Philippopoulos M, Lim C
Department of Chemistry, University of Toronto, Ontario, Canada.
J Mol Biol. 1995 Dec 8;254(4):771-92. doi: 10.1006/jmbi.1995.0654.
A 500 ps molecular dynamics simulation of Escherichia coli RNase H1 in the presence of explicit water molecules has been carried out to aid in the interpretation of NMR N-H backbone model free parameters and X-ray B-factor values of the free enzyme. Both experimental techniques have revealed unusual structural and dynamic features of the protein. Atomic fluctuations (B-factors) and re-orientational motions of the backbone heteronuclear bonds (order parameters) computed from the simulation are compared with results obtained from experiments. Qualitative agreement is obtained between the computed and X-ray B-factors, whereas the agreement between the computed and NMR generalized order parameters is as good as quantitative for most residues. Reasons for significant discrepancies, the physical basis and the plausible biological consequences of the observed protein dynamics are discussed.
在存在明确水分子的情况下，对大肠杆菌核糖核酸酶H1进行了500皮秒的分子动力学模拟，以辅助解释游离酶的核磁共振N-H主链无模型参数和X射线B因子值。这两种实验技术都揭示了该蛋白质不同寻常的结构和动力学特征。将模拟计算得到的原子涨落（B因子）和主链异核键的重新取向运动（序参量）与实验结果进行了比较。计算得到的B因子与X射线B因子之间获得了定性的一致性，而对于大多数残基，计算得到的和核磁共振广义序参量之间的一致性达到了定量水平。讨论了显著差异的原因、观察到的蛋白质动力学的物理基础以及可能的生物学后果。
