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Biophys. J. BioFAST: First Published May 12, 2006. doi:10.1529/biophysj.106.085100
© 2006 by the Biophysical Society.

A more recent version of this article appeared on August 1, 2006.
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BIOPHYSICAL THEORY AND MODELING

Tryptophan Rotamers as Evidenced by X-Ray, Fluorescence Lifetimes and Molecular Dynamics Modeling

Samuel L. C. Moors 1, Mario Hellings 2, Marc De Maeyer 2, Yves Engelborghs 2 and Arnout Ceulemans 1*

1 University of Leuven
2 K.U. Leuven

* To whom correspondence should be addressed. E-mail: arnout.ceulemans{at}chem.kuleuven.be.

Submitted on March 15, 2006
Revised on April 25, 2006
Accepted on 25 April 2006


  Abstract
We investigated the native-state dynamics of the Bacillus caldolyticus cold shock protein mutant Bc-Csp L66E, using fluorescence and appropriate molecular dynamics methods. Two fluorescence lifetimes were found, the amplitudes of which agree very well with tryptophan rotamer populations, obtained from parallel tempering calculations. Rotamer lifetimes were predicted by transition state theory from high-temperature simulations. Transition pathways were extracted from the transition rates between individual rotameric states. The molecular dynamics also reveal the loop fluctuations in the native state.

Key Words: cold shock protein, dead-end elimination, molecular dynamics, parallel tempering, rotamer transition, transition path




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[Abstract] [Full Text] [PDF]


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Copyright © 2006 by the Biophysical Society.