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

这个子项目是许多利用资源的研究子项目之一 由NIH/NCRR资助的中心拨款提供。子项目的主要支持 而子项目的主要调查员可能是由其他来源提供的， 包括其它NIH来源。 列出的子项目总成本可能 代表子项目使用的中心基础设施的估计数量， 而不是由NCRR赠款提供给子项目或子项目工作人员的直接资金。 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轨迹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. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. 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