THEORETICAL STUDIES ON THE DYNAMIC ASPECTS OF MACROMOLECULAR FUNCTION

一氧化氮合成反应的动力学研究 模拟了肌红蛋白的光解离过程。 分子动力学。动力学进程曲线，通过平均得到 100个轨迹，可以通过一个简单的模型很好地再现 朗之万粒子在平均力势中运动的计算公式 非反应性轨迹。从能量井中逃逸的速度 与亚铁血红素相邻的值与由 实验数据表明，多井模型提供了一个 对非指数重结合动力学的合理解释。一个 布朗动力学算法，最初设计用于计算 扩散控制反应速率，已被用来计算 跨大气层流体动摩擦力(即 扩散系数)。这项工作在 Effect利用了两个看似不相关的物理模型之间的深层类比 数量，并导致了一种新颖而高效的计算方法 大分子的扩散系数。有一种理论认为 为DNA分子的电泳法而开发的 微光刻法构建的合成凝胶，由一种 基本上是柱子的二维规则阵列。具体地说， 一个DNA分子挂在一根柱子上的平均“解钩”时间 形成U型结构进行了计算。达成了很好的一致意见 在理论和实验之间，表明一个基本方面 长度分馏的机制可以在一个 微观层面。本实验室开发的一种高效算法 计算大分子的静电性质一直以来都是 应用于细胞色素c-细胞色素过氧化物酶系统 静电相互作用对自由基氧化还原电位的影响 络合物形成能和电子转移效率。在……里面 除了成功预测突变对这些人的影响之外 属性，这些计算揭示了 氧化还原电位和选举转移速率由 蛋白质环境。

The kinetics of the geminate rebinding of nitric oxide following photodissociation to myoglobin was simulated using the technique of molecular dynamics. The kinetic progress curve, obtained by averaging 100 trajectories, could be well reproduced by a simple model of a Langevin particle moving in a potential of mean force calculated from nonreactive trajectories. The rate of escape from the energy well adjacent to the heme was in good agreement with the value calculated from experimental data, suggesting that a multiple-well model provides a plausible explanation for the nonexponential rebinding kinetics. A Brownian dynamics algorithm, originally devised for calculating diffusion-controlled reaction rates, has been adapted to calculate the transalational hydrodynamic friction (i.e., the reciprocal of the diffusion coefficient) of objects with complex shapes. This work in effect exploits a deep analogy between two seemingly unrelated physical quantities, and leads to a novel and highly efficient way of calculating the diffusion coefficients of macromolecules. A theory has been developed for the electrophoresis of DNA molecules in microlithographically constructed synthetic gels consisting of an essentially two dimensional regular array of posts. Specifically, the average "unhooking" time for a DNA molecule that got hooked on a post to form a U-shaped structure was calculated. Good agreement was found between theory and experiment, indicating that one fundamental aspect of the mechanism of length fractionation can be fully understood on a microscopic level. An efficient algorithm developed in this laboratory to calculate the electrostatic properties of macromolecules has been applied to the cytochrome c-cytochrome peroxidase system to elucidate the influence of electrostatic interactions on redox potentials, the free energy of complex formation and the efficiency of electron transfer. In addition to successfully predicting the effect of mutations on those properties, these calculations revealed the structural basis of how the redox potential and the rate of election transfer is controlled by the protein environment.