PMID: 9533620Apr 9, 1998Paper

IMPALA: a simple restraint field to simulate the biological membrane in molecular structure studies

Proteins
P DucarmeRobert Brasseur

Abstract

The lipid bilayer is crucial for the folding of integral membrane proteins. This article presents an empirical method to account for water-lipid interfaces in the insertion of molecules interacting with bilayers. The interactions between the molecule and the bilayer are described by restraint functions designed to mimic the membrane effect. These functions are calculated for each atom and are proportional to the accessible surface of the latter. The membrane is described as a continuous medium whose properties are varying along the axis perpendicular to the bilayer plane. The insertion is analyzed by a Monte Carlo procedure applied to the restraint functions. The method was successfully applied to small alpha peptides of known configurations. It provides insights of the behaviors of the peptide dynamics that cannot be obtained with statistical approaches (e.g., hydropathy analysis).

Citations

Sep 15, 2005·Journal of Bacteriology·Karsten R O HazlettJustin D Radolf
Sep 16, 2006·Proceedings of the National Academy of Sciences of the United States of America·Ngoc-Quynh-Nhu NguyenIngrid Struman
Jul 3, 2007·BMC Structural Biology·Andrei L LomizeHenry I Mosberg
Mar 29, 2011·Journal of Chemical Information and Modeling·Andrei L LomizeHenry I Mosberg
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Jan 6, 2006·Proteins·Madhusoodanan MottamalThemis Lazaridis
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Feb 5, 2011·Biochimica Et Biophysica Acta·Myriam OuberaiMarie-Paule Mingeot-Leclercq
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Nov 9, 2005·Biophysical Journal·L LinsR Brasseur
Jun 1, 2007·Biochimica Et Biophysica Acta·N FaM-P Mingeot-Leclercq

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