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首页> 美国卫生研究院文献>Biophysical Journal >A Structure-Based Simulation Approach for Electron Paramagnetic Resonance Spectra Using Molecular and Stochastic Dynamics Simulations
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A Structure-Based Simulation Approach for Electron Paramagnetic Resonance Spectra Using Molecular and Stochastic Dynamics Simulations

机译：基于分子和随机动力学模拟的基于结构的电子顺磁共振谱模拟方法

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Electron paramagnetic resonance (EPR) spectroscopy using site-directed spin-labeling is an appropriate technique to analyze the structure and dynamics of flexible protein regions as well as protein-protein interactions under native conditions. The analysis of a set of protein mutants with consecutive spin-label positions leads to the identification of secondary and tertiary structure elements. In the first place, continuous-wave EPR spectra reflect the motional freedom of the spin-label specifically linked to a desired site within the protein. EPR spectra calculations based on molecular dynamics (MD) and stochastic dynamics simulations facilitate verification or refinement of predicted computer-aided models of local protein conformations. The presented spectra simulation algorithm implies a specialized in vacuo MD simulation at 600 K with additional restrictions to sample the entire accessible space of the bound spin-label without large temporal effort. It is shown that the distribution of spin-label orientations obtained from such MD simulations at 600 K agrees well with the extrapolated motion behavior during a long timescale MD at 300 K with explicit water. The following potential-dependent stochastic dynamics simulation combines the MD data about the site-specific orientation probabilities of the spin-label with a realistic rotational diffusion coefficient yielding a set of trajectories, each more than 700 ns long, essential to calculate the EPR spectrum. Analyses of a structural model of the loop between helices E and F of bacteriorhodopsin are illustrated to demonstrate the applicability and potentials of the reported simulation approach. Furthermore, effects on the motional freedom of bound spin-labels induced by solubilization of bacteriorhodopsin with Triton X-100 are examined.
机译：使用定点自旋标记的电子顺磁共振（EPR）光谱技术是分析柔性蛋白质区域的结构和动力学以及天然条件下蛋白质与蛋白质相互作用的一种合适技术。具有连续自旋标记位置的一组蛋白质突变体的分析导致二级和三级结构元件的鉴定。首先，连续波EPR光谱反映了与蛋白质内所需位点特异性连接的自旋标记的运动自由度。基于分子动力学（MD）和随机动力学模拟的EPR光谱计算有助于验证或改进预测的局部蛋白构象的计算机辅助模型。提出的光谱模拟算法暗示了在600 K下进行专门的真空MD模拟，并附加了一些限制，可以在不花费大量时间的情况下对结合的自旋标记物的整个可访问空间进行采样。结果表明，从这种在600 K的MD模拟中获得的自旋标记取向分布与外在水在300 K的长时标MD下的外推运动行为非常吻合。以下与电位相关的随机动力学模拟将有关自旋标记的特定位置定向概率的MD数据与真实的旋转扩散系数结合在一起，产生了一组轨迹，每条轨迹的长度均超过700 ns，这对于计算EPR光谱至关重要。细菌视紫红质的螺旋E和F之间的环的结构模型的分析说明，以证明所报道的模拟方法的适用性和潜力。此外，研究了用Triton X-100溶解细菌视紫红质对诱导的自旋标记物运动自由度的影响。

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