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A program for flexible lattice energy minimization ( FLATER ) and its application to the study of protein–lipid copacking
Author(s) -
Wang Jing,
Pullman Alberte
Publication year - 1991
Publication title -
international journal of quantum chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.484
H-Index - 105
eISSN - 1097-461X
pISSN - 0020-7608
DOI - 10.1002/qua.560400728
Subject(s) - molecule , energy minimization , chemistry , chemical physics , membrane , lattice (music) , helix (gastropod) , lattice energy , crystallography , computational chemistry , crystal structure , physics , organic chemistry , ecology , biochemistry , snail , acoustics , biology
In distinction to the classical strategy of molecular modeling minimizing the energy of a small number of molecules, a procedure ( FLATER ) is developed to treat an aggregate of molecules organized in an array. The molecular energy of a unit cell in the array is minimized relative to a set of general coordinates defining the conformations and arrangement of molecules and the global geometry of the lattice, while allowing complete flexibility of the system. A test performed on the 1,2‐dilauroyl‐ DL ‐phosphatidylethanolamine:acetic acid crystal of known structure shows that the molecular structures obtained by the procedure are reliable. An application of the procedure to the study of the copacking of lipids and hydrophobic polypetide α‐helices in membranes is reported. Its results indicate that the interplay of the interactions that exist in the hydrocarbon region of a membrane concur to favor the assemblage of the helices rather than their dispersion in the lipid phase. This situation springs from the dominance of the helix–helix interactions, insured by the nature and number of the hydrophobic amino acid involved. This program is particularly well suited to studies of the interactions and architecture of molecules in multicomponent membranes.