Aggregation of polyalanine in a hydrophobic environment

Patricia Soto, Andrij Baumketner, Joan Emma Shea

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20 Scopus citations


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 Β -hairpin conformation, dimeric phases exist in an equilibrium between random coil, α -helical, Β -sheet, and Β -hairpin states. A thermodynamic characterization of the dimeric phases reveals that electric dipole-dipole interactions and optimal side-chain packing stabilize α -helical conformations, while hydrogen bond interactions favor Β -sheet conformations. Possible pathways leading to the formation of α -helical and Β -sheet dimers are discussed.

Original languageEnglish (US)
Article number134904
JournalJournal of Chemical Physics
Issue number13
StatePublished - Apr 7 2006

All Science Journal Classification (ASJC) codes

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry


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