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Biophys. J. BioFAST: First Published December 13, 2004. doi:10.1529/biophysj.104.051342
© 2004 by the Biophysical Society.

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

How similar are protein folding and protein binding nuclei? Examination of fluctuations of energy hot spots and conserved residues

Turkan Haliloglu 1, Ozlem Keskin 2, Buyong Ma 3 and Ruth Nussinov 4*

1 bogazici university
2 koc university and NCI at Frederick
3 NCI-Frederick
4 Tel-Aviv University and NCI-Frederick

* To whom correspondence should be addressed. E-mail: ruthn{at}nciiris.ncifcrf.gov.

Submitted on August 13, 2004
Revised on September 14, 2004
Accepted on 24 November 2004


  Abstract
The underlying physico-chemical principles of the interactions between domains in protein folding are similar to those between protein molecules in binding. Here we show that conserved residues and experimental hot spots at inter-molecular binding interfaces overlap residues that vibrate with high frequencies. Similarly, conserved residues and hot spots are found in protein cores and are also observed to vibrate with high frequencies. In both cases, these residues contribute significantly to the stability. Hence, these observations validate the proposition that binding and folding are similar processes. In both packing plays a critical role, rationalizing the residue conservation and the experimental alanine scanning hot spots. We further show that high frequency vibrating residues distinguish between protein binding sites and the remainder of the protein surface.

Key Words: Gaussian Network Model (GNM), binding site prediction, fluctuations, hot spots, protein binding and folding, protein-protein interactions




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Copyright © 2004 by the Biophysical Society.