Izumi Keisuke, Saho Eitaro, Kutomi Ayuka, Tomoike Fumiaki, Okada Tetsuji
Department of Life Science, Gakushuin University, Tokyo, Japan.
PeerJ. 2020 Feb 11;8:e8606. doi: 10.7717/peerj.8606. eCollection 2020.
All living organisms have evolved to contain a set of proteins with variable physical and chemical properties. Efforts in the field of structural biology have contributed to uncovering the shape and the variability of each component. However, quantification of the variability has been performed mostly by multiple pair-wise comparisons. A set of experimental coordinates for a given protein can be used to define the "morphness/unmorphness". To understand the evolved repertoire in an organism, here we show the results of global analysis of more than a thousand proteins, by the recently introduced method, distance scoring analysis (DSA). By collecting a new index "UnMorphness Factor" (UMF), proposed in this study and determined from DSA for each of the proteins, the lowest and the highest boundaries of the experimentally observable structural variation are comprehensibly defined. The distribution plot of UMFs obtained for represents the first view of a substantial fraction of non-redundant proteome set of an organism, demonstrating how rigid and flexible components are balanced. The present analysis extends to evaluate the growing data from single particle cryo-electron microscopy, providing valuable information on effective interpretation to structural changes of proteins and the supramolecular complexes.
所有生物都进化出了一套具有可变物理和化学性质的蛋白质。结构生物学领域的研究工作有助于揭示每个组分的形状和变异性。然而，变异性的量化大多是通过多对多比较来进行的。一组给定蛋白质的实验坐标可用于定义“形态性/非形态性”。为了了解生物体中进化出的全部蛋白质，我们在此展示了通过最近引入的距离评分分析（DSA）方法对一千多种蛋白质进行全局分析的结果。通过收集本研究中提出并由DSA为每种蛋白质确定的新指标“非形态性因子”（UMF），可全面定义实验可观察到的结构变异的最低和最高界限。为[具体内容缺失]获得的UMF分布图代表了生物体非冗余蛋白质组的很大一部分的首次视图，展示了刚性和柔性组分是如何平衡的。目前的分析扩展到评估来自单颗粒冷冻电子显微镜的不断增长的数据，为有效解释蛋白质和超分子复合物的结构变化提供了有价值的信息。
