X-ray diffuse scattering and rigid-body motion in crystalline lysozyme probed by molecular dynamics simulation
X-ray diffuse scattering and rigid-body motion in crystalline lysozyme probed by molecular dynamics simulation
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DOI：
10.1006/jmbi.1998.1754
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发表时间：
1998-05-29
影响因子：
5.6
通讯作者：
Smith, JC
中科院分区：
文献类型：
--
作者：
Héry, S;Genest, D;Smith, JC
刚体运动确定从Ins分子动力学模拟的正交鸡蛋白溶菌酶的单位细胞和它们的贡献，X射线漫散射强度进行检查。使用动态集群技术，集团的骨干原子移动铝？从分子内原子间涨落矩阵导出了质子刚体。这些基团往往在序列中是局部的或通过二硫键连接，并且每个平均含有五个残基。X射线漫散射模式，这是敏感的集体运动，计算从完整的模拟轨迹（包括所有的蛋白质自由度）。结果再现了实验散射的主要特征。漫散射也从刚体的拟合轨迹计算。完整的模拟漫散射和原子位移被认为是很好地再现了一个模型，其中的骨干原子形成的刚性组确定使用动态集群技术和单独的侧链作为单独的刚体行为：所产生的X-因子与完整的模拟散射是5%。从蛋白质的二级结构元件被认为是刚性的轨迹中获得定量较差的一致性。刚性的全分子和域运动对蛋白质原子位移的贡献很小。最后，原子间涨落的相关性直接使用正则方法进行检查。(C)出版社：Academic Press Limited。
Rigid-body motions are determined from a Ins molecular dynamics simulation of the unit cell of orthorhombic hen egg-white lysozyme and their contribution to X-ray diffuse scattering intensities are examined. Using a dynamical cluster technique, groups of backbone atoms that move as al?proximately rigid bodies are derived from the intramolecular interatomic fluctuation matrix. These groups tend to be local in the sequence or connected by disulphide bonds, and contain on average five residues each. X-ray diffuse scattering patterns, which are sensitive to collective motions, are calculated from the full simulation trajectory (including all the protein degrees of freedom). The results reproduce the main features of the experimental scattering. Diffuse scattering is also calculated from fitted trajectories of the rigid bodies. The full simulation diffuse scattering and atomic displacements are found to be well reproduced by a model in which the backbone atoms form the rigid groups determined using the dynamical cluster technique and the individual side-chains behave as separate rigid bodies: the resulting X-factor with the full simulation scattering is 5%. Quantitatively poorer agreement is obtained from trajectories in which the secondary structural elements of the protein are considered rigid. Rigid whole-molecule and domain motions make only minor contributions to the protein atom displacements. Finally, correlations in the interatomic fluctuations are examined directly using a canonical method. (C) 1998 Academic Press Limited.