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首页> 外文期刊>The journal of physical chemistry, A. Molecules, spectroscopy, kinetics, environment, & general theory >Temperature Dependence of Peptide Conformational Equilibria from Simulations at a Single Temperature
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Temperature Dependence of Peptide Conformational Equilibria from Simulations at a Single Temperature

机译：肽构象均衡的温度依赖性在一次温度下模拟

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摘要

Understanding the structure of proteins is key to unraveling their function in biological processes. Thus, significant attention has been paid to the calculation of conformational free energies. In this paper, we demonstrate a simple extension of fluctuation theory that permits the calculation of the temperature derivative of the conformational free energy, and hence the internal energy and entropy, from single-temperature simulations. The method further enables the decomposition into the contribution of different interactions present in the system to the internal energy surface. We illustrate the method for the canonical test system of alanine dipeptide in aqueous solution, for which we examine the free energy as a function of two dihedral angles. This system, like many, is most effectively treated using accelerated sampling methods and we show how the present approach is compatible with an important class of these, those that introduce a bias potential, by implementing it within metadynamics.
机译：了解蛋白质的结构是揭示其在生物过程中功能的关键。因此，构象自由能的计算受到了极大的关注。在本文中，我们展示了涨落理论的一个简单扩展，它允许从单温度模拟计算构象自由能的温度导数，从而计算内能和熵。该方法还能够将系统中存在的不同相互作用分解为对内能面的贡献。我们说明了水溶液中丙氨酸二肽标准测试系统的方法，我们检验了自由能作为两个二面角的函数。与许多系统一样，使用加速采样方法对该系统进行了最有效的处理，我们通过在亚动力学中实现，展示了当前方法如何与其中一类重要的方法兼容，即引入偏置电位的方法。

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