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Molecular dynamics calculations were carried out on models of two synthetic leucine-serine ion channels: a tetrameric bundle with sequence (LSLLLSL)(3)NH(2) and a hexameric bundle with sequence (LSSLLSL)(3)NH(2). Each protein bundle is inserted in a palmitoyloleoylphosphatidylcholine bilayer membrane and solvated by simple point charge water molecules inside the pore and at both mouths. Both systems appear to be stable in the absence of an electric field during the 4 ns of molecular dynamics simulation. The water motion in the narrow pore of the four-helix bundle is highly restricted and may provide suitable conditions for proton transfer via a water wire mechanism. In the wider hexameric pore, the water diffuses much more slowly than in bulk but is still mobile. This, along with the dimensions of the pore, supports the observation that this peptide is selective for monovalent cations. Reasonable agreement of predicted conductances with experimentally determined values lends support to the validity of the simulations.

Original publication

DOI

10.1016/S0006-3495(99)77077-3

Type

Journal article

Journal

Biophys J

Publication Date

11/1999

Volume

77

Pages

2400 - 2410

Keywords

Amino Acid Sequence, Cell Membrane, Ion Channels, Leucine, Molecular Dynamics Simulation, Molecular Sequence Data, Phosphatidylcholines, Porosity, Protein Structure, Secondary, Serine, Substrate Specificity, Water