A Classification Model for the Second Extracellular Loop of Class A GPCRs

Alessandro Nicoli, Andreas Dunkel, Toni Giorgino, Chris de Graaf, and Antonella Di Pizio

This repository contains code for the web app providing interactive supplemental information about the classification model for the Second Extracellular Loop (ECL2) of Class A GPCR receptors. The web app is currently hosted at ecl2.giorginolab.it.

Reference

Alessandro Nicoli, Andreas Dunkel, Toni Giorgino, Chris de Graaf, and Antonella Di Pizio. Classification Model for the Second Extracellular Loop of Class A GPCRs. Journal of Chemical Information and Modeling. 2022. DOI: 10.1021/acs.jcim.1c01056.

• The extracellular loop 2 (ECL2) is the longest and the most diverse loop among class A G protein-coupled receptors (GPCRs). It connects the transmembrane (TM) helices 4 and 5 and contains a highly conserved cysteine through which it is bridged with TM3. In this paper, experimental ECL2 structures were analyzed based on their sequences, shapes, and intramolecular contacts. To take into account the flexibility, we incorporated into our analyses information from the molecular dynamics trajectories available on the GPCRmd website. Despite the high sequence variability, shapes of the analyzed structures, defined by the backbone volume overlaps, can be clustered into seven main groups. Conformational differences within the clusters can be then identified by intramolecular interactions with other GPCR structural domains. Overall, our work provides a reorganization of the structural information of the ECL2 of class A GPCR subfamilies, highlighting differences and similarities on sequence and conformation levels.