title: Aggregation of polyalanine in a hydrophobic environment.
abstract: 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 alpha-helical conformations, while hydrogen bond interactions favor beta-sheet conformations. Possible pathways leading to the formation of alpha-helical and beta-sheet dimers are discussed.
authors.affiliation: Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA.
authors.forename: Patricia
authors.initials: P
authors.lastname: Soto
authors.forename: Andrij
authors.initials: A
authors.lastname: Baumketner
authors.forename: Joan-Emma
authors.initials: JE
authors.lastname: Shea
mesh_terms: D000409:Alanine / Q000737:chemistry*; D003198:Computer Simulation; D003510:Cyclohexanes / Q000737:chemistry; D019281:Dimerization; D057927:Hydrophobic and Hydrophilic Interactions; D010455:Peptides / Q000737:chemistry*; D017433:Protein Structure, Secondary
chemical_list: D003510:Cyclohexanes; D010455:Peptides; C506365:Cyclohexane; D000409:Alanine