Equilibrium and nonequilibrium effects in the collapse of a model polypeptide.
We present results of molecular simulations of a model polypeptide whose hydrophobic collapse proceeds as a cascade of downhill transitions between distinct intermediate states. Different intermediates are stabilized by means of appropriate harmonic constraints, allowing explicit calculation of the equilibrium free energy landscape. Nonequilibrium collapse trajectories are simulated independently and compared to diffusion on the calculated free energy surface. We find that collapse generally adheres to this surface, but quantitative agreement is complicated by nonequilibrium effects and by dependence of the diffusion coefficient on position on the surface.
Denesyuk
Natalia A
NA
Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, USA.
Weeks
John D
JD
D003198:Computer Simulation; D057927:Hydrophobic and Hydrophilic Interactions; D007700:Kinetics; D008956:Models, Chemical; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D013816:Thermodynamics
D010455:Peptides