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Protein Folding Kinetics:  Barrier Effects in Chemical and Thermal Denaturation Experiments

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Contribution from the Department of Chemistry and Biochemistry, and Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland 20742
Cite this: J. Am. Chem. Soc. 2007, 129, 17, 5673–5682
Publication Date (Web):April 10, 2007
https://doi.org/10.1021/ja0689740
Copyright © 2007 American Chemical Society
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    Abstract

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    Recent experimental work on fast protein folding brings about an intriguing paradox. Microsecond-folding proteins are supposed to fold near or at the folding speed limit (downhill folding), but yet their folding behavior seems to comply with classical two-state analyses, which imply the crossing of high free energy barriers. However, close inspection of chemical and thermal denaturation kinetic experiments in fast-folding proteins reveals systematic deviations from two-state behavior. Using a simple one-dimensional free energy surface approach we find that such deviations are indeed diagnostic of marginal folding barriers. Furthermore, the quantitative analysis of available fast-kinetic data indicates that many microsecond-folding proteins fold downhill in native conditions. All of these proteins are then promising candidates for an atom-by-atom analysis of protein folding using nuclear magnetic resonance.1 We also find that the diffusion coefficient for protein folding is strongly temperature dependent, corresponding to an activation energy of ∼1 kJ·mol-1 per protein residue. As a consequence, the folding speed limit at room temperature is about an order of magnitude slower than the ∼ 1 μs estimates from high-temperature T-jump experiments. Our analysis is quantitatively consistent with the available thermodynamic and kinetic data on slow two-state folding proteins and provides a straightforward explanation for the apparent fast-folding paradox.

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