Simulation of nitroxide electron paramagnetic resonance spectra from Brownian trajectories and molecular dynamics simulations
Simulation of nitroxide electron paramagnetic resonance spectra from Brownian trajectories and molecular dynamics simulations
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DOI：
10.1529/biophysj.107.125419
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发表时间：
2008-05-15
影响因子：
3.4
通讯作者：
Hustedt, Eric J.
中科院分区：
文献类型：
--
作者：
DeSensi, Susan C.;Rangel, David P.;Hustedt, Eric J.
从自由感应衰减的傅里叶变换可以得到模拟的氮氧自由基自旋标记物的连续波电子顺磁共振谱。以前已经表明，自由感应衰减可以通过求解一组布朗轨迹的含时随机刘维尔方程来计算。从而改变标签的旋转动力学。在这项工作中，一个基于四元数的蒙特卡罗算法已被开发来生成描述自旋标记蛋白质的全局旋转扩散的布朗轨迹。此外，分子动力学模拟的两个自旋标记的T4溶菌酶，T4L F153R1，和T4L K65R1的突变体已被用来产生轨迹描述的内部动态的蛋白质和自旋标记侧链的本地动态。从分子动力学模拟结合轨迹描述的全球旋转扩散的蛋白质的轨迹被用来占所有的自旋标记的蛋白质的动力学。从这些组合的轨迹计算的光谱对应的实验光谱掩埋的网站T4L F153R1和螺旋表面网站T4L K65R1。这项工作提供了一个框架，以进一步探讨在各种各样的标签环境中遇到的定点自旋标记研究的自旋标记侧链的动力学建模。
A simulated continuous wave electron paramagnetic resonance spectrum of a nitroxide spin label can be obtained from the Fourier transform of a free induction decay. It has been previously shown that the free induction decay can be calculated by solving the time-dependent stochastic Liouville equation for a set of Brownian trajectories de. ning the rotational dynamics of the label. In this work, a quaternion-based Monte Carlo algorithm has been developed to generate Brownian trajectories describing the global rotational diffusion of a spin-labeled protein. Also, molecular dynamics simulations of two spin-labeled mutants of T4 lysozyme, T4L F153R1, and T4L K65R1 have been used to generate trajectories describing the internal dynamics of the protein and the local dynamics of the spin-label side chain. Trajectories from the molecular dynamics simulations combined with trajectories describing the global rotational diffusion of the protein are used to account for all of the dynamics of a spin-labeled protein. Spectra calculated from these combined trajectories correspond well to the experimental spectra for the buried site T4L F153R1 and the helix surface site T4L K65R1. This work provides a framework to further explore the modeling of the dynamics of the spin-label side chain in the wide variety of labeling environments encountered in site-directed spin labeling studies.