Choice of Force Fields and Water Models for Sampling Solution Conformations of Bacteriophage T4 Lysozyme

作     者：Xin-zheng Du Xin-fan Hua Zhi-yong Zhang Xin-zheng Du;Xin-fan Hua;Zhi-yong Zhang

作者机构：MOE Key Laboratory for Membraneless&Cellular DynamicsNational Science Center for Physical Sciences at the MicroscaleDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefei 230026China 

出 版 物：《Chinese Journal of Chemical Physics》 (化学物理学报（英文）)

年 卷 期：2021年第34卷第4期

页      面：487-496,I0004-I0010页

核心收录：

学科分类：081704[工学-应用化学] 07[理学] 08[工学] 0817[工学-化学工程与技术] 070303[理学-有机化学] 0703[理学-化学] 0702[理学-物理学] 

基　　金：This work was supported by the National Natu-ral Science Foundation of China(No.91953101 and No.21573205) the Strategic Priority Research Program of the Chinese Academy of Science(XDB37040202),the Hefei National Science Center Pilot Project Funds,and the New Concept Medical Research Fund of USTC 

主　　题：Molecular dynamics simulation Force eld Water model Domain motion Bacteriophage T4 lysozyme 

摘      要：A protein may exist as an ensem-ble of di erent conformations in solution,which cannot be repre-sented by a single static *** dy-namics(MD)simulation has become a useful tool for sampling protein conformations in solution,but force elds and water models are important *** work presents a case study of the bacteriophage T4 lysozyme(T4L).We have found that MD simulations using a classic AMBER99SB force eld and TIP4P water model cannot well describe hinge-bending domain motion of the wild-type T4L at the timescale of one *** combinations,such as a residue-speci c force eld called RSFF2+and a dispersion-corrected water model TIP4P-D,are able to sample reasonable solution conformations of T4L,which are in good agreement with experimental *** primary study may provide candidates of force elds and water models for further investigating conformational transition of T4L.