Accurate Evaluation of Ion Conductivity of the Gramicidin A Channel Using a Polarizable Force Field without Any Corrections

doi:10.1021/acs.jctc.6b00128

	Accurate Evaluation of Ion Conductivity of the Gramicidin A Channel Using a Polarizable Force Field without Any Corrections
	Peng, Xiangda 1,2; Zhang, Yuebin 1; Chu, Huiying 1; Li, Yan 1; Zhang, Dinglin 1; Cao, Liaoran 1; Li, Guohui 1
刊名	JOURNAL OF CHEMICAL THEORY AND COMPUTATION
	2016-06-01
卷号	12 期号:6 页码:2973-2982
ISSN号	1549-9618
DOI	10.1021/acs.jctc.6b00128
文献子类	Article
英文摘要	Classical molecular dynamic (MD) simulation of membrane proteins faces significant challenges in accurately reproducing and predicting experimental observables such as ion conductance and permeability due to its incapability of precisely describing the electronic interactions in heterogeneous systems. In this work, the free energy profiles of K+ and Na+ permeating through the gramicidin A channel are Characterized by using the AMOEBA polarizable force field with a total sampling time of 1 mu s. Our results indicated that by explicitly introducing the multipole terms and polarization into the electrostatic potentials, the permeation free energy barrier of K+ through the gA channel is considerably reduced compared to the overestimated results obtained from the fixed-charge model. Moreover; the estimated maximum conductance, without any corrections, for both K+ and Na+ passing through the gA channel are much closet to the experimental results than any classical MD simulations, demonstrating the power of AMOEBA in investigating the membrane proteins.
WOS关键词	MOLECULAR-DYNAMICS SIMULATIONS ; FREE-ENERGY PROFILE ; PARTICLE MESH EWALD ; MEMBRANE-PROTEINS ; AQUEOUS-SOLUTION ; MODEL MEMBRANE ; MONTE-CARLO ; A CHANNEL ; PERMEATION ; TRANSPORT
WOS研究方向	Chemistry ; Physics
语种	英语
出版者	AMER CHEMICAL SOC
WOS记录号	WOS:000378016000044
内容类型	期刊论文
源URL	[http://cas-ir.dicp.ac.cn/handle/321008/170522]
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
通讯作者	Li, Guohui
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 2.Univ Chinese Acad Sci, Chinese Acad Sci, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Peng, Xiangda,Zhang, Yuebin,Chu, Huiying,et al. Accurate Evaluation of Ion Conductivity of the Gramicidin A Channel Using a Polarizable Force Field without Any Corrections[J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION,2016,12(6):2973-2982.
APA	Peng, Xiangda.,Zhang, Yuebin.,Chu, Huiying.,Li, Yan.,Zhang, Dinglin.,...&Li, Guohui.(2016).Accurate Evaluation of Ion Conductivity of the Gramicidin A Channel Using a Polarizable Force Field without Any Corrections.JOURNAL OF CHEMICAL THEORY AND COMPUTATION,12(6),2973-2982.
MLA	Peng, Xiangda,et al."Accurate Evaluation of Ion Conductivity of the Gramicidin A Channel Using a Polarizable Force Field without Any Corrections".JOURNAL OF CHEMICAL THEORY AND COMPUTATION 12.6(2016):2973-2982.