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Originally published as Biophys J. BioFAST on July 29, 2005.
doi:10.1529/biophysj.105.065904
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Biophysical Journal 89:2395-2401 (2005)
© 2005 The Biophysical Society

The Role of Shape in Determining Molecular Motions

Mingyang Lu * and Jianpeng Ma * {dagger}

* Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030; and {dagger} Department of Bioengineering, Rice University, Houston, Texas 77005

Correspondence: Address reprint requests to Jianpeng Ma, 1 Baylor Plaza, BCM-125, Baylor College of Medicine, Houston, TX 77030. Tel.: 713-798-8187; Fax: 713-796-9438; E-mail: jpma{at}bcm.tmc.edu.

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 molecules 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.




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