Hydrophobic association of α-helices, steric dewetting, and enthalpic barriers to protein folding

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.

Theoretical and experimental demonstration of the importance of specific nonnative interactions in protein folding

“…For these reasons, the pairwise hydrophobic interactions in our model should provide predictive information about the kinetic process leading up to the folding transition state, i.e., before tight packing becomes overwhelmingly important. For the same reasons, however, our model may be less adequate for unfolding kinetics and overall folding cooperativity (which are not the focus of this study) because the present approach does not consider many-body interactions that are likely important for modeling tight packing and highly cooperative behaviors (44)(45)(46)(47)(48). The simulations and experimental work presented here have therefore focused only on folding rates and not unfolding rates or overall thermodynamic stability.…”

Dynamics of one-state downhill protein folding

“…S6). In principle, D could change with temperature due to changes in water viscosity and steric hindrance during peptide bond rotations [together Ϸ24 kJ/mol (35)], steric dewetting (36), and the roughness in the energy landscape that is smoothed out by the free energy projection. The latter could also make D decrease along the reaction coordinate (2) and produce superArrhenius temperature dependence (37).…”

Desolvation Barrier Effects Are a Likely Contributor to the Remarkable Diversity in the Folding Rates of Small Proteins

“…Figure 1b provides an assessment of this additivity assumption. Here, the PMF between two 20-residue α-helices simulated using an explicit-water model 78 is contrasted with an effective potential constructed for the same manybody system based on assuming pairwise additivitiy of our db potential. Figure 1b shows that the overall barrier to helix-helix association (at separation ∼ 1 nm) computed from explicit-water simulation (dashed curve) is lower than that calculated by a simple summation of contributions from our implicit-water potential for individual residue pairs (continuous curve).…”