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 

机构地区：[1]Laboratory of Molecular Modeling and Design,State Key Laboratory of Molecular Reaction Dynamics,Dalian Institute of Chemical Physics,Chinese Academy of Sciences,Dalian 116023,China [2]University of Chinese Academy of Sciences,Beijing 101408,China [3]State Key Laboratory of Fine Chemicals,School of Chemistry,Dalian University of Technology,Dalian 116024,China

出　　处：《Chinese Journal of Chemical Physics》2021年第4期471-479,I0003,共10页化学物理学报（英文）

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

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 time.In 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 dimer-ization.The 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 le.Results 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 values.Further 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.

关 键 词：DIMERIZATION CONDUCTANCE Gramicidin A AMOEBA force eld Umbrella sampling 

分 类 号：O629.73[理学—有机化学]