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Methods Mol Biol. 2013;1063:125-42. doi: 10.1007/978-1-62703-583-5_7.

Solvation models and computational prediction of orientations of peptides and proteins in membranes.

Author information

1
Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA.

Abstract

Membrane-associated peptides and proteins function in the highly heterogeneous environment of the lipid bilayer whose physico-chemical properties change non-monotonically along the bilayer normal. To simulate insertion of peptides and proteins into membranes and correctly reproduce the energetics of this process, an adequate solvation model and physically realistic representation of the lipid bilayer should be employed. We present a brief overview of the existing solvation models and their application for prediction of binding affinities and orientations of proteins in membranes. Particular emphasis is placed on the recently proposed PPM method, the corresponding web server, and the OPM database that were designed for positioning in membranes of integral and peripheral proteins with known three-dimensional structures.

PMID:
23975775
DOI:
10.1007/978-1-62703-583-5_7
[Indexed for MEDLINE]

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