the free energy landscapes of proteins. Taken together, these results demonstrate that the molecular fragment replacement strategy can be used in combination with chemical shift information to characterize not only the native structures of proteins but also their conformational fluctuations.