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Biophys. J. BioFAST: First Published December 13, 2004. doi:10.1529/biophysj.104.050252
© 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

Relaxation Kinetics and the Glassiness of Native Proteins: Coupling of Time Scales

Canan Baysal 1* and Ali Rana Atilgan 2

1 Sabanci University
2 Bogazici University

* To whom correspondence should be addressed. E-mail: canan{at}sabanciuniv.edu.

Submitted on July 22, 2004
Revised on August 6, 2004
Accepted on 1 December 2004


  Abstract
We provide evidence that the onset of functional dynamics of folded proteins with elevated temperatures is associated with the effective sampling of its energy landscape under physiological conditions. The analysis is based on data describing the relaxation phenomena governing the backbone dynamics of bovine pancreatic trypsin inhibitor derived from molecular dynamics simulations, previously reported by us [Biophys. J., 83, 699-705, 2002]. By representing the backbone dynamics of the folded protein by three distinct regimes, it is possible to decompose its seemingly complex dynamics, described by a stretch exponential decay of the backbone motions. Of these three regimes, one is associated with the slow time scales due to the activity along the envelope of the energy surface defining the folded protein. Another, with fast time scales, is due to the activity along the pockets decorating the folded-state envelope. The intermediate regime emerges at temperatures where jumps between the pockets become possible. It is at the temperature window where motions corresponding to all the three time scales become operative that the protein becomes active.

Key Words: dynamical transition, energy landscape, relaxation spectrum, residue fluctuations, temperature modulation




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Copyright © 2004 by the Biophysical Society.