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Biophys. J. BioFAST: First Published July 29, 2005. doi:10.1529/biophysj.105.065904
© 2005 by the Biophysical Society.

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

The Role of Shape in Determining Molecular Motions

mingyang lu 1 and Jianpeng Ma 1*

1 Baylor College of Medicine

* To whom correspondence should be addressed. E-mail: jpma{at}bcm.tmc.edu.

Submitted on May 5, 2005
Revised on June 9, 2005
Accepted on 15 July 2005


  Abstract
We examined the role of molecular shape in determining the patterns of low-frequency deformational motions of biological macromolecules. The low-frequency subspace of eigenvectors in normal mode analysis was found to be robustly similar upon randomization of the Hessian matrix elements as long as the structure of the matrix is maintained, which indicates that the global shape of molecule plays a more dominant role in determining the highly anisotropic low-frequency motions than the absolute values of stiffness and directionality of local interactions. The results provided a quantitative foundation for the validity of elastic normal mode analysis.

Key Words: Conformational motion, anisotropy, normal mode analysis, shape




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Copyright © 2005 by the Biophysical Society.