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Brownian Dynamics Simulations of Ion Transport through the VDAC
dc.contributor.author | Lee, Kyu, II | |
dc.contributor.author | Rui, Huan | |
dc.contributor.author | Pastor, Richard W. | |
dc.contributor.author | Im, Wonpil | |
dc.date.accessioned | 2015-04-22T19:11:39Z | |
dc.date.available | 2015-04-22T19:11:39Z | |
dc.date.issued | 2011-02-02 | |
dc.identifier.citation | Lee, Kyu Il, Huan Rui, Richard W. Pastor, and Wonpil Im. "Brownian Dynamics Simulations of Ion Transport through the VDAC." Biophysical Journal 100.3 (2011): 611-19. http://dx.doi.org/10.1016/j.bpj.2010.12.3708. | en_US |
dc.identifier.uri | http://hdl.handle.net/1808/17473 | |
dc.description | This is the publisher's version. Copyright 2011 by Elsevier. | en_US |
dc.description.abstract | It is important to gain a physical understanding of ion transport through the voltage-dependent anion channel (VDAC) because this channel provides primary permeation pathways for metabolites and electrolytes between the cytosol and mitochondria. We performed grand canonical Monte Carlo/Brownian dynamics (GCMC/BD) simulations to explore the ion transport properties of human VDAC isoform 1 (hVDAC1; PDB:2K4T) embedded in an implicit membrane. When the MD-derived, space-dependent diffusion constant was used in the GCMC/BD simulations, the current-voltage characteristics and ion number profiles inside the pore showed excellent agreement with those calculated from all-atom molecular-dynamics (MD) simulations, thereby validating the GCMC/BD approach. Of the 20 NMR models of hVDAC1 currently available, the third one (NMR03) best reproduces both experimental single-channel conductance and ion selectivity (i.e., the reversal potential). In addition, detailed analyses of the ion trajectories, one-dimensional multi-ion potential of mean force, and protein charge distribution reveal that electrostatic interactions play an important role in the channel structure and ion transport relationship. Finally, the GCMC/BD simulations of various mutants based on NMR03 show good agreement with experimental ion selectivity. The difference in ion selectivity between the wild-type and the mutants is the result of altered potential of mean force profiles that are dominated by the electrostatic interactions. | en_US |
dc.publisher | Elsevier | en_US |
dc.title | Brownian Dynamics Simulations of Ion Transport through the VDAC | en_US |
dc.type | Article | |
kusw.kuauthor | Lee, Kyu II | |
kusw.kuauthor | Rui, Huan | |
kusw.kuauthor | Im, Wonpil | |
kusw.kudepartment | Molecular Biosciences | en_US |
kusw.kudepartment | Center for Bioinformatics | en_US |
dc.identifier.doi | 10.1016/j.bpj.2010.12.3708 | |
kusw.oaversion | Scholarly/refereed, publisher version | |
kusw.oapolicy | This item does not meet KU Open Access policy criteria. | |
dc.rights.accessrights | openAccess |