Kurkal-Siebert Vandana, Smith Jeremy C
Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, Im Neuenheimer Feld 368, D-69120 Heidelberg, Germany.
J Am Chem Soc. 2006 Feb 22;128(7):2356-64. doi: 10.1021/ja055962q.
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.
对低温下低频集体蛋白质动力学的理解，可以为功能性蛋白质能量景观、蛋白质玻璃化转变的起源以及蛋白质-蛋白质相互作用提供有价值的信息。在此，对各种结晶肌红蛋白模型进行了分子动力学（MD）模拟和简正模式分析，以表征150K时蛋白质内部和蛋白质间的振动。MD轨迹的主成分分析表明，玻色子峰（动态结构因子中一个以约2 - 2.5毫电子伏为中心的宽峰）起源于约10²个集体谐波振动。发现准确描述环境对于再现实验玻色子峰的形式和位置至关重要。在较低能量下，计算得到的动态结构因子中还发现了其他强峰。对这些峰的表征表明，它们源于蛋白质彼此之间的谐波振动。这些振动可能为蛋白质-蛋白质相互作用的物理性质提供有价值的信息。
