Incipient structural and vibrational relaxation process of photolyzed carbonmonoxy myoglobin: statistical analysis by perturbation ensemble molecular dynamics method
Incipient structural and vibrational relaxation process of photolyzed carbonmonoxy myoglobin: statistical analysis by perturbation ensemble molecular dynamics method
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DOI：
10.1007/s00214-011-0992-y
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发表时间：
2011-12-01
影响因子：
1.7
通讯作者：
Nagaoka, Masataka
中科院分区：
文献类型：
--
作者：
Takayanagi, Masayoshi;Nagaoka, Masataka
通过扰动系综分子动力学（PEMD）方法分析了光解碳单氧肌红蛋白的初始结构和振动能量弛豫过程，其中执行多对扰动和未扰动MD模拟以进行系综平均，以通过抵消热波动来获得统计上显着的结果。首先，我们证明了实验报告的各向异性膨胀可以在光解后的皮秒内检测到。实验和计算结果之间的良好一致性表明，PEMD 方法可以合理地预测那些由扰动驱动的变化，即使这些变化可能很微妙且小于热波动。其次，成功分析了结构松弛，包括E和F螺旋中的“蛤壳旋转”。高时间分辨率分析阐明了亚皮秒时间尺度上的初期结构动力学：在血红素隆起和解离的 CO 配体碰撞之后，蛤壳式旋转从 His64、Val68 和 His93 开始。第三，从血红素到珠蛋白基质的振动能量弛豫不仅在时间上而且在空间上得到阐明。这是第一个关于球蛋白基质中光解 MbCO 的时空分辨多余动能重新分布的“彻底”报告，具有统计上显着的精度，+/- 1 K。初始各向异性振动弛豫通过“通过键”和“通过抛射”路径在垂直于血红素平面的方向上的皮秒内明显发生，然后各向同性弛豫通过“通过空间”路径进行。最后得出的结论是，PEMD 方法是理解扰动驱动的初始弛豫过程的有力工具。
The incipient structural and vibrational energy relaxation process of photolyzed carbonmonoxy myoglobin was analyzed by the perturbation ensemble molecular dynamics (PEMD) method, in which many pairs of perturbed and unperturbed MD simulations are executed for ensemble-averaging to obtain statistically significant results by canceling out thermal fluctuations. First, we have shown that the experimentally reported anisotropic expansion can be detected within a picosecond after photolysis. The good agreement between the experimental and computational results indicates that the PEMD method can predict legitimately those changes driven by perturbations even if the changes might be subtle and smaller than thermal fluctuations. Second, the structural relaxation including the "clamshell rotation" in E and F helices was successfully analyzed. The high time resolution analysis has clarified the incipient structural dynamics on a subpicosecond timescale: the clamshell rotation starts at His64, Val68, and His93 following both the heme doming and the dissociated CO ligand collision. Third, the vibrational energy relaxation from the heme to the globin matrix is elucidated not only temporally but also spatially. This is the first "thorough" report of the spacetime-resolved excess kinetic energy redistribution of photolyzed MbCO in the globin matrix with a statistically significant precision, +/- 1 K. The incipient anisotropic vibrational relaxation occurs clearly within a picosecond in the direction perpendicular to the heme plane by the "through-bond" and "through-projectile" pathways, and the isotropic relaxation then follows by the "through-space" pathway. Finally, it is concluded that the PEMD method is a powerful tool to understand the incipient relaxation process driven by the perturbation.