Sandbox Reserved 1722: Difference between revisions

The DRY motif is a proton microswitch that is located near the G-protein binding site C-terminal  on TM3 <ref name="Schonegge"/>.  It acts as an ion lock when the GPCR is not being activated, preventing unnecessary activation of the G-proteins <ref name="Zhou"/>. This motif is conserved in typical Class A GPCRS however, in MRGPRX2 it is only partially conserved. The arginine is conserved, while the aspartate is replaced by a glutamate and the tyrosine is replaced by a cysteine <ref name="Yang"/> <ref name="Sandoval">Sandoval, A., et al. "The Molecular Switching Mechanism at the Conserved D(E)RY Motif in Class-A GPCRs." Biophysical journal, 111(1), 79-89. https://doi.org/10.1016/j.bpj.2016.06.004 </ref>. The replacement of tyrosine for cysteine results in the helices coming closer together, creating a shallower binding pocket.<ref name="Zhou"/>  

MRGPRX2 consists of two binding pockets (seen in Figure 2). Sub-pocket 1 consists of acidic catalytic residues Asp-184 and Glu-164 that interact with substrates by making ion pairs. There are also some hydrophobic aromatic residues, Phe-170, Trp-243, and Phe-244, towards the top of the binding pocket.<ref name="Yang">Yang, Fan, et al. "Structure, function and pharmacology of human itch receptor complexes." Nature, Nature Publishing Group, 17 November 2021, https://www.nature.com/articles/s41586-021-04077-y</ref> These residues provide stabilization with ligands through stacking. Lastly, this pocket is in close proximity with the commonly conserved disulfide bond (formed by Cys-168 and Cys-180) seen in most Class A GPCRs. The second binding pocket forms hydrophobic interactions with larger substrates (seen in Figure 2), but is generally less studied.<ref name="Cao"/>

[[Image:Electro.PNG|450px|center|thumb|'''Figure 2''': Binding pocket of MRGPRX2 with cortistatin-14. Two different binding pockets are present in MRGPRX2 and cortistatin-14 interacts with both of them. <ref name="Cao"/>]]  

[[Image:Agoniststogether.PNG |400px|right|thumb|'''Figure 3''': Structure of MRGPRX2 Agonists. (A) Structure of R-Zinc 3573. A cationic ligand selected for binding to MRGPRX2.<ref name="Yang">Yang, Fan, et al. "Structure, function and pharmacology of human itch receptor complexes." Nature, Nature Publishing Group, 17 November 2021, https://www.nature.com/articles/s41586-021-04077-y</ref> (B) Structure of Cortistatin-14 with resolved amino acids highlighted in green. These ligands were used as a probes for MRGPRX2 function and stabilization for structure determination.<ref name="Yang">Yang, Fan, et al. "Structure, function and pharmacology of human itch receptor complexes." Nature, Nature Publishing Group, 17 November 2021, https://www.nature.com/articles/s41586-021-04077-y</ref>]]

<scene name='90/904328/Zinc/4'>(R)-Zinc-3573</scene> is a cation ligand that selectively binds to MRGPRX2 (Figure 3). Its N-dimethyl is inserted into subpocket 1 of the binding cavity with aromatic amino acid residues Phe-170, Trp-243, and Phe-244. In this <scene name='90/904328/Zizwithaa/5'>cavity</scene>, N-dimethyl group on the ligand makes ion pairs with Asp-184 and Glu-164. The ligand is then stabilized by stacking its ring with Trp-248 and the Cys-168 to Cys-180 disulfide bond <ref name="Yang">Yang, Fan, et al. "Structure, function and pharmacology of human itch receptor complexes." Nature, Nature Publishing Group, 17 November 2021, https://www.nature.com/articles/s41586-021-04077-y</ref>.

<scene name='90/904328/Overview_x2_c_pt_3/4'>Cortistatin-14</scene> is one of the peptide ligands that binds to MRGPRX2 (Figure 3). Cortistatin-14 interacts with the binding pocket through an <scene name='90/904328/Zic14_pt_3/5'>electrostatic</scene> interaction in sub-pocket 1 between Lys-3 on the peptide and Glu-164 and Asp-184 on MRGPRX2 <ref name="Cao"/>. Additionally, there are hydrophobic interactions in sub-pocket 2 between the peptide and the binding pocket due to the large hydrophobic amino acids on Cortistatin-14.  

[[Image:Gq_and_Gi_snip.PNG|300px|right|thumb|'''Figure 4''': Comparison of the conformational change for MRGPRX2 (light blue) coupled with Gq (teal) and MRGPRX2 (pink) coupled with Gi (purple).<ref name="Cao"/> PDB entry [https://www.rcsb.org/structure/7S8N 7S8N] and [https://www.rcsb.org/structure/7S8O 7S8O]]]

Once the ligand is bound, MRGPRX2 undergoes a conformational change that is transmitted through to the [https://en.wikipedia.org/wiki/G_protein#:~:text=G%20proteins%2C%20also%20known%20as,a%20cell%20to%20its%20interior. G-protein]. This conformational change is affected by the aforementioned deviances from Class A GPCRs. Rather than a large conformational change, a subtle one is induced. This will allow MRGPRX2 to interact with a G-protein. <scene name='90/904327/Gproteins/2'>G-proteins</scene> are composed of 3 subunits; α, β, and γ. When activated, the receptor acts as a Guanine nucleotide factor (GEF) which will allow the Gα subunit to have its GDP be replaced by a GTP. This will cause the Gα subunit to dissociate from the dimer Gβγ. The Gα subunit is then able to act as a secondary messenger to begin the signal transduction in the cell. MRGPRX2 interacts with two different types of G-proteins; Gi and Gq. These G-proteins are activated by similar interactions with the receptor however, they are structurally different and changes in the induced conformation are observed (Figure 4).   

[[Image:Zinc_and_drugs_snip.PNG|450px|right|thumb|'''Figure 5''': Structures of (R)-Zinc-3573, Dextromethorphan, Morphine, and Codeine. The blue circles indicate conserved basic N-dimethyl group and the green squares show the conserved benzene rings.<ref name="Cao"/>]]

MRGPRX2 activation is associated with chronic itching or anaphylaxis reactions, a common side effect of many prescribed medications. <ref name="Cao"/> Among these drugs are opiods [https://en.wikipedia.org/wiki/Morphine morphine] and [https://en.wikipedia.org/wiki/Codeine codeine] and [https://en.wikipedia.org/wiki/Dextromethorphan dextromethorphan]. By analyzing the structures of these drugs, it can be seen that they contain chemical features similar to <scene name='90/904328/Zizwithaa/5'>agonist R-Zinc-3573</scene> (see Figure 5). They contain a conserved benzene ring that stabilizes them in binding pocket one (see Figure 5). Similarly, they contain an N-dimethyl group that would allow them to form key bonds with residues Asp-184 and Glu-164. Lastly, these drugs have a similar shape and size to that of the agonist R-Zinc-3573.<ref name="Babina"> Babina, M., et al. "MRGPRX2 Is the Codeine Receptor of Human Skin Mast Cells: Desensitization through β-Arrestin and Lack of Correlation with the FcεRI Pathway." Journal of Investigative Dermatology, 141(6), 1286-1296. https://doi.org/10.1016/j.jid.2020.09.017</ref> These structural and chemical similarities indicate the possibility of a similar binding mechanism.