利用广泛的极化力场自由能模拟方法来协调 HIV-1 核衣壳蛋白 NCp7 的 NMR 结构。
Reconciling NMR Structures of the HIV-1 Nucleocapsid Protein NCp7 Using Extensive Polarizable Force Field Free-Energy Simulations.
机构信息
LCT, Sorbonne Université, UMR 7616 CNRS, F-75005 Paris, France.
UR EGP, Centre d'Analyses et de Recherche, Faculté des Sciences, Université Saint-Joseph de Beyrouth, Beirut 1107 2050, Lebanon.
出版信息
J Chem Theory Comput. 2020 Apr 14;16(4):2013-2020. doi: 10.1021/acs.jctc.9b01204. Epub 2020 Mar 30.
Abstract
Using polarizable (AMOEBA) and nonpolarizable (CHARMM) force fields, we compare the relative free energy stability of two extreme conformations of the HIV-1 nucleocapsid protein NCp7 that had been previously experimentally advocated to prevail in solution. Using accelerated sampling techniques, we show that they differ in stability by no more than 0.75-1.9 kcal/mol depending on the reference protein sequence. While the extended form appears to be the most probable structure, both forms should thus coexist in water explaining the differing NMR findings.
摘要
利用极化（AMOEBA）和非极化（CHARMM）力场，我们比较了此前实验证明在溶液中占主导地位的 HIV-1 核衣壳蛋白 NCp7 的两种极端构象的相对自由能稳定性。使用加速采样技术，我们发现它们的稳定性差异不超过 0.75-1.9 kcal/mol，具体取决于参考蛋白序列。虽然伸展构象似乎是最可能的结构，但这两种构象都应该在水中共存，这可以解释不同的 NMR 发现。
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