Bridging the Missing Link between Structure and Fidelity of the RNA-Dependent RNA Polymerase from Poliovirus through Free Energy Simulations

	Bridging the Missing Link between Structure and Fidelity of the RNA-Dependent RNA Polymerase from Poliovirus through Free Energy Simulations
	Shen, Hujun; Li, Guohui
刊名	journal of chemical theory and computation
	2014-11-01
卷号	10 期号:11 页码:5195-5205
通讯作者	李国辉
英文摘要	rna-dependent rna polymerases (rdrps) are enzymes catalyzing rna replication from a rna template. active-site closure in rdrps, normally induced by correct nucleotide triphosphate (ntp) binding, is a prerequisite for the cycle of nucleotide incorporation. so, a complete understanding of polymerase function (in particular polymerase fidelity) of a rdrp requires more complete knowledge of active-site closure in the rdrp. in this work, based on solved crystal structures, we have built different models for the rna-dependent rna polymerase from poliovirus (termed pv 3d(pol)). through md simulations and free energy calculations of these pv 3dpol models, we have revealed the dynamic correlation between motif a and motif d and between motif a and incoming ntp, have deepened our understanding of polymerase fidelity from dynamic aspects, and have provided an explanation to the puzzle that arises from different observations based on kinetic studies and structural data.
学科主题	物理化学
WOS标题词	science & technology ; physical sciences
类目[WOS]	chemistry, physical ; physics, atomic, molecular & chemical
研究领域[WOS]	chemistry ; physics
关键词[WOS]	state kinetic-analysis ; molecular-dynamics simulations ; histogram analysis method ; ribonucleotide incorporation ; reverse-transcriptase ; nucleotidyl transfer ; mechanism ; rna-polymerase-(3d(pol)) ; motions ; protein
收录类别	SCI
语种	英语
WOS记录号	WOS:000344905300039
公开日期	2016-05-09
内容类型	期刊论文
源URL	[http://cas-ir.dicp.ac.cn/handle/321008/144007]
专题	大连化学物理研究所_中国科学院大连化学物理研究所
作者单位	Chinese Acad Sci, Dalian Inst Chem Phys, State Key Lab Mol React Dynam, Lab Mol Modeling & Design, Dalian 116023, Peoples R China
推荐引用方式 GB/T 7714	Shen, Hujun,Li, Guohui. Bridging the Missing Link between Structure and Fidelity of the RNA-Dependent RNA Polymerase from Poliovirus through Free Energy Simulations[J]. journal of chemical theory and computation,2014,10(11):5195-5205.
APA	Shen, Hujun,&Li, Guohui.(2014).Bridging the Missing Link between Structure and Fidelity of the RNA-Dependent RNA Polymerase from Poliovirus through Free Energy Simulations.journal of chemical theory and computation,10(11),5195-5205.
MLA	Shen, Hujun,et al."Bridging the Missing Link between Structure and Fidelity of the RNA-Dependent RNA Polymerase from Poliovirus through Free Energy Simulations".journal of chemical theory and computation 10.11(2014):5195-5205.