Diffusive model of protein folding dynamics with Kramers turnover in rate
Diffusive model of protein folding dynamics with Kramers turnover in rate
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DOI：
10.1103/physrevlett.96.228104
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发表时间：
2006-06-09
影响因子：
8.6
通讯作者：
Hummer, G
中科院分区：
文献类型：
--
作者：
Best, RB;Hummer, G
我们用一个粗大的聚合物模型研究了一个三螺旋集束蛋白的折叠动力学。折叠动力学可以由沿着选择来捕捉过渡态的反应坐标的一维扩散来准确地表示。通过改变溶剂摩擦力，我们证明了位置相关的扩散系数是由粗略能量面上的微观跃迁决定的。在这些微观动力学中，通过扩散系数来调节折叠速度，在中间摩擦时折叠速度的最大值被解释为“Kramers周转”；整体折叠即使接近于零摩擦也保持扩散。对于水摩擦，我们发现Kramers折叠模型中的“尝试频率”(或“速度限制”)约为2亩S(-1)，激活势垒约为2k(B)T，折叠过渡路径持续时间约为100 ns，比折叠时间约为10亩S少2个数量级。
We study the folding kinetics of a three-helix bundle protein using a coarse polymer model. The folding dynamics can be accurately represented by one-dimensional diffusion along a reaction coordinate selected to capture the transition state. By varying the solvent friction, we show that position-dependent diffusion coefficients are determined by microscopic transitions on a rough energy landscape. A maximum in the folding rate at intermediate friction is explained by "Kramers turnover" in these microscopic dynamics that modulates the rate via the diffusion coefficient; overall folding remains diffusive even close to zero friction. For water friction, we find that the "attempt frequency" (or "speed limit") in a Kramers model of folding is about 2 mu s(-1), with an activation barrier of about 2k(B)T, and a folding transition path duration of approximate to 100 ns, 2 orders of magnitude less than the folding time of approximate to 10 mu s.