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Biophys. J. BioFAST: First Published May 6, 2005. doi:10.1529/biophysj.105.063305
© 2005 by the Biophysical Society.

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

Probing the local dynamics of nucleotide-binding pocket coupled to the global dynamics: myosin versus kinesin

Wenjun Zheng 1* and Bernard R Brooks 2

1 NIH
2 National Institutes of Health

* To whom correspondence should be addressed. E-mail: zhengwj{at}helix.nih.gov.

Submitted on March 22, 2005
Revised on April 15, 2005
Accepted on 25 April 2005


  Abstract
Based on the elastic network model, we develop a new analysis for protein complexes, which analyzes the local dynamics of a subsystem that is elastically coupled to a fluctuating environment. This method is applied to a comparative dynamical analysis of the nucleotide-binding pocket of two motor proteins - myosins and kinesins. In myosins, the observed structural changes in the nucleotide-pocket from the transition state to the rigor-like state are dominated by the lowest normal mode that involves significant movements in both switch I and switch II; in kinesins, the measured conformational changes in the nucleotide-pocket are also dominated by the lowest mode, which, however, only involves large movement in switch I. We then compute the global structural changes induced by the nucleotide-pocket deformations as described by the dominant 'pocket' mode, which yield encouraging results: in myosins, multiple hinge motions involving the opening/closing of the cleft between the upper and lower 50kda subdomains and the swinging movement of the converter are induced, which are dominated by precisely the same global mode that has been recently identified by us as important to the dynamical correlations among the nucleotide-pocket, the actin-binding site and the converter; in kinesins, the induced global conformational changes are well described by a highly collective global mode which hints for a dynamical pathway spanning from the nucleotide-pocket to the neck-linker via the H6 helix.

Key Words: elastic network model, kinesin, myosin, normal modes analysis, nucleotide-binding pocket




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Copyright © 2005 by the Biophysical Society.