Effect of Protein Dimerization on Ion Conductivity of Gramicidin A Channel Studied Using Polarizable Force Field

作     者：Jun-ben Weng Chen-yi Liao Yan Li Ding-lin Zhang Guo-hui Li An-hui Wang Jun-ben Weng;Chen-yi Liao;Yan Li;Ding-lin Zhang;Guo-hui Li;An-hui Wang

作者机构：Laboratory of Molecular Modeling and DesignState Key Laboratory of Molecular Reaction DynamicsDalian Institute of Chemical PhysicsChinese Academy of SciencesDalian 116023China University of Chinese Academy of SciencesBeijing 101408China State Key Laboratory of Fine ChemicalsSchool of ChemistryDalian University of TechnologyDalian 116024China 

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：471-479,I0003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] 

基　　金：This work is supported by the National Natural Sci-ence Foundation of China(No.21933010) 

主　　题：Dimerization Conductance Gramicidin A AMOEBA force eld Umbrella sampling 

摘      要：In studies of ion channel systems,due to the huge computational cost of polarizable force elds,classical force elds remain the most widely used for a long *** this work,we used the AMOEBA polarizable atomic multipole force eld in enhanced sampling simula-tions of single-channel gramicidin A(gA)and double-channel gA systems and investigated its reliability in characterizing ion-transport properties of the gA ion channel under *** inuence of gA dimerization on the permeation of potassium and sodium ions through the channel was described in terms of conductance,di usion coeffcient,and free energy pro *** from the polarizable force eld simulations show that the conductance of potassium and sodium ions passing through the single-and double-channel agrees well with experimental *** data analysis reveals that the molecular mechanism of protein dimerization a ects the ion-transport properties of gA channels,i.e.,protein dimer-ization accelerates the permeation of potassium and sodium ions passing through the double-channel by adjusting the environment around gA protein(the distribution of phospholipid head groups,ions outside the channel,and bulk water),rather than directly adjusting the conformation of gA protein.