Chemogenomic Analysis of G-Protein Coupled Receptors and Their Ligands Deciphers Locks and Keys Governing Diverse Aspects of Signalling

Jörg D Wichard,Gerd Krause,Nikolaus Heinrich,Gunnar Kleinau,Antonius Ter Laak,Ronald Kühne

doi:10.1371/journal.pone.0016811

Abstract

Understanding the molecular mechanism of signalling in the important super-family of G-protein-coupled receptors (GPCRs) is causally related to questions of how and where these receptors can be activated or inhibited. In this context, it is of great interest to unravel the common molecular features of GPCRs as well as those related to an active or inactive state or to subtype specific G-protein coupling. In our underlying chemogenomics study, we analyse for the first time the statistical link between the properties of G-protein-coupled receptors and GPCR ligands. The technique of mutual information (MI) is able to reveal statistical inter-dependence between variations in amino acid residues on the one hand and variations in ligand molecular descriptors on the other. Although this MI analysis uses novel information that differs from the results of known site-directed mutagenesis studies or published GPCR crystal structures, the method is capable of identifying the well-known common ligand binding region of GPCRs between the upper part of the seven transmembrane helices and the second extracellular loop. The analysis shows amino acid positions that are sensitive to either stimulating (agonistic) or inhibitory (antagonistic) ligand effects or both. It appears that amino acid positions for antagonistic and agonistic effects are both concentrated around the extracellular region, but selective agonistic effects are cumulated between transmembrane helices (TMHs) 2, 3, and ECL2, while selective residues for antagonistic effects are located at the top of helices 5 and 6. Above all, the MI analysis provides detailed indications about amino acids located in the transmembrane region of these receptors that determine G-protein signalling pathway preferences.

Highlights

G-protein-coupled receptors (GPCRs) constitute a large superfamily of transmembrane receptors which convey extracellular signals into the intracellular region to effect sensory perception, chemotaxis, neurotransmission, cell communication and several other physiological events
Apart from a few exceptions such as the Glycoprotein hormone receptors (GPHRs) and Leucine-rich repeat containing G-protein coupled receptors (LGRs 4-8) [49], family A GPCRs are characterized by ligand binding close to or inside the transmembrane helices and the extracellular loops [11,50,51]
This is in contrast to other GPCR families and it has been proposed that this circumstance may be the basis for their evolutionary success, reflected by the highest number of members compared to the more structurally complex receptor proteins that have long ligandbinding N termini [9]

Summary

Introduction

G-protein-coupled receptors (GPCRs) constitute a large superfamily of transmembrane receptors which convey extracellular signals into the intracellular region to effect sensory perception, chemotaxis, neurotransmission, cell communication and several other physiological events. GPCRs are subdivided into several families [6], whereby the largest family is the rhodopsin-like family A Understanding these complex proteins and related signaling systems is of enormous importance, not least for drug discovery [7,8,9,10,11]. This is reflected by the fact that GPCRs are the largest target group for therapeutics [12] including up to 40% of currently marketed drugs [13]

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