Identification of ligand-specific G protein-coupled receptor states and prediction of downstream efficacy via data-driven modeling

Abstract

Ligand binding stabilizes different G protein-coupled receptor states via a complex allosteric process that is not completely understood. Here, we have derived free energy landscapes describing activation of the β2 adrenergic receptor bound to ligands with different efficacy profiles using enhanced sampling molecular dynamics (MD) simulations. These reveal shifts towards active-like states at the G protein binding site for receptors bound to partial and full agonists and that the ligands modulate the conformational ensemble of the receptor by tuning protein microswitches. We indeed find an excellent correlation between the conformation of the microswitches close to the ligand binding site and in the transmembrane region and experimentally reported cAMP signaling responses. Dimensionality reduction further reveals the similarity between the unique conformational states induced by different ligands and examining the output of classifiers highlights two distant hotspots governing agonism on transmembrane helices 5 and 7.

Modeling of CCR5 Recognition by HIV-1 gp120: How the Viral Protein Exploits the Conformational Plasticity of the Coreceptor

“…Compared to free CCR5, the receptor bound to gp120 shows reorientations of the intracellular ends of TM5, TM6 and TM7, which are the three regions in class A GPCRs whose concerted movements upon agonist binding allow the outward movement of TM6 and coupling to G protein. In the prototypic class A GPCR β2 adrenergic receptor (β2AR), stabilization of an active state involves key interactions along the TM5–TM7 interface that act as microswitches connecting the orthosteric binding site to the G protein binding region [ 66 ]. In our simulations of CD4–gp120–CCR5, TM5 adopts a strict canonical α-helical structure for two-thirds of its length on the intracellular side, except for the residues Met210–Ile212, Pro206, which are conserved in the GPCR family, and Gly202, whose position corresponds to the TM5 bulge of the β2AR.…”

“…In our simulations of CD4–gp120–CCR5, TM5 adopts a strict canonical α-helical structure for two-thirds of its length on the intracellular side, except for the residues Met210–Ile212, Pro206, which are conserved in the GPCR family, and Gly202, whose position corresponds to the TM5 bulge of the β2AR. In β2AR, the TM5 bulge represents the most proximal microswitch and its structural rearrangement is highly correlated with agonist efficacy [ 66 ]. In our simulations of CD4–gp120–CCR5, the gp120s also induce a characteristic bending in TM6.…”

“…Our MD simulations and mutagenesis data, however, suggest that other Envs, including primary Envs that are characterized by huge sequence variability [ 73 , 74 , 75 ], may exhibit distinct signaling properties. Indeed, the four gp120s studied here differentially shape the CCR5 transmembrane cavity, a process that may translate into distinct patterns of receptor activation [ 18 , 66 ]. The gp120s also differ in that they reorient differently the intracellular ends of TM5–7 ( Figure 4 ) and even more strikingly ICL3 ( Figure 3 , Figures S6e and S7 ).…”

Cooperative protein allosteric transition mediated by a fluctuating transmission network

“…For example, a repacking of a hydrophobic core as well as switching of polar interaction partners was reported for the nitrogen regulartory protein C 14 . Moreover, the above described lever-arm effect is reminiscent of structural changes in G protein-coupled receptors, where small changes in the ligand binding site are structurally amplified to large-scale protein surface changes at the G protein binding site 37,38 . A similar effect was also reported for the microbial rhodopsin bacteriorhodopsin, where the retinal cofactor pushing against Trp182 causes a large-scale outward motion of helix F 39 , and for the connection between ATP hydrolysis and protein conformational changes in heat shock protein 90 17 .…”

Allosteric Effect of Nanobody Binding on Ligand-Specific Active States of the β2 Adrenergic Receptor

“…The conformational ensembles were sampled using kinetically trapped active-like state sampling, or single state sampling, a recently published enhanced sampling technique. 29 In this relatively simple framework, 24 simulation replicas, each of 7.5 ns length, were launched from the starting structure ( Table 1 ). Their center point, c , was computed in a high-dimensional space spanned by a set of collective variables (CVs), which have previously been shown to well characterize the β2AR’s activation mechanism.…”