Dehydration-driven solvent exposure of hydrophobic surfaces as a driving force in peptide folding

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 104; no. 39; pp. 15230 - 15235
• Main Authors: Daidone, Isabella, Ulmschneider, Martin B, Di Nola, Alfredo, Amadei, Andrea, Smith, Jeremy C
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 25.09.2007; National Acad Sciences
• Subjects: Amyloid - chemistry; Atoms; Biological Sciences; Biophysics; Computer Simulation; Diffusion; Free energy; Humans; Hydrogen bonds; Kinetics; Mathematical minima; Modeling; Models, Statistical; Molecular Conformation; Molecules; Peptides; Peptides - chemistry; Physical Sciences; Prions - chemistry; Protein Denaturation; Protein Folding; Protein Structure, Secondary; Proteins; Simulation; Simulations; Solvents; Solvents - chemistry; Surface areas; Thermodynamics; Water - chemistry
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.0701401104

Recent work has shown that the nature of hydration of pure hydrophobic surfaces changes with the length scale considered: water hydrogen-bonding networks adapt to small exposed hydrophobic species, hydrating or "wetting" them at relatively high densities, whereas larger hydrophobic areas are "dewetted" [Chandler D (2005), Nature 29:640-647]. Here we determine whether this effect is also present in peptides by examining the folding of a β-hairpin (the 14-residue amyloidogenic prion protein H1 peptide), using microsecond time-scale molecular dynamics simulations. Two simulation models are compared, one explicitly including the water molecules, which may thus adapt locally to peptide configurations, and the other using a popular continuum approximation, the generalized Born/surface area implicit solvent model. The results obtained show that, in explicit solvent, peptide conformers with high solvent-accessible hydrophobic surface area indeed also have low hydration density around hydrophobic residues, whereas a concomitant higher hydration density around hydrophilic residues is observed. This dewetting effect stabilizes the fully folded β-hairpin state found experimentally. In contrast, the implicit solvent model destabilizes the fully folded hairpin, tending to cluster hydrophobic residues regardless of the size of the exposed hydrophobic surface. Furthermore, the rate of the conformational transitions in the implicit solvent simulation is almost doubled with respect to that of the explicit solvent. The results suggest that dehydration-driven solvent exposure of hydrophobic surfaces may be a significant factor determining peptide conformational equilibria.