Abstract
Efficient protein folding implies a microscopic funnel-like multidimensional free-energy landscape. Macroscopically, conformational entropy reduction can manifest itself as part of an empirical barrier in the traditional view of folding, but experiments show that such barriers can also entail significant unfavorable enthalpy changes. This observation raises the puzzling possibility, irrespective of conformational entropy, that individual microscopic folding trajectories may encounter large uphill moves and thus the multidimensional free-energy landscape may not be funnel-like. Here, we investigate how nanoscale hydrophobic interactions might underpin this salient enthalpic effect in biomolecular assembly by computer simulations of the association of two preformed polyalanine or polyleucine helices in water. We observe a high, positive enthalpic signature at room temperature when the helix separation is less than a single layer of water molecules. Remarkably, this unfavorable enthalpy change, with a parallel increase in void volume, is largely compensated for by a concomitant increase in solvent entropy, netting only a small or nonexistent microscopic free-energy barrier. Thus, our findings suggest that high enthalpic folding barriers can be consistent with a funnel picture of folding and are mainly a desolvation phenomenon indicative of a cooperative mechanism of simultaneous formation of multiple side-chain contacts at the rate-limiting step.