Department of Chemical Engineering, Pusan National University, Busan, 609-735, Republic of Korea.
Department of Physics, Pukyong National University, Busan, 608-737, Republic of Korea.
Sci Rep. 2017 Nov 9;7(1):15205. doi: 10.1038/s41598-017-15513-3.
Joint-based descriptor is a new level of macroscopic descriptor for protein structure using joints of secondary structures as a basic element. Here, we propose how the joint-based descriptor can be applied to examine the conformational distances or differences of transmembrane (TM) proteins. Specifically, we performed three independent studies that measured the global and conformational distances between GPCR A family and its related structures. First, the conformational distances of GPCR A family and other 7TM proteins were evaluated. This provided the information on the distant and close families or superfamilies to GPCR A family and permitted the identification of conserved local conformations. Second, computational models of GPCR A family proteins were validated, which enabled us to estimate how much they reproduce the native conformation of GPCR A proteins at global and local conformational level. Finally, the conformational distances between active and inactive states of GPCR proteins were estimated, which identified the difference of local conformation. The proposed macroscopic joint-based approach is expected to allow us to investigate structural features, evolutionary relationships, computational models and conformational changes of TM proteins in a more simplistic manner.
基于关节的描述符是一种新的蛋白质结构宏观描述符，它使用二级结构的关节作为基本元素。在这里，我们提出了如何将基于关节的描述符应用于检查跨膜（TM）蛋白的构象距离或差异。具体来说，我们进行了三项独立的研究，测量了 GPCR A 家族与其相关结构之间的全局和构象距离。首先，评估了 GPCR A 家族和其他 7TM 蛋白的构象距离。这提供了有关与 GPCR A 家族遥远和密切的家族或超家族的信息，并允许识别保守的局部构象。其次，验证了 GPCR A 家族蛋白的计算模型，这使我们能够估计它们在全局和局部构象水平上对 GPCR A 蛋白的天然构象的再现程度。最后，估计了 GPCR 蛋白的活性和非活性状态之间的构象距离，确定了局部构象的差异。所提出的基于宏观关节的方法有望使我们能够以更简单的方式研究 TM 蛋白的结构特征、进化关系、计算模型和构象变化。
