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Relaxation Kinetics and the Glassiness of Native Proteins: Coupling of Timescales

Canan Baysal ^* and Ali Rana Atilgan 

^* Laboratory of Computational Biology, Faculty of Engineering and Natural Sciences, Sabanci University, Orhanli 34956, Tuzla, Istanbul, Turkey; and School of Engineering, Bogazici University, Bebek 34342, Istanbul, Turkey

Correspondence: Address reprint requests to Canan Baysal, Tel.: 90-216-483-9523; Fax: 90-216-483-9550; E-mail: canan{at}sabanciuniv.edu.

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. 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 timescales due to the activity along the envelope of the energy surface defining the folded protein. Another, with fast timescales, 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 three timescales become operative that the protein becomes active.

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