A Novel “Activation Switch” Motif Common to All Aminergic Receptors

Abstract

Aminergic receptors are G protein-coupled receptors (GPCRs) that transduce signals from small endogenous biogenic amines to regulate intracellular signaling pathways. Agonist binding in the ligand binding pocket on the extracellular side opens and prepares a cavity on the intracellular face of the receptors to interact with and activate G proteins and β-arrestins. Here, by reviewing and analyzing all available aminergic receptor structures, we seek to identify activation-related conformational changes that are independent of the specific scaffold of the bound agonist, which we define as “activation conformational changes” (ACCs). While some common intracellular ACCs have been well-documented, identifying common extracellular ACCs, including those in the ligand binding pocket, is complicated by local adjustments to different ligand scaffolds. Our analysis shows no common ACCs at the extracellular ends of the transmembrane helices. Furthermore, the restricted access to the ligand binding pocket identified previously in some receptors is not universal. Notably, the Trp6.48 toggle switch and the Pro5.50-Ile3.40-Phe6.44 (PIF) motif at the bottom of the ligand binding pocket have previously been proposed to mediate the conformational consequences of ligand binding to the intracellular side of the receptors. Our analysis shows that common ACCs in the ligand binding pocket are associated with the PIF motif and nearby residues, including Trp6.48, but fails to support a shared rotamer toggle associated with activation. However, we identify two common rearrangements between the extracellular and middle subsegments, and propose a novel “activation switch” motif common to all aminergic receptors. This motif includes the middle subsegments of transmembrane helices 3, 5, and 6 and integrates both the PIF motif and Trp6.48.

Unraveling Activation-Related Rearrangements and Intrinsic Divergence from Ligand-Specific Conformational Changes of the Dopamine D3 and D2 Receptors

“…This rotation appears to be independent of whether an agonist can form hydrogen bonds with these serine residues, although such interactions may facilitate the rearrangement. Despite the pivotal significance attributed to TM5 serine residues for catecholamine receptors, , our comprehensive analysis of the entire aminergic family did not uncover any consistent rotamer changes of TM5 serine and threonine during activation . This absence of a common trend aligns with the lack of necessity for an agonist to form hydrogen bonds with these serine residues.…”

“…To ensure accuracy, these analyses require the receptor being analyzed to have high-resolution structures available for both the inactive and active states, which is the situation for both the D2R and D3R (Table S1). Thus, in the current study, utilizing these metrics and analysis protocols, we first carried out an in-depth investigation to determine whether there are additional ACCs shared between these two receptors, in addition to those commonly found for the aminergic family …”

“…To detect conformational differences between a pair of structures, we developed several analyses based on pairwise distance of various structural elements defined above …”

“…Recently, we developed an analysis infrastructure that allows for superposition-independent comparisons of GPCR structures. Using this infrastructure, we have analyzed the available structures of aminergic receptors to identify common ACCs that are independent of LCCs . While our analysis reveals no shared ACCs at the extracellular end of the transmembrane (TM) domain, we found common ACCs associated with the Pro 5.50 -Ile 3.40 -Phe 6.44 (PIF) motif (the superscripts denote Ballesteros-Weinstein numbering) and nearby residues, including the previously proposed toggle switch Trp 6.48 , at the bottom of the ligand binding pocket.…”

“…The ligands of these two receptors have been used, or are being developed, for the treatments of various neuropsychiatric disorders. Specifically, the D2R antagonists are used for schizophrenia, and the D3R antagonists or partial agonists are being actively developed for substance use disorders, , while agonists targeting these receptors have demonstrated promising results in mitigating the symptoms of Parkinson’s disease. − The different distributions of the D2R and D3R in the brain regions and their functional distinctions prompt the development of subtype-selective ligands with potentially fewer side effects. , However, it has been challenging to rationally develop subtype-selective D2R or D3R ligands with controlled efficacy and specificity for signaling pathways, due to the high sequence homology between these two receptors, as well as the difficulty in identifying activation-related conformational changes (ACCs) in their ligand binding pockets. ,− …”