Equilibrium and nonequilibrium effects in the collapse of a model polypeptide

Details Equilibrium and nonequilibrium effects in the collapse of a model polypeptide Equilibrium and nonequilibrium effects in the collapse of a model polypeptide

2009-02-16

arxiv.org/abs/0902.2763v1

Physics

Condensed Matter

Soft Condensed Matter

3 figures

Scientific paper

10.1103/PhysRevLett.102.108101

We present results of molecular simulations of a model protein 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.

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