Sameer Varma

Learn More
To understand ion permeation, one must assign correct ionization states to titratable amino acid residues in protein channels. We report on the effects of physical and methodological assumptions in calculating the protonation states at neutral bulk pH of titratable residues lining the lumen of the native Escherichia coli OmpF channel, and five mutants. We(More)
K+ ions seemingly permeate K-channels rapidly because channel binding sites mimic coordination of K+ ions in water. Highly selective ion discrimination should occur when binding sites form rigid cavities that match K+, but not the smaller Na+, ion size or when binding sites are composed of specific chemical groups. Although conceptually attractive, these(More)
Several groups, including our own, have found molecular dynamics (MD) calculations to result in the size of the pore of an outer membrane bacterial porin, OmpF, to be reduced relative to its size in the x-ray crystal structure. At the narrowest portion of its pore, loop L3 was found to move toward the opposite face of the pore, resulting in decreasing the(More)
The level of complexity with which any biological ion interaction mechanism can be investigated, whether it is a binding mechanism in proteins or a permeation mechanism in ion channels, is invariably limited by the state-of-the-art of our understanding of the characteristic properties of ion solvation. Currently, our understanding of the energetic(More)
Transferring Na(+) and K(+) ions from their preferred coordination states in water to states having different coordination numbers incurs a free energy cost. In several examples in nature, however, these ions readily partition from aqueous-phase coordination states into spatial regions having much higher coordination numbers. Here we utilize statistical(More)
The chemical property of methyl groups that renders them indispensable to biomolecules is their hydrophobicity. Quantum mechanical studies undertaken here to understand the effect of point substitutions on potassium (K-) channels illustrate quantitatively how methyl-induced polarization also contributes to biomolecular function. K- channels regulate(More)
The hydration of K(+) is studied using a hierarchy of theoretical approaches, including ab initio Born-Oppenheimer molecular dynamics and Car-Parrinello molecular dynamics, a polarizable force field model based on classical Drude oscillators, and a nonpolarizable fixed-charge potential based on the TIP3P water model. While models based more directly on(More)
Please note that Yu et al. (2010. J. Amer. Chem. Soc. 132:10847–10856) cited the wrong LJ parameter set used for Na+ and K+ ions (Andersen, O.S., and B. Roux, personal communication). In their study, Yu et al. (2010) did not use the parameter set from Beglov and Roux (1994. J. Chem. Phys. 100:9050–9063), but instead the parameter set from Noskov and Roux(More)
This paper describes the design and operation of an integrated multiscale computational environment for design of nanoscale ion channel semiconductors, the Ion Channel Workbench. The present work builds on an earlier multiscale calculation from our lab [1] in which we showed that this approach could provide a close correspondence to experimental(More)
The physical properties of lipid bilayers can be remodeled by a variety of environmental factors. Here we investigate using molecular dynamics simulations the specific effects of nanoscopic substrates or external contact points on lipid membranes. We expose palmitoyl-oleoyl phosphatidylcholine bilayers unilaterally and separately to various model nanosized(More)