论文标题
生物分子活化动力学中的动能流动
Kinetic energy flows in activated dynamics of biomolecules
论文作者
论文摘要
蛋白质构象变化是激活蛋白质功能必不可少的过程。蛋白质中的激活与小分子中的激活不同，因为它涉及通过在蛋白质结构中编码的首选通道的定向和系统的能量流。了解这些能量流通道的性质以及在激活过程中如何通过它们流过它们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机械框架，以了解势能流。在这里，我们以动力流的严格理论来完成这个理论框架：当印象力反对惯性力时，动力和动能互换时，而动能在惯性相互反对时直接从一个坐标向另一种坐标转移。该理论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。在此过程的两个必需能量流通道中，二面性phi面对激活屏障，而二面体theta则从势能流中接收能量。有趣的是，Theta通过直接动能流将PHI转移到PHI上，帮助PHI越过激活屏障，所有能量的收到的所有能量：势能流动引起的theta的增加变为PHI的增加。作为补偿，Theta通过直接机制和键角β通过间接机制从键角α接收动能。
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.
