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A comparative study on the ability of two implicit solvent lipid models to predict transmembrane helix tilt angles.

ABSTRACT: Free-energy profiles describing the relative orientation of membrane proteins along predefined coordinates can be efficiently calculated by means of umbrella simulations. Such simulations generate reliable orientational distributions but are difficult to converge because of the very long equilibration times of the solvent and the lipid bilayer in explicit representation. Two implicit lipid membrane models are here applied in combination with the umbrella sampling strategy to the simulation of the transmembrane (TM) helical segment from virus protein U (Vpu). The models are used to study both orientation and energetics of this ?-helical peptide as a function of hydrophobic mismatch. We observe that increasing the degree of positive hydrophobic mismatch increased the tilt angle of Vpu. These findings agree well with experimental data and as such validate the solvation models used in this study.

SUBMITTER: Frank A

PROVIDER: S-EPMC3030950 | biostudies-literature | 2011 Jan

REPOSITORIES: biostudies-literature

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A comparative study on the ability of two implicit solvent lipid models to predict transmembrane helix tilt angles.

Frank Aaron A Andricioaei Ioan I

The Journal of membrane biology 20101209 1-2

Free-energy profiles describing the relative orientation of membrane proteins along predefined coordinates can be efficiently calculated by means of umbrella simulations. Such simulations generate reliable orientational distributions but are difficult to converge because of the very long equilibration times of the solvent and the lipid bilayer in explicit representation. Two implicit lipid membrane models are here applied in combination with the umbrella sampling strategy to the simulation of th ...[more]

PMID: 21152910

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