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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Simulation method for calculating the entropy and free energy of peptides and proteins.
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Simulation method for calculating the entropy and free energy of peptides and proteins.

机译：计算肽和蛋白质的熵和自由能的模拟方法。

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摘要

A method called complete hypothetical scanning Monte Carlo has been introduced for calculating the absolute entropy, S, and free energy, F, of fluids. Here, the method is extended to peptide chains in vacuum. Thus, S is calculated from a given sample by reconstructing each conformation step-by-step by using transition probabilities (TPs); at each step, part of the chain coordinates have already been determined (the "frozen past"), and the TP is obtained from a Monte Carlo simulation of the (future) part of the chain whose TPs as yet have not been calculated. Very accurate results for S and F are obtained for the helix, extended, and hairpin microstates of a simplified model of decaglycine (Gly)(10) and (Gly)(16). These results agree well with results obtained by the quasiharmonic approximation and the local states method. The complete HSMC method can be applied to a macromolecule with any degree of flexibility, ranging from local fluctuations to a random coil. Also, the difference in stability, Delta F(mn) = F(m) - F(n) between significantly different microstates m and n can be obtained from two simulations only without the need to resort to thermodynamic integration. Our long-term goal is to extend this method to any peptide and apply it to a peptide immersed in a box with explicit water.
机译：为了计算流体的绝对熵S和自由能F，引入了一种称为完全假设扫描Monte Carlo的方法。在此，该方法扩展到真空中的肽链。因此，通过使用转移概率（TP）逐步重构每个构象，从给定样本中计算出S；在每个步骤中，已经确定了部分链坐标（“冻结过去”），并且从尚未计算TP的链的（未来）部分的蒙特卡洛模拟中获得了TP。对于十甘氨酸（Gly）（10）和（Gly）（16）简化模型的螺旋，扩展和发夹状微状态，S和F的结果非常准确。这些结果与通过拟谐波近似和局部状态方法获得的结果非常吻合。完整的HSMC方法可以应用到具有从局部波动到随机线圈的任何程度的灵活性的高分子。同样，仅通过两种模拟就可以得到明显不同的微状态m和n之间的稳定性差异Delta F（mn）= F（m）-F（n），而无需诉诸热力学积分。我们的长期目标是将这种方法扩展到任何肽，并将其应用于浸入有清水的盒子中的肽。

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