Low-temperature protein dynamics: a simulation analysis of interprotein vibrations and the boson peak at 150 k.
Low-temperature protein dynamics: a simulation analysis of interprotein vibrations and the boson peak at 150 k.
复制标题
DOI：
10.1021/ja055962q
复制
发表时间：
2006-02
影响因子：
15
通讯作者：
Vandana Kurkal-Siebert;Jeremy C. Smith
中科院分区：
文献类型：
--
作者：
Vandana Kurkal-Siebert;Jeremy C. Smith
了解低温下的低频集体蛋白质动力学可以为功能性蛋白质能量景观、蛋白质玻璃化转变的起源和蛋白质-蛋白质相互作用提供有价值的信息。在这里，对结晶肌红蛋白的各种模型进行了分子动力学 (MD) 模拟和简正模式分析，以表征 150 K 下的蛋白内和蛋白间振动。MD 轨迹的主成分分析表明，玻色子峰是动态结构因子中以约 2-2.5 meV 为中心的宽峰，源自约 10(2) 集体谐波振动。人们发现，对环境的准确描述对于再现实验玻色子峰的形状和位置至关重要。在较低能量下，在计算的动态结构因子中发现了其他强峰。这些峰的表征表明它们是由蛋白质相对于彼此的简谐振动产生的。这些振动可能提供有关蛋白质-蛋白质相互作用的物理性质的有价值的信息。
An understanding of low-frequency, collective protein dynamics at low temperatures can furnish valuable information on functional protein energy landscapes, on the origins of the protein glass transition and on protein-protein interactions. Here, molecular dynamics (MD) simulations and normal-mode analyses are performed on various models of crystalline myoglobin in order to characterize intra- and interprotein vibrations at 150 K. Principal component analysis of the MD trajectories indicates that the Boson peak, a broad peak in the dynamic structure factor centered at about approximately 2-2.5 meV, originates from approximately 10(2) collective, harmonic vibrations. An accurate description of the environment is found to be essential in reproducing the experimental Boson peak form and position. At lower energies other strong peaks are found in the calculated dynamic structure factor. Characterization of these peaks shows that they arise from harmonic vibrations of proteins relative to each other. These vibrations are likely to furnish valuable information on the physical nature of protein-protein interactions.