Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.
J Phys Chem B. 2013 Feb 14;117(6):1838-43. doi: 10.1021/jp3106666. Epub 2013 Feb 1.
It has been recently proposed that NMR chemical shifts can be used as replica-averaged structural restraints in molecular dynamics simulations to determine the conformational fluctuations of proteins. In this work, we assess the accuracy of this approach by considering its application to the case of ribonuclease A. We found that the agreement between experimental and calculated chemical shifts improves on average when the chemical shifts are used as replica-averaged restraints with respect to the cases in which X-ray structures or ensembles of structures obtained by standard molecular dynamics simulations are considered. These results indicate that the use of chemical shifts as structural restraints enables a bias of the conformational sampling to be introduced in a system-specific manner to reproduce accurately the conformational fluctuations of proteins.
最近有人提出，NMR 化学位移可以用作分子动力学模拟中的复制平均结构约束，以确定蛋白质的构象波动。在这项工作中，我们通过考虑其在核糖核酸酶 A 情况下的应用来评估该方法的准确性。我们发现，当将化学位移用作复制平均约束时，与考虑 X 射线结构或通过标准分子动力学模拟获得的结构集合的情况相比，实验和计算化学位移之间的一致性平均得到改善。这些结果表明，使用化学位移作为结构约束可以以系统特定的方式引入构象采样的偏差，以准确再现蛋白质的构象波动。
