A general approach for prediction of motional EPR spectra from Molecular Dynamics (MD) simulations: application to spin labelled protein
A general approach for prediction of motional EPR spectra from Molecular Dynamics (MD) simulations: application to spin labelled protein
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DOI：
10.1039/c0cp01068e
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发表时间：
2011-01-01
影响因子：
3.3
通讯作者：
Oganesyan, Vasily S.
中科院分区：
文献类型：
--
作者：
Oganesyan, Vasily S.
本文介绍了一种从分子动力学（MD）模拟产生的单动力学轨道直接和完全预测EPR谱的一般方法。该方法适用于任意系统的电子和核自旋所描述的一般形式的自旋哈密顿的整个运动范围。它表明，对于一个可靠的模拟运动EPR谱只有一个单一的截断动力学轨迹生成，直到旋转动力学的相关函数完全放松时的点是必需的。该模拟算法是基于一个组合的传播的自旋密度矩阵在刘维尔空间为这个初始的时间间隔和使用定义良好的参数计算完全从动态轨迹的自旋密度矩阵的演变预测在较长的时间。一种新的方法是说明与应用程序连接到蛋白质抹香鲸肌红蛋白的氮氧自旋标记MTSL。结果表明，EPR谱的模拟，这是非常符合实验，可以实现从一个单一的MD轨迹。计算揭示了复杂的性质的自旋标签的动态，这是一个叠加的二面角状态内的快速librational运动，缓慢的旋转异构的动态之间的不同构象状态的氮氧系链和缓慢的旋转扩散的蛋白质本身。的氮氧系链的EPR谱的整体形状的缓慢旋转异构动力学的意义进行了分析和讨论。
A general approach for the prediction of EPR spectra directly and completely from single dynamical trajectories generated from Molecular Dynamics (MD) simulations is described. The approach is applicable to an arbitrary system of electron and nuclear spins described by a general form of the spin-Hamiltonian for the entire motional range. It is shown that for a reliable simulation of motional EPR spectra only a single truncated dynamical trajectory generated until the point when correlation functions of rotational dynamics are completely relaxed is required. The simulation algorithm is based on a combination of the propagation of the spin density matrix in the Liouville space for this initial time interval and the use of well defined parameters calculated entirely from the dynamical trajectory for prediction of the evolution of the spin density matrix at longer times. A new approach is illustrated with the application to a nitroxide spin label MTSL attached to the protein sperm whale myoglobin. It is shown that simulation of the EPR spectrum, which is in excellent agreement with experiment, can be achieved from a single MD trajectory. Calculations reveal the complex nature of the dynamics of a spin label which is a superposition of the fast librational motions within dihedral states, of slow rotameric dynamics among different conformational states of the nitroxide tether and of the slow rotational diffusion of the protein itself. The significance of the slow rotameric dynamics of the nitroxide tether on the overall shape of the EPR spectrum is analysed and discussed.