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Biophys. J. BioFAST: First Published September 8, 2005. doi:10.1529/biophysj.104.055590
© 2005 by the Biophysical Society.

A more recent version of this article appeared on December 1, 2005.
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BIOPHYSICAL THEORY AND MODELING

A Molecular Dynamics Study of the Formation, Stability and Oligomerization State of two Designed Coiled Coils: Possibilities and limitations

Angel Pineiro 1, Alessandra Villa 2, Toni Vagt 3, Beate Koksch 3 and Alan E Mark 4*

1 Nacional Autónoma de México
2 J. W. Goethe University
3 Free University Berlin
4 University of Groningen

* To whom correspondence should be addressed. E-mail: a.e.mark{at}rug.nl.

Submitted on November 5, 2004
Revised on March 14, 2005
Accepted on 8 August 2005


  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 while peptide E is apparently random coil under these conditions. The peptides are complementary to each other with peptide E forming a coiled coil when mixed with peptide B. Molecular dynamics (MD) simulations show that combinations of B + B and B + E readily form a dimeric coiled coil whereas E + E does not in line with the experimental data. However, the simulations strongly suggest the preferred orientation of the helices in the homodimeric coiled coil is anti-parallel with interactions at the interface quite different to that of the idelized model. In addition, MD simulations suggest equilibrium between dimers, trimers and tetramers of {alpha}-helices for peptide B.

Key Words: Molecular dynamics, coiled coils, protein folding




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O. J. Brown, S. A. Lopez, A. O. Fuller, and T. Goodson III
Formation and Reversible Dissociation of Coiled Coil of Peptide to the C-Terminus of the HSV B5 Protein: A Time-Resolved Spectroscopic Analysis
Biophys. J., August 1, 2007; 93(3): 1068 - 1078.
[Abstract] [Full Text] [PDF]


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Copyright © 2005 by the Biophysical Society.