生物分子活化动力学中的动能流
Kinetic energy flows in activated dynamics of biomolecules
摘要：
蛋白质构象变化是蛋白质功能所必需的活化过程。蛋白质中的活化不同于小分子中的活化，因为它涉及通过蛋白质结构中编码的优选通道的定向和系统的能量流。了解这些能量流动通道的性质以及在激活过程中能量如何通过它们流动对于理解蛋白质构象变化至关重要。我们最近开发了一个严格的统计力学框架来理解势能流。在这里，我们完成了这个理论框架与严格的理论动能流：潜在的和动能相互转换时，强制力反对惯性力，而动能直接从一个坐标转移到另一个时，惯性力反对对方。该理论被应用于分析生物分子构象动力学的原型系统：丙氨酸二肽的异构化。在这一过程的两个基本能量流通道中，二面角φ面对活化势垒，而二面角θ从势能流接收能量。有趣的是，theta通过直接的动能流将它所接收的所有能量转移到phi上，从而帮助phi越过活化势垒：势能流引起的theta的增加转化为phi的增加。作为补偿，θ通过直接机制从键角α接收动能，通过间接机制从键角β接收动能。
英文摘要：
Protein conformational changes are activated processes essential for protein functions. Activation in a protein differs from activation in a small molecule in that it involves directed and systematic energy flows through preferred channels encoded in the protein structure. Understanding the nature of these energy flow channels and how energy flows through them during activation is critical for understanding protein conformational changes. We recently developed a rigorous statistical mechanical framework for understanding potential energy flows. Here we complete this theoretical framework with a rigorous theory for kinetic energy flows: potential and kinetic energy inter-convert when impressed forces oppose inertial forces whereas kinetic energy transfers directly from one coordinate to another when inertial forces oppose each other. This theory is applied to analyzing a prototypic system for biomolecular conformational dynamics: the isomerization of an alanine dipeptide. Among the two essential energy flow channels for this process, dihedral phi confronts the activation barrier, whereas dihedral theta receives energy from potential energy flows. Intriguingly, theta helps phi to cross the activation barrier by transferring to phi via direct kinetic energy flow all the energy it received: increase in theta caused by potential energy flow converts into increase in phi. As a compensation, theta receives kinetic energy from bond angle alpha via direct mechanism and bond angle beta via indirect mechanism.
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