Computer Modeling and Theoretical Studies of Biopolymers

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Summary: A series of classical molecular dynamics simulations of a water wire in a DPPC bilayer yielded lifetimes tau of up to 90 ps, with <tau> = 37 ? 8 ps (not including wires that broke within 4 ps). This is sufficiently long to conduct protons across the bilayer through a quantum mechanical hopping mechanism, similar to proton conduction in ice. Lifetimes of wires in the octane region of a water/octane/water sandwich-like arrangement were qualitatively similar (<tau> = 36 ?3 ps), demonstrating the usefulness of the water/octane system in exploratory membrane studies. A report of this research has been submitted for publication to the Journal of Chemical Physics. The asymmetric boundary condition P21 was shown to yield equivalent results to P1 in molecular dynamics simulations of bulk water, a water/vacuum interface, and pure DPPC bilayers with an equal numbers of lipids per leaflet; equivalence of Pc and P1 was also demonstrated for the former two systems. P21 was further tested in simulations involving the spreading of an octane film on water, and equilibration of a DPPC bilayer from an initial condition containing different number of lipids in the two leaflets. Lastly, a simulation of a DOPC/melittin membrane in P21 showed significant redistribution of lipids from an ostensibly reasonable initial condition. These results highlight the utility of simulating membranes and other heterogeneous interfacial systems with asymmetric boundary conditions. A report of this research has been submitted for publication to the Biophysical Journal. Results from a 20 ns molecular dynamcis simulation of a DPPC bilayer were compared with simple models of lipid dynamics. A consistent picture emerges. Individual lipids, through fast internal motions, average themselves into relatively cylindrical shapes on the 100 ps time scale, and wobble in a cone-like potential on the ns time scale. These motions take place in a highly fluid environment, much like a liquid alkane. Lateral diffusion of the lipids is on a significantly longer time scale because of restrictions at the bilayer/water interface, not because the interior of the bilayer is highly viscous. A report of this research has been submitted for publication to Accounts of Chemical Research. Simulations of aquaporin in a DOPC bilayer have commenced. Preliminary results show transport of water consistent with experimental observations, and potentially explain why aquaporin can conduct protons, but not water.