Atomic solvation parameters for proteins in a membrane environment. Application to transmembrane α-helices

DE Nolde, AS Arseniev, G Vergoten… - Journal of Biomolecular …, 1997 - Taylor & Francis
DE Nolde, AS Arseniev, G Vergoten, RG Efremov
Journal of Biomolecular Structure and Dynamics, 1997Taylor & Francis
Several sets of atomic solvation parameters imitating:(i) nonpolar environment of
hydrocarbon core of a membrane,(ii) aqueous solution, and (iii) weakly-polar solvents have
been developed. The parameters have been incorporated into the ECEPP/2 and CHARMM
force fields and employed in non-restrained Monte Carlo and molecular dynamics
simulations of membrane-spanning a-helical peptides (segment A of bacteriorhodopsin,
melittin). Through these simulations, the structure and energetics of the helices have been …
Abstract
Several sets of atomic solvation parameters imitating: (i) nonpolar environment of hydrocarbon core of a membrane, (ii) aqueous solution, and (iii) weakly-polar solvents have been developed. The parameters have been incorporated into the ECEPP/2 and CHARMM force fields and employed in non-restrained Monte Carlo and molecular dynamics simulations of membrane-spanning a-helical peptides (segment A of bacteriorhodopsin, melittin). Through these simulations, the structure and energetics of the helices have been examined as a function of the solvation term in the potential energy function. For the peptides under study, the set (i) of atomic solvation parameters reveals good retention of the a-helical conformation. By contrast, the simulations in vacuum or with the parameters imitating a polar solvent (sets (ii) or (iii)) show fast helix destabilization and tight packing of the structure accompanied by significant decreasing of the surface area accessible to solvent. Increased helical propensity for amino acid residues, population of side-chain rotamers as well as hydrogen-bonding pattern in nonpolar membrane-like environment agree well with available experimental and computational data. The problems related to further applications of the membrane-mimicking sets of atomic solvation parameters to simulations of membrane proteins and peptides are addressed.
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