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

该子项目是利用 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得主要资金， 因此可以在其他CRISP条目中表示。列出的机构是 中心，不一定是研究者的机构。 从运动模型出发模拟氮氧自由基自旋标记物的电子自旋共振谱，是对实验谱进行定量分析的必要条件。我们已经开发了一个框架，通过使用轨迹，如从分子动力学（MD）模拟结合随机治疗的全球蛋白质翻滚的自旋标签动态建模。这是在开发了两个有效的数值积分器之后在时域中实现的：一个用于自旋的量子动力学，另一个用于经典旋转扩散。对于量子动力学，我们在希尔伯特空间中传播自旋密度矩阵的相关部分。对于扩散翻滚，我们使用四元数，这使得在作为球谐函数之和展开的势中能够处理各向异性扩散。时间平均参数被用来弥合MD轨道的较小时间步长和适合于旋转扩散和/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