Effect of Protein Dimerization on Ion Conductivity of Gramicidin A Channel Studied Using Polarizable Force Field |
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| Authors: | Jun-ben Weng Chen-yi Liao Yan Li Ding-lin Zhang Guo-hui Li An-hui Wang |
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| Affiliation: | a.Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Chinab.University of Chinese Academy of Sciences, Beijing 101408, Chinac.State Key Laboratory of Fine Chemicals, School of Chemistry, Dalian University of Technology, Dalian 116024, China |
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| Abstract: | In studies of ion channel systems, due to the huge computational cost of polarizable force fields, classical force fields remain the most widely used for a long time. In this work, we used the AMOEBA polarizable atomic multipole force field in enhanced sampling simulations 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 dimerization. The influence of gA dimerization on the permeation of potassium and sodium ions through the channel was described in terms of conductance, diffusion coefficient, and free energy profile. Results from the polarizable force field 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 affects the ion-transport properties of gA channels, i.e., protein dimerization 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. |
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| Keywords: | Dimerization Conductance Gramicidin A AMOEBA force field Umbrella sampling |
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