Department of Chemistry & Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States.
J Phys Chem B. 2011 Jun 23;115(24):7991-5. doi: 10.1021/jp201998c. Epub 2011 May 27.
The response of a protein to variation of a specific coordinate can provide insights into the role of the overall architecture in the structural change. Given that the calculated potential of mean force governing the fluctuation of an electron transfer donor-acceptor distance in the NAD(P)H:Flavin oxidoreductase (Fre)/FAD complex was shown to agree with experiment, an analysis of the structural response of the rest of the protein to that distance change was made. Significant displacements are found throughout much of the protein, and the coupling pathway resulting in the structural changes was determined. A covariance analysis based on the quasiharmonic modes of the unperturbed protein was used to provide information concerning how the residue motions are correlated. It is found that, of the three regions identified as moving together in an NMR study, two undergo significant structural changes when the electron donor-acceptor distance is varied, and the third does not.
蛋白质对特定坐标变化的响应可以深入了解整体结构在结构变化中的作用。鉴于计算出的平均力势能可以很好地描述 NAD(P)H：黄素氧化还原酶（Fre）/FAD 复合物中电子转移供体-受体距离的波动，因此分析了该蛋白质其余部分对距离变化的结构响应。结果发现，在整个蛋白质中都存在明显的位移，并且确定了导致结构变化的耦合途径。基于未受扰蛋白质的准谐模式的协方差分析用于提供有关残基运动如何相关的信息。结果发现，在 NMR 研究中被确定为共同运动的三个区域中，有两个在电子供体-受体距离变化时会发生明显的结构变化，而第三个区域则不会。
