The dimerization of polyalanine peptides in a hydrophobic environment was explored using replica exchange molecular dynamics simulations.A nonpolar solvent (cyclohexane) was used to mimic,among other hydrophobic environments,the hydrophobic interior of a membrane in which the peptides are fully embedded.Our simulations reveal that while the polyalanine monomer preferentially adopts a beta-hairpin conformation,dimeric phases exist in an equilibrium between random coil,alpha-helical,beta-sheet,and beta-hairpin states.A thermodynamic characterization of the dimeric phases reveals that electric dipole-dipole interactions and optimal side-chain packing stabilize a-helical conformations,while hydrogen bond interactions favor beta-sheet conformations.Possible pathways leading to the formation of a-helical and beta-sheet dimers are discussed.
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