Phase Behavior of a Lattice Hydrophobic Oligomer in Explicit Water

Consistent Treatment of Hydrophobicity in Protein Lattice Models Accounts for Cold Denaturation

The hydrophobic effect stabilizes the native structure of proteins by minimizing the unfavorable interactions between hydrophobic residues and water through the formation of a hydrophobic core. Here, we include the entropic and enthalpic contributions of the hydrophobic effect explicitly in an implicit solvent model. This allows us to capture two important effects: a length-scale dependence and a temperature dependence for the solvation of a hydrophobic particle. This consistent treatment of the hydrophobic effect explains cold denaturation and heat capacity measurements of solvated proteins.

Thermal stability of hydrophobic helical oligomers: a lattice simulation study in explicit water

We investigate the thermal stability of helical hydrophobic oligomers using a three-dimensional, water-explicit lattice model and the Wang-Landau Monte Carlo method. The degree of oligomer helicity is controlled by the parameter ε(mm) < 0, which mimics monomer-monomer hydrogen bond interactions leading to the formation of helical turns in atomistic proteins. We vary |ε(mm)| between 0 and 4.5 kcal/mol and therefore investigate systems ranging from flexible homopolymers (i.e., those with no secondary structure) to helical oligomers that are stable over a broad range of temperatures. We find that systems with |ε(mm)| ≤ 2.0 kcal/mol exhibit a broad thermal unfolding transition at high temperature, leading to an ensemble of random coils. In contrast, the structure of conformations involved in a second, low-temperature, transition is strongly dependent on |ε(mm)|. Weakly helical oligomers are observed when |ε(mm)| ≤ 1.0 kcal/mol and exhibit a low-temperature, cold-unfolding-like transition to an ensemble of strongly water-penetrated globular conformations. For higher |ε(mm)| (1.7 kcal/mol ≤ |ε(mm)| ≤ 2.0 kcal/mol), cold unfolding is suppressed, and the low-temperature conformational transition becomes a "crystallization", in which a "molten" helix is transformed into a defect-free helix. The molten helix preserves ≥50% of the helical contacts observed in the "crystal" at a lower temperature. When |ε(mm)| = 4.5 kcal/mol, we find that conformational transitions are largely suppressed within the range of temperatures investigated.