title: Protein folding kinetics: barrier effects in chemical and thermal denaturation experiments.
abstract: 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 approximately 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 approximately 1 micros 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.
authors.affiliation: Department of Chemistry and Biochemistry, and Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland 20742, USA.
authors.forename: Athi N
authors.initials: AN
authors.lastname: Naganathan
authors.forename: Urmi
authors.initials: U
authors.lastname: Doshi
authors.forename: Victor
authors.initials: V
authors.lastname: Muñoz
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D004735:Energy Transfer; D019277:Entropy; D007700:Kinetics; D008956:Models, Chemical; D011489:Protein Denaturation / Q000187:drug effects; D017510:Protein Folding; D013499:Surface Properties; D013696:Temperature; D013816:Thermodynamics