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 language | English |
|---|---|
| Article number | 134904 |
| Journal | Journal of Chemical Physics |
| Volume | 124 |
| Issue number | 13 |
| DOIs | |
| State | Published - Apr 7 2006 |
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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 journal › Article
}
TY - JOUR
T1 - Aggregation of polyalanine in a hydrophobic environment
AU - Soto, Patricia
AU - Baumketner, Andrij
AU - Shea, Joan Emma
PY - 2006/4/7
Y1 - 2006/4/7
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=34547648530&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=34547648530&partnerID=8YFLogxK
U2 - 10.1063/1.2179803
DO - 10.1063/1.2179803
M3 - Article
C2 - 16613474
AN - SCOPUS:34547648530
VL - 124
JO - Journal of Chemical Physics
JF - Journal of Chemical Physics
SN - 0021-9606
IS - 13
M1 - 134904
ER -