The Barriers in the Bimolecular and Unimolecular Folding Reactions of the Dimeric Core Domain of Escherichia coli Trp Repressor Are Dominated by Enthalpic Contributions

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Abstract
The kinetic folding mechanism of the isolated dimerization domain of E. coli Trp repressor, [2−66]2 TR, consists of a nearly diffusion-limited association reaction to form a dimeric intermediate, I2, which is then converted to the native, folded dimeric species, N2 by a first-order folding step (preceding paper in this issue). The two transition states traversed in the folding of [2−66]2 TR were characterized by monitoring the folding and unfolding reactions by stopped-flow fluorescence as a function of temperature and urea. For both transition states, the barriers are dominated by the enthalpic component; the entropic component accelerates the association reaction but has little effect on the subsequent rearrangement reaction. The transition state between I2 and N2 is relatively nativelike, as determined by the sensitivity of the rate constants to denaturant. This study also highlights the key role of solvent entropy in determining the magnitude of the relative free energy of the transition states and the ground states. The positive entropy change for the I2 to N2 reaction, presumably arising from the release of solvent from hydrophobic surfaces, is the driving force for this final folding step, offsetting an unfavorable enthalpic term.