Dehydration-driven solvent exposure of hydrophobic surfaces as a driving force in peptide folding.
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 beta-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 beta-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.
Daidone
Isabella
I
Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany.
Ulmschneider
Martin B
MB
Di Nola
Alfredo
A
Amadei
Andrea
A
Smith
Jeremy C
JC
D000682:Amyloid / Q000737:chemistry; D003198:Computer Simulation; D004058:Diffusion; D006801:Humans; D007700:Kinetics; D015233:Models, Statistical; D008968:Molecular Conformation; D010455:Peptides / Q000737:chemistry*; D011328:Prions / Q000737:chemistry; D011489:Protein Denaturation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D012997:Solvents / Q000737:chemistry*; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
D000682:Amyloid; D010455:Peptides; D011328:Prions; D012997:Solvents; D014867:Water