GPCRana: A web server for quantitative analysis of GPCR structures

Yu Guo; Qingtong Zhou; Bin Wei; Ming-Wei Wang; Suwen Zhao

doi:10.1016/j.str.2023.06.008

GPCRana: A web server for quantitative analysis of GPCR structures

Structure. 2023 Sep 7;31(9):1132-1142.e2. doi: 10.1016/j.str.2023.06.008. Epub 2023 Jun 30.

Authors

Yu Guo¹, Qingtong Zhou², Bin Wei³, Ming-Wei Wang⁴, Suwen Zhao⁵

Affiliations

¹ iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China; Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China.
² Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; Research Center for Deepsea Bioresources, Sanya, Hainan 572025, China. Electronic address: zhouqt@fudan.edu.cn.
³ Research Center for Deepsea Bioresources, Sanya, Hainan 572025, China.
⁴ Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; Research Center for Deepsea Bioresources, Sanya, Hainan 572025, China; Department of Chemistry, School of Science, The University of Tokyo, Tokyo 113-0033, Japan. Electronic address: mwwang@simm.ac.cn.
⁵ iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China. Electronic address: zhaosw@shanghaitech.edu.cn.

PMID: 37392740
DOI: 10.1016/j.str.2023.06.008

Abstract

G protein-coupled receptors (GPCRs) attract tremendous attention from both industrial and academic researchers with currently over 900 released structures. Structural analysis is widely used to understand receptor functionality and pharmacology, but more user-friendly tools are needed. Residue-residue contact score (RRCS) is an atomic distance-based method that allows a quantitative description of GPCR structures. Here, we present GPCRana, a web server that provides a user-friendly interface to analyze GPCR structures. After uploading selected structures, GPCRana immediately generates a comprehensive report covering four aspects: (i) RRCS for all residue pairs incorporated with real-time 3D visualization; (ii) ligand-receptor interactions; (iii) activation pathway analysis; and (iv) RRCS_TMs that indicates the global movements of transmembrane helices. Moreover, conformational changes between two structures can be analyzed. Applying GPCRana on AlphaFold2-predicted models reveals differentiated inter-helical packing forms in a receptor-dependent manner. Our web server offers a fast and precise way to study GPCR structures and is freely available at http://gpcranalysis.com/#/.

Keywords: GPCR; GPCR activation; protein-ligand interactions; residue-residue contact score; structure analysis; web server.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Internet
Models, Molecular
Receptors, G-Protein-Coupled* / chemistry
Software*

Substances

Receptors, G-Protein-Coupled