Prediction of interfaces for oligomerizations of G‐protein coupled receptors

Abstract

Several lines of biochemical and pharmacological evidence have suggested that some G-protein-coupled receptors (GPCRs) form homo oligomers, hetero oligomers or both. The GPCRs oligomerizations are considered to be related to signal transduction and some diseases. Therefore, an accurate prediction of the residues that interact upon oligomerization interface would further our understanding of signal transduction and the diseases in which GPCRs are involved. One of the complications for such a prediction is that the interfaces differ with the subtypes, even within the same GPCR family. Focusing on the distribution of residues conserved on the molecular surface in a particular subtype, we developed a new method to predict the interface for the GPCR oligomers, and applied it to several subtypes of known GPCRs to check the sensitivity. Subsequently, we found that predicted interfaces of rhodopsin, D(2) dopamine receptor and beta(2) adrenergic receptor agreed with the experimentally suggested interfaces, despite difference in the interface region among the three subtypes. Moreover, a highly conserved residue detected from the D(2) dopamine receptor corresponded to a residue involved in a missense change found in the large family of myoclonus dystonia. Our observation suggests the possibility that the disease is caused by the disorder of the oligomerization, although the molecular mechanism of the disease has not been revealed yet. The benefits and the pitfalls of the new method will be discussed, based on the results of the applications.

The stoichiometric ‘signature’ ofRhodopsin-family G protein-coupled receptors

“…It is noteworthy that of 26 receptors previously reported to be dimers, often in multiple publications (Table S3), 21 behaved as monomers in our assays. The new data are in closer agreement with the growing body of single-molecule microscopy data that has failed to report constitutive dimerization in most cases (9,(22)(23)(24)34). The present data also argue against a general model of allosteric regulation of GPCR homodimers founded, principally, on pharmacological analysis.…”

“…To further confirm that Rhodopsin-family GPCRs do indeed adopt one of two different stoichiometric states, we used single-molecule cross-color coincidence detection (SMCCCD (34)). Briefly, candidate GPCRs were transiently expressed in Chinese Hamster Ovary (CHO) K1 cells under the control of a weak promoter to ensure approximately physiological i.e.…”

Oligomerization of G-Protein-Coupled Receptors: Lessons from the YeastSaccharomyces cerevisiae

“…However, these and their related receptors may also oligomerize via their transmembrane domains, because oligomers persist when disulfide bonds are reduced or C-terminal interaction domains are removed (9,77,116). Indeed, putative oligomerization interfaces in GPCR transmembrane domains have been predicted by computational methods (71). Understanding the mechanisms by which GPCRs form specific homo-and hetero-oligomeric assemblies ultimately will require detailed investigation at the structural level.…”

Role of iso-receptors in receptor-receptor interactions with a focus on dopamine iso-receptor complexes

“…In this respect, the evidence that intrinsically disordered domains play a significant role in protein-protein interaction (Hilser and Thompson, 2007) was particularly intriguing, and the analysis of intrinsic disorder is a presently followed strategy to identify GPCR regions potentially linked to RRIs (Agnati et al, 2008b;Tovo-Rodrigues et al, 2014). The analysis of disordered domains, however, does not help in the prediction of putative interaction sites located in the TM helices and other methods are needed to estimate favorable contact surfaces on the TM helices of GPCR (see Nemoto and Toh, 2005). -The second aspect concerns the estimate of the possible geometrical arrangements the receptor complex can assume.…”

“…Following a consensus approach is of particular importance in this field (Ferron et al, 2006;Agnati et al, 2008b), since it increases the reliability of disorder prediction minimizing the falsepositive rates (Huang et al, 2014). -Evolutionary trace method, in combination with experimentally determined structure data of rhodopsin and β-adrenergic receptors, has been proposed by Nemoto and Toh (2005) to predict the likely hetero-and homo-oligomerization interfaces of family A GPCR. Such a procedure can be accessed through the GRIP server (http://grip.cbrc.jp/GRIP/) and appears particularly suited to identify potential interaction interfaces present in the well-structured TM domains of DA-Rs .…”