Active-State Models of Ternary GPCR Complexes: Determinants of Selective Receptor-G-Protein Coupling

Abstract

Based on the recently described crystal structure of the β2 adrenergic receptor - Gs-protein complex, we report the first molecular-dynamics simulations of ternary GPCR complexes designed to identify the selectivity determinants for receptor-G-protein binding. Long-term molecular dynamics simulations of agonist-bound β2AR-Gαs and D2R-Gαi complexes embedded in a hydrated bilayer environment and computational alanine-scanning mutagenesis identified distinct residues of the N-terminal region of intracellular loop 3 to be crucial for coupling selectivity. Within the G-protein, specific amino acids of the α5-helix, the C-terminus of the Gα-subunit and the regions around αN-β1 and α4-β6 were found to determine receptor recognition. Knowledge of these determinants of receptor-G-protein binding selectivity is essential for designing drugs that target specific receptor/G-protein combinations.

A Transient Interaction between the Phosphate Binding Loop and Switch I Contributes to the Allosteric Network between Receptor and Nucleotide in Gαi1

“…A similar interaction is observed in structures of inhibited G␣ subunits (76 -78) and in the context of the G␤␥ subunits (16,17) prompting an analogy to a "seatbelt" that prevents GDP release (16). Consistent with the role of this interaction in controlling nucleotide release, the distance between the closest Glu-43O⑀ and Arg-178N atoms lengthens under conditions that promote nucleotide exchange (75).…”

“…Molecular dynamics simulations proposed that receptor recognition stabilizes the ␣N-␤1 junction and the ␤2-␤3 hairpin of the G␣ subunit (74,75), and fluorescence studies indeed revealed receptor-mediated changes in the solvent accessibility of these regions (7,72) (Fig. 9, orange).…”

“…Although the ␣5 helix has been the most extensively studied contributor to G␣ activation, additional conformational changes have been identified using mutagenesis (67,72,73), biophysical (18,69,72), and computational approaches (71,74,75). Molecular dynamics simulations proposed that receptor recognition stabilizes the ␣N-␤1 junction and the ␤2-␤3 hairpin of the G␣ subunit (74,75), and fluorescence studies indeed revealed receptor-mediated changes in the solvent accessibility of these regions (7,72) (Fig.…”

An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G-Protein-Coupled Receptor Ligands

“…A model for the G αi -protein was constructed, using a previously published model for active-state G i in complex with the D 2 dopaminergic receptor. 67 The D 2 -G αi ternary complex was aligned to the ADRB2-G αs complex and the BU72-μOR complex, followed by substituting the Nb9-8 with the G αi .…”

Structure versus function—The impact of computational methods on the discovery of specific GPCR–ligands

“…A structural model for the bradykinin B 2 receptor indicated the presence of the ionic lock and showed, in combination with mutational studies, its role for the stabilization of the inactive receptor state [11]. Kling et al [12] used an active-state homology model of the dopamine D 2 receptor-Gα i protein-complex. Their simulations revealed ligand-dependent conformational changes of the G protein binding epitopes that show substantial differences for full or partial agonist bound complexes.…”