A protein may exist as an ensem-ble of di erent conformations in solution,which cannot be repre-sented by a single static structure.Molecular dy-namics(MD)simulation has become a useful tool for sampling protein confo...A protein may exist as an ensem-ble of di erent conformations in solution,which cannot be repre-sented by a single static structure.Molecular dy-namics(MD)simulation has become a useful tool for sampling protein conformations in solution,but force elds and water models are important issues.This 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 microsecond.Other 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 data.This primary study may provide candidates of force elds and water models for further investigating conformational transition of T4L.展开更多
1 Introduction Viruses are the most abundant biological entities on Earth.They can influence the succession of individual microbial populations,biogeochemical cycles of C/N and,ultimately,microbial community structure...1 Introduction Viruses are the most abundant biological entities on Earth.They can influence the succession of individual microbial populations,biogeochemical cycles of C/N and,ultimately,microbial community structure through killing展开更多
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.
文摘A protein may exist as an ensem-ble of di erent conformations in solution,which cannot be repre-sented by a single static structure.Molecular dy-namics(MD)simulation has become a useful tool for sampling protein conformations in solution,but force elds and water models are important issues.This 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 microsecond.Other 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 data.This primary study may provide candidates of force elds and water models for further investigating conformational transition of T4L.
基金supported by the National Natural Science Foundation of China (Grant Nos. 41002123 & 41030211)the National Basic Research Program of China (Grant No. 2011CB808800)+1 种基金State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (No. GBL11201)the Fundamental Research Funds for National University, China University of Geosciences (Wuhan)
文摘1 Introduction Viruses are the most abundant biological entities on Earth.They can influence the succession of individual microbial populations,biogeochemical cycles of C/N and,ultimately,microbial community structure through killing
