Wood K, Grudinin S, Kessler B, Weik M, Johnson M, Kneller G R, Oesterhelt D, Zaccai G
Institut Laue-Langevin, 6 rue Jules Horowitz, B.P. 156, 38042 Grenoble Cedex 9, France.
J Mol Biol. 2008 Jul 11;380(3):581-91. doi: 10.1016/j.jmb.2008.04.077. Epub 2008 May 11.
Components of biological macromolecules, complexes and membranes are animated by motions occurring over a wide range of time and length scales, the synergy of which is at the basis of biological activity. Understanding biological function thus requires a detailed analysis of the underlying dynamical heterogeneity. Neutron scattering, using specific isotope labeling, and molecular dynamics simulations were combined in order to study the dynamics of specific amino acid types in bacteriorhodopsin within the purple membrane (PM) of Halobacterium salinarum. Motions of leucine, isoleucine and tyrosine residues on the pico- to nanosecond time scale were examined separately as a function of temperature from 20 to 300 K. The dynamics of the three residue types displayed different temperature dependence: isoleucine residues have larger displacements compared to the global PM above 120 K; leucine residues have displacements similar to that of PM in the entire temperature range studied; and tyrosine residues have displacements smaller than that of the average membrane in an intermediate temperature range. Experimental features were mostly well reproduced by molecular dynamics simulations performed at five temperatures, which allowed the dynamical characterisation of the amino acids under study as a function of local environment. The resulting dynamical map of bacteriorhodopsin revealed that movements of a specific residue are determined by both its environment and its residue type.
生物大分子、复合物和膜的组成部分由发生在广泛时间和长度尺度上的运动驱动，这些运动的协同作用是生物活性的基础。因此，理解生物功能需要对潜在的动态异质性进行详细分析。利用特定的同位素标记，将中子散射和分子动力学模拟相结合，以研究嗜盐菌紫膜（PM）中细菌视紫红质中特定氨基酸类型的动力学。在20至300K的温度范围内，分别研究了亮氨酸、异亮氨酸和酪氨酸残基在皮秒到纳秒时间尺度上的运动随温度的变化。这三种残基类型的动力学表现出不同的温度依赖性：在120K以上，异亮氨酸残基的位移比整个PM的位移大；在整个研究温度范围内，亮氨酸残基的位移与PM的位移相似；在中间温度范围内，酪氨酸残基的位移比平均膜的位移小。在五个温度下进行的分子动力学模拟大多很好地再现了实验特征，这使得能够根据局部环境对所研究的氨基酸进行动力学表征。由此得到的细菌视紫红质动力学图谱表明，特定残基的运动由其环境和残基类型共同决定。
