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学科主题: 物理化学
题名: Bridging the Missing Link between Structure and Fidelity of the RNA-Dependent RNA Polymerase from Poliovirus through Free Energy Simulations
作者: Shen, Hujun1;  Li, Guohui1
通讯作者: 李国辉
刊名: JOURNAL OF CHEMICAL THEORY AND COMPUTATION
发表日期: 2014-11-01
DOI: 10.1021/ct5006449
卷: 10, 期:11, 页:5195-5205
收录类别: SCI
文章类型: Article
WOS标题词: Science & Technology ;  Physical Sciences
类目[WOS]: Chemistry, Physical ;  Physics, Atomic, Molecular & Chemical
研究领域[WOS]: Chemistry ;  Physics
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.
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
语种: 英语
WOS记录号: WOS:000344905300039
Citation statistics: 
内容类型: 期刊论文
URI标识: http://cas-ir.dicp.ac.cn/handle/321008/144007
Appears in Collections:中国科学院大连化学物理研究所_期刊论文

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作者单位: 1.Chinese Acad Sci, Dalian Inst Chem Phys, State Key Lab Mol React Dynam, Lab Mol Modeling & Design, Dalian 116023, Peoples R China

Recommended Citation:
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.
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