Applied field nonequilibrium molecular dynamics simulations of ion exit from a beta-barrel model of the L-type calcium channel

Biochimica Et Biophysica Acta
Vivek RamakrishnanDavid D Busath

Abstract

We present results of applied field nonequilibrium molecular dynamics simulations (AF NEMD) of a minimal beta-barrel model channel intended to represent an L-type calcium channel that suggests a possible relationship between glutamate side chain conformational changes and ion flux in calcium channels. The beta-barrel is used to provide a scaffolding for glutamate side chains and a confinement for electrolyte of dimensions similar to the expected channel structure. It was preloaded with ions to explore relative rates of ion exit for different occupancy configurations. Our simulations with an asymmetrical flexible selectivity filter represented by four glutamate side chains (EEEE), one of which differs in initial dihedrals from the other three, indicate a plausible mechanism for the observed anomalous mole fraction effect seen in calcium channels. Apparent rates of electric field-induced exit from channels preloaded with three Na+ ions are much higher than for channels with one Ca2+ followed by two Na+ ions, consistent with the common notion that Ca2+ block of Na+ current is due to competition between the Ca2+ and Na+ ions for the negatively charged (EEEE) locus. In our model, the Ca2+ ion ligates simultaneously to the four negat...Continue Reading

Citations

May 21, 2005·Biochimica Et Biophysica Acta·Ben CorryShin-Ho Chung
Aug 7, 2007·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·A V Raghunathan, N R Aluru
Aug 15, 2012·The Journal of Physical Chemistry. B·Todor Dudev, Carmay Lim
Oct 25, 2014·Accounts of Chemical Research·Todor Dudev, Carmay Lim

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