模型多肽塌缩过程中的平衡和非平衡效应
Equilibrium and nonequilibrium effects in the collapse of a model polypeptide
摘要：
我们提出了一个模型蛋白质的疏水性崩溃作为一个级联的不同中间状态之间的下坡过渡的分子模拟结果。通过适当的谐波约束，不同的中间体是稳定的，允许明确计算的平衡自由能景观。非平衡崩溃轨迹独立模拟和比较计算的自由能表面上的扩散。我们发现，崩溃一般坚持这个表面，但定量协议是复杂的非平衡效应和依赖的扩散系数的表面上的位置。
英文摘要：
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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