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. 2008:443:213-27.
doi: 10.1007/978-1-59745-177-2_12.

Transmembrane protein models based on high-throughput molecular dynamics simulations with experimental constraints

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Transmembrane protein models based on high-throughput molecular dynamics simulations with experimental constraints

Andrew J Beevers et al. Methods Mol Biol. 2008.

Abstract

Elucidating the structure of transmembrane proteins domains with high-resolution methods is a difficult and sometimes impossible task. Here, we explain the method of combining a limited amount of experimental data with automated high-throughput molecular dynamics (MD) simulations of alpha-helical transmembrane bundles in an explicit lipid bilayer/water environment. The procedure uses a systematic conformational search of the helix rotation with experimentally constrained MDs simulations. The experimentally determined helix tilt and rotational angle of a labeled residue with site-specific infrared dichroism allows us to select a unique high-resolution model from a number of possible energy minima encountered in the systematic conformational search.

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