Sandbox Reserved 1722

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This Sandbox is Reserved from February 28 through September 1, 2022 for use in the course CH462 Biochemistry II taught by R. Jeremy Johnson at the Butler University, Indianapolis, USA. This reservation includes Sandbox Reserved 1700 through Sandbox Reserved 1729.

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Human Itch GPCR

Structure of MRGPRX2 with transmembrane helices shown in blue, Gαq shown in purple, Gβ1 shown in yellow, and Gγ2 shown in pink (PDB entry 7S8L)

Drag the structure with the mouse to rotate

Figure 1:MRGPRX2 in the cellular membrane. ^[1]

1 G-Protein Coupled Receptors
- 1.1 Class A GCPRs
- 1.2 MRGPRs
2 Changes in MRGPRX2 from Standard Class A GPCRS
3 Binding Pocket
- 3.1 Agonists
  - 3.1.1 Cation
  - 3.1.2 Peptide
4 MRGPRX2 Signaling Pathway
5 Clinical Relevance

G-Protein Coupled Receptors

G-protein coupled receptors(GCPRs) are a large family of cell surface membrane receptors. Once bound to a wide variety of extracellular ligands, GCPRs undergo a conformational change and relay information to intracellular secondary messengers ^[2]. This G protein activation results in a cellular response dependent on the ligand bound and location of the GPCR in the body. GCPRs can be broken down into five families: the rhodopsin family (class A), the secretin family (class B), the adhesion family, the glutamate family (class C), and the frizzled/taste family (class F) ^[3]. All of the families have a similar transmembrane (TM) domain consisting of seven complexed with intracellular G proteins.

Class A GCPRs

Class A GPCRS or rhodopsin-like GPCRS are the largest and most studied type of GPCRS. Due to the diversity of these receptors they are found in many aspects of physiology. For example, in skin, liver, and kidney diseases. They are characterized by conserved motifs including DRY, PIF, Sodium Binding, and the CWxP ^[4]. A common example of a class A GPCRS is the β2AR receptor.

MRGPRs

The human itch GPCR, or Mas-related G-protein coupled receptor (MRGPR), is a Class A GPCR found in human sensory neurons and is responsible for the sensation of “itching” caused by skin irritation and diseases, insect bites, and hypersensitivity to certain drugs. MRGPR's are broken into 4 groups consisting of MRGPRX1, MRGPRX2, MRGPRX3, and MRGPRX4. MRGPRX4 is responsible for cholestatic itching, an intense itching felt during pregnancy on the soles of the feet and palms of hands. Meanwhile, MRGPRX2 regulates degranulation and hypersensitivity itch reactions ^[1]. These two, chiefly MRGPRX2, are often targets for drugs that result in mast cell degranulation and hypersensitivity side effects, such as swelling and itching. In comparison to other Class A GPCRs, MRGPRX2 binds to an even wider range of ligands, including agonists such as cationic small molecules and peptide ligands.

Changes in MRGPRX2 from Standard Class A GPCRS

Toggle Switch

In β2AR, and other Class A GPCRs, a “toggle switch” of which limits the proximity of the TM helices as tryptophan sterically occludes tight interaction. This results in a deep binding pocket for ligand binding. In contrast, in MRGPRX2 Trp-286 is replaced by ^[1] ^[5]. Glycine is a much smaller amino acid and thus allows the helices to close the base of the binding pocket. This causes MRGPRX2 to have a much shallower binding site and allows more promiscuous ligand binding. This can be seen in a shorter distance from the toggle switch to the ligand in β2AR compared to MRGPRX2.

Disulfide bonds

In common Class A GPCRs the disulfide bond associated with the initiation of signal transduction is located on the extracellular domain of the 7 transmembrane helices. ^[3] The , a well studied Class A GPCR, occurs between transmembrane three (TM3) C106 and extracellular loop (EL) C191. This loop crosses through the middle of the extracellular domain, creating a barrier for bulkier substrates. In MRGPRX2, the is located between (TM4) C168 and (TM5) C180. This is a TM to TM disulfide bond as compared to a TM to EL disulfide bond seen in typical Class A GPCRs. This lack of interaction with the extracellular loop seen in MRGPRX2 causes the extracellular loop to flip on top of the TM4 and TM5 resulting in an open space for larger substrates to be able to interact with the receptor.

PIF Motif

MRGPRX2 also differs from typical Class A GPCRs based on substitutions in the PIF/connector motif, which acts as a microswitch. PIF plays a role in connecting the binding pocket to conformational rearrangements required for receptor activation^[6]. The PIF motif is located towards the base of the TM domains. In a Class A GPCR, like β2AR, the consists of Phe-211, Ile-121, and Phe-282 on TM domains 5, 3, and 6, respectively. However, for MRGPRX2, this is replaced with Leu-194 on TM5, Leu-117 on TM3, and Phe-232 on TM6.

DRY Motif

The DRY motif is a proton microswitch that is located near the G-protein binding site C-terminal on TM3 ^[6]. It acts as an ion lock when the GPCR is not being activated, preventing unnecessary activation of the G-proteins ^[4]. 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 ^[5] ^[7]. The replacement of tyrosine for cysteine results in the helices coming closer together, creating a shallower binding pocket.^[4]

Sodium Binding

The sodium site motif facilitates the conformational change of GPCR upon activation.^[8] A sodium molecule sits in the middle of the TM7 helices where it is stabilized by conserved residues aspartate (TM2), serine (TM2), and three water molecules. The sodium is able to make a salt bridge with the aspartate at this position. The sodium acts similar to a ball joint in which it allows for the TM helices be spread apart and induce larger conformational change upon binding. In MRGPRX2 this motif is only partially conserved. The aspartate (TM2) is conserved while the serine is replaced by a glycine.^[5] This creates a less favorable environment for the stabilization of sodium. Currently, in crystallization structures no sodium has been seen at this site. Thus making it inconclusive on whether it plays a role in the conformational change to activate G-proteins upon binding to the receptor.^[5]

Binding Pocket

MRGPRX2 consists of two binding pockets (seen in Figure 2). Sub-pocket 1 consists of primarily hydrophobic aromatic residues; Phe-170, Trp-243, and Phe-244.^[5] These residues provide stabilization with ligands through stacking. This pocket also contains acidic catalytic residues Asp-184 and Glu-164 that interact with substrates by making ion pairs. 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 electrostatic interactions with larger substrates (seen in Figure 2), but is generally less studied.^[1]

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. ^[1]

Agonists

Figure 3: Structure of MRGPRX2 Agonists. (A) Structure of R-Zinc 3573. A cationic ligand selected for binding to MRGPRX2.^[5] (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.^[5]

Cation

is a cation ligand that selectively binds to MRGPRX2. 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 , 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 ^[5].

Peptide

is one of the peptide ligands that binds to MRGPRX2. Cortistatin-14 interacts with the binding pocket through an interaction in sub-pocket 1 between Lys-3 on the peptide and Glu-164 and Asp-184 on MRGPRX2 ^[1]. 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.

MRGPRX2 Signaling Pathway

MRGPRX2 mediates degranulation of mast cells through interaction with Gq and Gi subunits. Gq activation signals through Phospholipase C, which catalyzes the cleavage of Phosphatidylinositol bisphosphate into diacylglycerol (DAG) and inositol trisphosphate (IP3). DAG is then able to increase the activity of protein kinase C. IP3 receptor is ligand gated calcium channel on the endoplasmic reticulum (ER), that causes the release of calcium in cytoplasm. Subsequently, this results in muscle contraction and enzyme activation.

MRGPRX2 also interacts with Gi or G-protein inhibitory, which is structurally homologous to Gs (G-protein stimulatory), and will inhibit adenylyl cyclase and therefore lowers (cAMP). Gi is stimulated when somatostatin binds to receptor in pancreas.

Clinical Relevance

Figure 4: Structures of (R)-Zinc-3573, Dextromethorphan, Morphine, and Codeine. The red circles indicate conserved basic N-dimethyl group and the blue squares show the conserved benzene rings.^[1]

Many drugs activate MRGPRX2 as a side effect that causes the sensation of itchiness ^[1]. Among these drugs are morphine, codeine, and dextromethorphan. These drugs contain similar chemical features that are also found in (R)- ZINC-3573, introducing the idea of a similar binding mechanism ^[9].

Due to mutations in key structural features of typical Class A GPCRS, MRGPRX2, it is able to bind to a variety of substrates that then mediate the signaling pathway for the sensation of itching.

References

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 Cao, Can, et al. "Structure, function and pharmacology of human itch GPCRs." Nature, Nature Publishing Group, 17 November 2021, https://www.nature.com/articles/s41586-021-04126-6
↑ Thal, David M., et al. "Structural insights into G-protein-coupled receptor allostery." Nature, Nature Publishing Group, 04 July 2018, https://www.nature.com/articles/s41586-018-0259-z
↑ ^3.0 ^3.1 Zhang D, Zhao Q, Wu B. Structural Studies of G Protein-Coupled Receptors. Mol Cells. 2015 Oct;38(10):836-42. doi: 10.14348/molcells.2015.0263. Epub 2015, Oct 15. PMID:26467290 doi:http://dx.doi.org/10.14348/molcells.2015.0263
↑ ^4.0 ^4.1 ^4.2 Zhou Q, Yang D, Wu M, Guo Y, Guo W, Zhong L, Cai X, Dai A, Jang W, Shakhnovich EI, Liu ZJ, Stevens RC, Lambert NA, Babu MM, Wang MW, Zhao S. Common activation mechanism of class A GPCRs. Elife. 2019 Dec 19;8. pii: 50279. doi: 10.7554/eLife.50279. PMID:31855179 doi:http://dx.doi.org/10.7554/eLife.50279
↑ ^5.0 ^5.1 ^5.2 ^5.3 ^5.4 ^5.5 ^5.6 ^5.7 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
↑ ^6.0 ^6.1 Schonegge, Anne-Marie, et al. "Evolutionary action and structural basis of the allosteric switch controlling β2AR functional selectivity." Nature, Nature Publishing Group, 18 December 2017, https://www.nature.com/articles/s41467-017-02257-x
↑ 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
↑ Katritch V, Fenalti G, Abola EE, Roth BL, Cherezov V, Stevens RC. Allosteric sodium in class A GPCR signaling. Trends Biochem Sci. 2014 May;39(5):233-44. doi: 10.1016/j.tibs.2014.03.002. Epub , 2014 Apr 21. PMID:24767681 doi:http://dx.doi.org/10.1016/j.tibs.2014.03.002
↑ 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

Retrieved from "http://52.214.119.220/wiki/index.php/Sandbox_Reserved_1722"

@@ Line 40: / Line 40: @@
 == Binding Pocket ==
+MRGPRX2 consists of two binding pockets (seen in Figure 2). Sub-pocket 1 consists of primarily hydrophobic aromatic residues; Phe-170, Trp-243, and Phe-244.<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. This pocket also contains acidic catalytic residues Asp-184 and Glu-164 that interact with substrates by making ion pairs. 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 electrostatic interactions with larger substrates (seen in Figure 2), but is generally less studied.<ref name="Cao"/>
-MRGPRX2 consists of two binding pockets (seen in Figure 2). Sub-pocket 1 consists of primarily hydrophobic aromatic residues; Phe-170, Trp-243, and Phe-244. These residues provide stabilization with ligands through stacking. This pocket also contains acidic catalytic residues Asp-184 and Glu-164 that interact with substrates by making ion pairs. 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 electrostatic interactions with larger substrates (seen in Figure 2), but is generally less studied.
+[[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:Electro.PNG|350px|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"/>]]
 ==== Agonists ====
+[[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>]]
 ===== Cation =====
@@ Line 54: / Line 55: @@
 <scene name='90/904328/Overview_x2_c_pt_3/4'>Cortistatin-14</scene> is one of the peptide ligands that binds to MRGPRX2. Cortistatin-14 interacts with the binding pocket through an <scene name='90/904328/Zic14_pt_3/4'>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:Agoniststogether.PNG |450px|center|thumb|'''Figure 3''': Structure of MRGPRX2 Agonists. (A) Structure of R-Zinc 3573. A cationic ligand selected for binding to MRGPRX2. This ligand was used as a probe 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> (B) Structure of Cortistatin-14 with resolved amino acids highlighted in green.<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>]]
@@ Line 69: / Line 68: @@
 [[Image:Drugs_and_zinc.PNG|400px|right|thumb|'''Figure 4''': Structures of (R)-Zinc-3573, Dextromethorphan, Morphine, and Codeine. The red circles indicate conserved basic N-dimethyl group and the blue squares show the conserved benzene rings.<ref name="Cao"/>]]
 Many drugs activate MRGPRX2 as a side effect that causes the sensation of itchiness <ref name="Cao"/>. Among these drugs are morphine, codeine, and dextromethorphan. These drugs contain similar chemical features that are also found in (R)- ZINC-3573, introducing the idea of a similar binding mechanism <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>.