Krishnan M, Kurkal-Siebert V, Smith Jeremy C
Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, Im Neuenheimer Feld 368, D-69120, Heidelberg, Germany.
J Phys Chem B. 2008 May 1;112(17):5522-33. doi: 10.1021/jp076641z. Epub 2008 Apr 10.
The role of methyl groups in the onset of low-temperature anharmonic dynamics in a crystalline protein at low temperature is investigated using atomistic molecular dynamics (MD) simulation. Anharmonicity appears at approximately 150 K, far below the much-studied solvent-activated dynamical transition at approximately 220 K. A significant fraction of methyl groups exhibit nanosecond time scale rotational jump diffusion at 150 K. The splitting and shift in peak position of both the librational band (around 100 cm(-1)) and the torsional band (around 270-300 cm(-1)) also differ significantly among methyl groups, depending on the local environment. The simulation results provide no evidence for a correlation between methyl dynamics and solvent exposure, consistent with the hydration-independence of the low-temperature anharmonic dynamics observed in neutron scattering experiments. The calculated proton mean-square fluctuation and methyl NMR order parameters show a systematic nonlinear dependence on the rotational barrier which can be described using model functions. The methyl groups that exhibit many rotational excitations are located near xenon cavities, suggesting that cavities in proteins act as activation centers of anharmonic dynamics. The dynamic heterogeneity and the environmental sensitivity of motional parameters and low-frequency spectral bands of CH(3) groups found here suggest that methyl dynamics may be used as a probe to investigate the relation between low-energy structural fluctuations and packing defects in proteins.
利用原子分子动力学（MD）模拟研究了甲基在低温下结晶蛋白中低温非谐动力学起始过程中的作用。非谐性出现在约150 K，远低于在约220 K时被广泛研究的溶剂激活动力学转变温度。相当一部分甲基在150 K时表现出纳秒时间尺度的旋转跳跃扩散。根据局部环境的不同，甲基的 librational 带（约100 cm⁻¹）和扭转带（约270 - 300 cm⁻¹）的峰位分裂和位移也有显著差异。模拟结果没有提供甲基动力学与溶剂暴露之间存在相关性的证据，这与中子散射实验中观察到的低温非谐动力学的水合独立性一致。计算得到的质子均方涨落和甲基核磁共振序参量显示出对旋转势垒的系统非线性依赖性，可用模型函数来描述。表现出许多旋转激发的甲基位于氙气腔附近，这表明蛋白质中的腔作为非谐动力学的激活中心。这里发现的甲基基团运动参数和低频光谱带的动态非均匀性以及环境敏感性表明，甲基动力学可作为一种探针来研究蛋白质中低能量结构涨落与堆积缺陷之间的关系。
