A molecular dynamics study of the formation, stability, and oligomerization state of two designed coiled coils: Possibilities and limitations

Pineiro, A., Villa, A., Vagt, T., Koksch, B. and Mark, A. E. (2005) A molecular dynamics study of the formation, stability, and oligomerization state of two designed coiled coils: Possibilities and limitations. Biophysical Journal, 89 6: 3701-3713. doi:10.1529/biophysj.104.055590


Author Pineiro, A.
Villa, A.
Vagt, T.
Koksch, B.
Mark, A. E.
Title A molecular dynamics study of the formation, stability, and oligomerization state of two designed coiled coils: Possibilities and limitations
Journal name Biophysical Journal   Check publisher's open access policy
ISSN 0006-3495
Publication date 2005-12
Year available 2005
Sub-type Article (original research)
DOI 10.1529/biophysj.104.055590
Volume 89
Issue 6
Start page 3701
End page 3713
Total pages 13
Place of publication Bethesda
Publisher Biophysical Society
Language eng
Abstract The formation, relative stability, and possible stoichiometries of two (self-) complementary peptide sequences (B and E) designed to form either a parallel homodimeric (B + B) or an antiparallel heterodimeric ( B + E) coiled coil have been investigated. Peptide B shows a characteristic coiled coil pattern in circular dichroism spectra at pH 7.4, whereas peptide E is apparently random coiled under these conditions. The peptides are complementary to each other, with peptide E forming a coiled coil when mixed with peptide B. Molecular dynamics simulations show that combinations of B + B and B + E readily form a dimeric coiled coil, whereas E + E does not fall in line with the experimental data. However, the simulations strongly suggest the preferred orientation of the helices in the homodimeric coiled coil is antiparallel, with interactions at the interface quite different to that of the idealized model. In addition, molecular dynamics simulations suggest equilibrium between dimers, trimers, and tetramers of alpha-helices for peptide B.
Keyword Biophysics
Alpha-helix Dipole
Leucine-zipper
Transmembrane Domain
Crystal-structure
Membrane-fusion
Protein
Simulations
Association
Assemblies
Program
Q-Index Code C1

Document type: Journal Article
Sub-type: Article (original research)
Collections: Excellence in Research Australia (ERA) - Collection
School of Chemistry and Molecular Biosciences
 
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