Nonexponential Kinetics of Loop Formation in Proteins and Peptides: A Signature of Rugged Free Energy Landscapes?
Nonexponential Kinetics of Loop Formation in Proteins and Peptides: A Signature of Rugged Free Energy Landscapes?
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DOI：
10.1021/acs.jpcb.7b07075
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发表时间：
2017-10-19
影响因子：
3.3
通讯作者：
Paci, Emanuele
中科院分区：
文献类型：
--
作者：
Gowdy, James;Batchelor, Matthew;Paci, Emanuele
环形成的动力学，即多肽的两个原子之间接触的发生，仍然是持续关注的焦点。其中一个原因是，接触形成是折叠和结合等过程的基本事件。更重要的是，它是实验可测量的，并且可以从理论上预测理想聚合物。偏离单指数动力学有时被解释为崎岖的、蛋白质样的、自由能景观的标志。在这里，我们提出模拟，与不同的原子模型，短肽具有不同的结构倾向，和结构蛋白。结果表明，长时间接触形成动力学（或弛豫）呈指数，短时间接触形成动力学呈幂律弛豫。在中间时间，可以观察到偏离幂律或简单指数动力学的现象，这似乎是具有特异性或非特异性吸引相互作用的多肽的特征，但如果没有吸引相互作用则会消失。我们的结果与最近对肽和蛋白质的实验测量一致，并为它们提供了全面的解释。
The kinetics of loop formation, i.e., the occurrence of contact between two atoms of a polypeptide, remains the focus of continuing interest. One of the reasons is that contact formation is the elementary event underlying processes such as folding and binding. More importantly, it is experimentally measurable and can be predicted theoretically for ideal polymers. Deviations from single exponential kinetics have sometimes been interpreted as a signature of rugged, protein-like, free energy landscapes. Here we present simulations, with different atomistic models, of short peptides with varied structural propensity, and of a structured protein. Results show exponential contact formation kinetics (or relaxation) at long times, and a power law relaxation at very short times. At intermediate times, a deviation from either power law or simple exponential kinetics is observed that appears to be characteristic of polypeptides with either specific or nonspecific attractive interactions but disappears if attractive interactions are absent. Our results agree with recent experimental measurements on peptides and proteins and offer a comprehensive interpretation for them.