Calculating slow-motional electron paramagnetic resonance spectra from molecular dynamics using a diffusion operator approach
Calculating slow-motional electron paramagnetic resonance spectra from molecular dynamics using a diffusion operator approach
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DOI：
10.1021/jp054738k
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发表时间：
2006-03-16
影响因子：
2.9
通讯作者：
Fajer, PG
中科院分区：
文献类型：
--
作者：
Budil, DE;Sale, KL;Fajer, PG
许多研究小组利用分子动力学 (MD) 来计算附着在生物分子上的自旋标记的慢运动电子顺磁共振 (EPR) 谱。几乎所有此类计算都是基于 Robinson、Slutsky 和 Auteri 引入的轨迹方法的某些变体（J. Chem. Phys. 1992, 96, 2609-2616）。在这里，我们提出了一种替代方法，该方法专门适用于基于扩散算子的随机刘维尔方程 (SLE) 形式，该形式也广泛用于计算慢运动 EPR 线形状。具体来说，该方法利用 MD 轨迹来导出扩散参数，例如旋转扩散张量、扩散倾斜角和定向势的展开系数，然后将其用作 SLE 线形程序的直接输入。与基于轨迹的方法相比，这种方法可显着提高计算效率，特别是对于高频、高场 EPR。它还为解卷积局部自旋标记运动和标记分子或域的整体运动的影响提供了基础：一旦通过这种方法表征了局部运动，则可以将标记扩散参数与较低 EPR 频率下的线形分析结合使用来表征全局运动。通过将 MD 预测线形与实验高频 (250 GHz) EPR 谱进行比较来验证该方法。
A number of groups have utilized molecular dynamics (MD) to calculate slow-motional electron paramagnetic resonance (EPR) spectra of spin labels attached to biomolecules. Nearly all such calculations have been based on some variant of the trajectory method introduced by Robinson, Slutsky and Auteri (J. Chem. Phys. 1992, 96, 2609-2616). Here we present an alternative approach that is specifically adapted to the diffusion operator-based stochastic Liouville equation (SLE) formalism that is also widely used to calculate slow-motional EPR line shapes. Specifically, the method utilizes MD trajectories to derive diffusion parameters such as the rotational diffusion tensor, diffusion tilt angles, and expansion coefficients of the orienting potential, which are then used as direct inputs to the SLE line shape program. This approach leads to a considerable improvement in computational efficiency over trajectory-based methods, particularly for high frequency, high field EPR. It also provides a basis for deconvoluting the effects of local spin label motion and overall motion of the labeled molecule or domain: once the local motion has been characterized by this approach, the label diffusion parameters may be used in conjunction with line shape analysis at lower EPR frequencies to characterize global motions. The method is validated by comparison of the MD predicted line shapes to experimental high frequency (250 GHz) EPR spectra.