Desolvation barrier effects are a likely contributor to the remarkable diversity in the folding rates of small proteins.
The variation in folding rate among single-domain natural proteins is tremendous, but common models with explicit representations of the protein chain are either demonstrably insufficient or unclear as to their capability for rationalizing the experimental diversity in folding rates. In view of the critical role of water exclusion in cooperative folding, we apply native-centric, coarse-grained chain modeling with elementary desolvation barriers to investigate solvation effects on folding rates. For a set of 13 proteins, folding rates simulated with desolvation barriers cover approximately 4.6 orders of magnitude, spanning a range essentially identical to that observed experimentally. In contrast, folding rates simulated without desolvation barriers cover only approximately 2.2 orders of magnitude. Following a Hammond-like trend, the folding transition-state ensemble (TSE) of a protein model with desolvation barriers generally has a higher average number of native contacts and is structurally more specific, that is, less diffused, than the TSE of the corresponding model without desolvation barriers. Folding is generally significantly slower in models with desolvation barriers because of their higher overall macroscopic folding barriers as well as slower conformational diffusion speeds in the TSE that are approximately 1/50 times those in models without desolvation barriers. Nonetheless, the average root-mean-square deviation between the TSE and the native conformation is often similar in the two modeling approaches, a finding suggestive of a more robust structural requirement for the folding rate-limiting step. The increased folding rate diversity in models with desolvation barriers originates from the tendency of these microscopic barriers to cause more heightening of the overall macroscopic folding free-energy barriers for proteins with more nonlocal native contacts than those with fewer such contacts. Thus, the enhancement of folding cooperativity by solvation effects is seen as positively correlated with a protein's native topological complexity.
Ferguson
Allison
A
Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8.
Liu
Zhirong
Z
Chan
Hue Sun
HS
D008956:Models, Chemical; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
D011506:Proteins