Hidden GPCR structural transitions addressed by multiple walker supervised molecular dynamics (mwSuMD)

Abstract

The structural basis for the pharmacology of G protein-coupled receptors (GPCR), the most abundant membrane proteins and the target of about 35% of approved drugs, is still a matter of intense study. What makes GPCRs challenging to study is the inherent flexibility and the metastable nature of interaction with extra- and intracellular partners that drive their effects. Here, we present a molecular dynamics (MD) adaptive sampling algorithm, namely multiple walker supervised molecular dynamics (mwSuMD), to address complex structural transitions involving GPCRs without energy input. By increasing the complexity of the simulated process, we first report the binding and unbinding of the vasopressin peptide from its receptor V 2 . Successively, we show the stimulatory (G s ) and inhibitory (G i ) G proteins binding to the adrenoreceptor β 2 (β 2 AR), and the adenosine 1 receptor (A 1 R), respectively. Then we present the complete transition of the glucagon-like peptide-1 receptor (GLP-1R) from inactive to active, agonist and G s -bound state, and the GDP release from the activated G s . Finally, we report the heterodimerization between the adenosine receptor A 2 (A 2A R) and the dopamine receptor D 2 (D 2 R) and subsequent bivalent ligand binding. We demonstrate that mwSuMD can address, without or with limited energetic bias, complex binding processes such as G protein selectivity and homo- and heterodimerization that are intrinsically linked to the dynamics of the protein and out of reach of classic MD.