SIMULATING ESR SPECTRA OF NITROXIDE SPIN LABELS FROM MD & STOCH TRAJECTORIES

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 从运动模型模拟氮氧化物自旋标记物的电子自旋共振谱对于定量分析实验光谱是必要的。我们开发了一个框架，通过使用来自分子动力学(MD)模拟的轨迹并结合全球蛋白质翻滚的随机处理来建模自旋标签动力学。这是在开发了两个有效的数值积分器后在时间域实现的：一个用于自旋的量子动力学，另一个用于经典的旋转扩散。对于量子动力学，我们在希尔伯特空间中传播了自旋密度矩阵的相关部分。对于扩散滚流，我们使用了四元数，这使得各向异性扩散能够处理在作为球谐和展开的势中。利用时间平均自变量来弥合MD轨迹的较小时间步长和适用于旋转扩散和/或量子自旋动力学的较大时间步长之间的差距

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Simulating electron spin resonance spectra of nitroxide spin labels from motional models is necessary for the quantitative analysis of experimental spectra. We have developed a framework for modeling the spin label dynamics by using trajectories such as those from molecular dynamics (MD) simulations combined with stochastic treatment of the global protein tumbling. This was achieved in the time domain after two efficient numerical integrators were developed: One for the quantal dynamics of the spins and the other for the classical rotational diffusion. For the quantal dynamics, we propagated the relevant part of the spin density matrix in Hilbert space. For the diffusional tumbling, we worked with quaternions, which enabled the treatment of anisotropic diffusion in a potential expanded as a sum of spherical harmonics. Time-averaging arguments were invoked to bridge the gap between the smaller time step of the MD trajectories and the larger time steps appropriate for the rotational diffusion and/or quantal spin dynamics