Unsupervised Classification of G-Protein Coupled Receptors and Their Conformational States Using IChem Intramolecular Interaction Patterns

Abstract

Over the last decade, the ever-growing structural information on G-protein coupled receptors (GPCRs) has revealed the three-dimensional (3D) characteristics of a receptor structure that is competent for G-protein binding. Structural markers are now commonly used to distinguish GPCR functional states, especially when analyzing molecular dynamics simulations. In particular, the position of the sixth helix within the seven transmembrane domain (TM) is directly related to the coupling of the G-protein. Here we show that the structural pattern defined by intramolecular hydrogen bonds (excluding backbone/backbone interactions), ionic bonds and aromatic interactions in the TM suits the comparison of GPCR 3D structures and the unsupervised distinction of the receptor states. Firstly, we analyze a microsecond long molecular dynamic simulation of the human ß2-adrenergic receptor (ADRB2). Clustering of the 3D structures by pattern similarity identifies stable states which match the conformational classes defined by structural markers. Furthermore, the method directly spots the few state-specific interactions. Transforming pattern into graph, we extent the method to the comparison of different GPCRs. Clustering all GPCR experimentally-determined structures by clique relative size firstly separates receptors, then their conformational states, thereby suggesting that the interaction patterns are specific of the receptor sequence and that the interaction signatures of conformational states are not shared across distant homologs.