Calcium Block of Sodium Current in a Model Calcium Channel: Cylindrical Atomistic Pore with Glutamate Side Chains

Na(+)/Ca(2+) selectivity in the bacterial voltage-gated sodium channel NavAb

The recent publication of a number of high resolution bacterial voltage-gated sodium channel structures has opened the door for the mechanisms employed by these channels to distinguish between ions to be elucidated. The way these channels select between Na⁺ and K⁺ has been investigated in computational studies, but the selectivity for Na⁺ over Ca²⁺ has not yet been studied in this way. Here we use molecular dynamics simulations to calculate the energetics of Na⁺ and Ca²⁺ transport through the channel. Single ion profiles show that Ca²⁺ experiences a large barrier midway through the selectivity filter that is not seen by Na⁺. This barrier is caused by the need for Ca²⁺ to partly dehydrate to pass through this region and the lack of compensating interactions with the protein. Multi-ion profiles show that ions can pass each other in the channel, which is why the presence of Ca²⁺ does not block Na⁺ conduction despite binding more strongly in the pore.

DYNAMICS OF SIMPLE FLUIDS CONFINED IN CYLINDRICAL PORE: EFFECT OF PORE SIZE

We study the thermodynamic and dynamical properties of Weeks–Chandler–Anderson (WCA) fluids confined in a cylindrical pore by means of a canonical molecular dynamics simulation method. The pore model is an infinitely long cylinder consisted of a thermal wall and mimics a typical carbon nanotube. The thermodynamic properties are obtained for relatively high density fluids over a wide range of pore diameters at a given temperature. The size dependence of the self-diffusion coefficients in the cylindrical pore is also investigated. It is found that, as the pore diameter decreases, the potential energy and axial component of the pressure exhibit a sharp rise and the self-diffusion coefficient decreases. The observed behaviors can be understood in terms of the geometrical confinement and attenuation of transport induced by dispersive fluid-wall interaction. In addition, anomalous diffusion is observed at the pore size corresponding to twice the particle diameter.

Computational studies of gramicidin permeation: an entry way sulfonate enhances cation occupancy at entry sites

The impact on the cation-transport free-energy profile of replacing the C-terminal ethanolamine in the gramicidin A channel with a taurine residue is studied using molecular dynamics simulations of gramicidin A (1JNO) embedded in a lipid bilayer (DMPC) with 1 mol/kg NaCl saline solution. The potential of mean force for ion transport is obtained by umbrella sampling. The presence of a negatively charged sulfonate group at the entrance of the gramicidin channel affects the depth and the location of the binding sites, producing a strong attraction for the cations in the bulk. The potential of mean force by the sulfonate acting directly through electrostatics and van der Waals interactions on the test ion is highly modulated by indirect effects (i.e., sulfonate effects on other components of the system that, in turn, affect the ion free-energy profile in the channel). Because the "entry" sites are located symmetrically at both entry and exit of the channel, the deeper free-energy wells should inhibit exit. Given that the channel has increased conductance experimentally, the simulation results suggest that the channel conductance is normally entry limited.

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

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 negatively charged glutamate side chains and sterically blocks the permeation pathway. Ca2+-relief of Ca2+-block is suggested by a much higher rate of exit for channels preloaded with three Ca2+ ions than for channels with two Ca2+ ions.