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Update of the GRIP web service
Journal of Receptors and Signal Transduction ( IF 2.8 ) Pub Date : 2020-03-08 , DOI: 10.1080/10799893.2020.1734821
Akira Saito 1 , Daiki Tsuchiya 1 , Seiji Sato 2 , Atsushi Okamoto 2 , Yoichi Murakami 3, 4 , Kenji Mizuguchi 3 , Hiroyuki Toh 5 , Wataru Nemoto 1, 6
Affiliation  

Abstract G protein-coupled receptors (GPCRs) can form homodimers, heterodimers, or higher-order molecular complexes (oligomers). The reports on the change of functions through the oligomerization have been accumulated. Inhibition of GPCR oligomerization without affecting the protomer’s overall structure would clarify the oligomer-specific functions although inhibition experiments are costly and require accurate information about the interface location. Unfortunately, the number of experimentally determined interfaces is limited. The precise prediction of the oligomerization interfaces is, therefore, useful for inhibition experiments to examine the oligomer-specific functions, which would accelerate investigations of the GPCR signaling. However, interface prediction for GPCR oligomerization is difficult because different GPCR subtypes belonging to the same subfamily often use different structural regions as their interfaces. We previously developed a high-performance method to predict the interfaces for GPCR oligomerization, by identifying the conserved surfaces with the sequence and structure information. Then, the structural characteristic of a GPCR structure is regarded to be a thick-tube like conformation that is approximately perpendicular to the membrane plane. Our method had successfully predicted all of the interfaces available on that day. We had launched a web server for our interface prediction of GPCRs (GRIP). We have improved the previous version of GRIP server and enhanced its usability. First, we discarded the approximation of the GPCR structure as the thick-tube-like conformation. This improvement increased the number of structures for the prediction. Second, the FUGUE-based template recommendation service was introduced to facilitate the choice of an appropriate structure for the prediction. The new prediction server is available at http://grip.b.dendai.ac.jp/∼grip/.

中文翻译:

GRIP 网络服务的更新

摘要 G蛋白偶联受体(GPCRs)可以形成同源二聚体、异源二聚体或高阶分子复合物(寡聚体)。已经积累了关于通过低聚作用改变功能的报告。在不影响原聚体整体结构的情况下抑制 GPCR 寡聚化将阐明寡聚体特定的功能,尽管抑制实验成本高昂,并且需要有关界面位置的准确信息。不幸的是,实验确定的界面数量是有限的。因此,对寡聚化界面的精确预测对于检查寡聚体特异性功能的抑制实验很有用,这将加速 GPCR 信号的研究。然而,GPCR 寡聚化的界面预测是困难的,因为属于同一亚家族的不同 GPCR 亚型通常使用不同的结构区域作为它们的界面。我们之前开发了一种高性能方法,通过识别具有序列和结构信息的保守表面来预测 GPCR 寡聚化的界面。然后,GPCR结构的结构特征被认为是近似垂直于膜平面的粗管状构象。我们的方法成功预测了当天可用的所有接口。我们已经启动了一个网络服务器,用于我们对 GPCR (GRIP) 的界面预测。我们改进了先前版本的 GRIP 服务器并增强了其可用性。第一的,我们丢弃了 GPCR 结构的近似值作为粗管状构象。这种改进增加了预测的结构数量。其次,引入了基于 FUGUE 的模板推荐服务,以方便选择合适的预测结构。新的预测服务器可从 http://grip.b.dendai.ac.jp/∼grip/ 获得。
更新日期:2020-03-08
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