Vibrational frequency shifts and relaxation rates for a selected vibrational mode in cytochrome c
Vibrational frequency shifts and relaxation rates for a selected vibrational mode in cytochrome c
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DOI：
10.1016/s0006-3495(03)74575-5
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发表时间：
2003-09-01
影响因子：
3.4
通讯作者：
Straub, JE
中科院分区：
文献类型：
--
作者：
Bu, LT;Straub, JE
用平衡态分子动力学模拟和简正模分析方法研究了细胞色素c分子中一个选定的振动模式--Met 80末端甲基的C-D伸缩振动的振动能弛豫。正如Romesberg及其同事的开创性工作所证明的那样，烷基侧链中C-H（到C-D）拉伸的同位素标记将拉伸频率转移到蛋白质态密度的透明区域，使其成为蛋白质结构和动力学的有效和通用探针。溶剂化细胞色素c的分子动力学轨迹运行在300 K，振动布居弛豫时间估计使用经典的Landau-Teller-Zwanzig模型和一些共振和双声子振动弛豫过程的半经典理论。C-D伸缩振动布居弛豫时间估计为T-1 = 14 - 40 ps;各种半经典T-1估计值之间的相对接近的一致性支持了这些表达式的适用性。简正模计算用于识别蛋白质和C-D振子之间的主导耦合。所有强烈耦合到C-D拉伸的浴模式都非常接近。角弯曲模式在终端甲基Met 80似乎是最有可能的受体模式de。讨论了C-D振动的布居弛豫机制。
The vibrational energy relaxation of a selected vibrational mode in cytochrome c - a C-D stretch in the terminal methyl group of Met80- has been studied using equilibrium molecular dynamics simulation and normal mode analysis methods. As demonstrated in the pioneering work of Romesberg and co-workers, isotopic labeling of the C-H ( to C-D) stretch in alkyl side chains shifts the stretching frequency to the transparent region of the protein's density of states, making it an effective and versatile probe of protein structure and dynamics. Molecular dynamics trajectories of solvated cytochrome c were run at 300 K, and vibrational population relaxation times were estimated using the classical Landau-Teller-Zwanzig model and a number of semiclassical theories of resonant and two-phonon vibrational relaxation processes. The C-D stretch vibrational population relaxation time is estimated to be T-1 = 14 - 40 ps; the relatively close agreement between various semiclassical estimates of T-1 lends support to the applicability of those expressions. Normal mode calculations were used to identify the dominant coupling between the protein and C-D oscillator. All bath modes strongly coupled to the C-D stretch are in close proximity. Angle bending modes in the terminal methyl group of Met80 appear to be the most likely acceptor modes de. ning the mechanism of population relaxation of the C-D vibration.