Aggregation of polyalanine in a hydrophobic environment

Patricia Soto, Andrij Baumketner, Joan Emma Shea

Research output: Contribution to journalArticle

19 Citations (Scopus)

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 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
Article number134904
JournalJournal of Chemical Physics
Volume124
Issue number13
DOIs
StatePublished - Apr 7 2006

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Conformations
Agglomeration
peptides
Peptides
Dimerization
dimerization
replicas
Dimers
cyclohexane
electric dipoles
Molecular dynamics
Hydrogen bonds
coils
simulation
monomers
Monomers
dimers
interactions
Thermodynamics
hydrogen bonds

All Science Journal Classification (ASJC) codes

  • Atomic and Molecular Physics, and Optics

Cite this

Aggregation of polyalanine in a hydrophobic environment. / Soto, Patricia; Baumketner, Andrij; Shea, Joan Emma.

In: Journal of Chemical Physics, Vol. 124, No. 13, 134904, 07.04.2006.

Research output: Contribution to journalArticle

Soto, Patricia ; Baumketner, Andrij ; Shea, Joan Emma. / Aggregation of polyalanine in a hydrophobic environment. In: Journal of Chemical Physics. 2006 ; Vol. 124, No. 13.
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