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IMPALA: A simple restraint field to simulate the biological membrane in molecular structure studies
Author(s) -
Ducarme Ph.,
Rahman M.,
Brasseur R.
Publication year - 1998
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/(sici)1097-0134(19980301)30:4<357::aid-prot3>3.0.co;2-g
Subject(s) - bilayer , lipid bilayer , membrane , monte carlo method , molecular dynamics , biological membrane , chemical physics , folding (dsp implementation) , perpendicular , chemistry , molecule , biophysics , biological system , statistical physics , physics , computational chemistry , mathematics , geometry , biology , engineering , biochemistry , statistics , organic chemistry , electrical engineering
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 α 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). Proteins 30:357–371, 1998. © 1998 Wiley‐Liss, Inc.