help button home button Biophys. J.
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Briki, F.
Right arrow Articles by Etchebest, C.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Briki, F.
Right arrow Articles by Etchebest, C.

Biophys J, October 2002, p. 1774-1783, Vol. 83, No. 4

A Procedure for Refining a Coiled Coil Protein Structure Using X-Ray Fiber Diffraction and Modeling

Fatma Briki,* Jean Doucet,* and Catherine Etchebestdagger

 *LURE, Bât 209D, Centre Universitaire Paris-Sud, F-91898 Orsay Cedex, France;  dagger Bioinformatique Génomique et Moléculaire, INSERM U436, Université Paris 7, 75251 Paris Cedex 05, France

We describe a combined use of experimental and simulation techniques to configure side chains in a coiled coil structure. As already demonstrated in a previous work, x-ray diffraction patterns from hard alpha -keratin fibers in the 5.15 Å meridian zone reflect the global configuration of the chi 1 dihedral angle of the coiled coil side chains. Molecular simulations, such as energy minimization and molecular dynamics, and rotameric representation in the PDB, are used here on a heterodimeric coiled coil to investigate the dihedral angle distribution along the sequence. Different procedures have been used to build the structure, the quality assessment was based on the agreement between the simulated diffraction patterns and the experimental ones in the fingerprint region of coiled coils (5.15 Å). The best one for building a realistic coiled coil structure consists of placing the side chains using molecular dynamics (MD) simulations, followed by side chain positioning using SMD or SCWRL procedures. The side chains and the backbone are equilibrated during the MD until they reach an equilibrium state for the t/g+ ratio. Positioning the side chains on the resulting backbone, using the above procedures, gives rise to a well-defined 5.15 Å meridian reflection.

Biophys J, October 2002, p. 1774-1783, Vol. 83, No. 4
© 2002 by the Biophysical Society   0006-3495/02/10/1774/10  $2.00


This article has been cited by other articles:


Home page
 Biophys. JHome page
A. Pineiro, A. Villa, T. Vagt, B. Koksch, and A. E. Mark
A Molecular Dynamics Study of the Formation, Stability, and Oligomerization State of Two Designed Coiled Coils: Possibilities and Limitations
Biophys. J., December 1, 2005; 89(6): 3701 - 3713.
[Abstract] [Full Text] [PDF]

Home page
 J. Cell Biol.Home page
K. M. Bernot, C.-H. Lee, and P. A. Coulombe
A small surface hydrophobic stripe in the coiled-coil domain of type I keratins mediates tetramer stability
J. Cell Biol., March 14, 2005; 168(6): 965 - 974.
[Abstract] [Full Text] [PDF]


HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
Copyright © 2002 by the Biophysical Society.