Sandbox Reserved 1701: Difference between revisions
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[[Image:PIF_resized.png|500px|right|thumb|'''Figure 3.''' Conserved PIF motif in 5HT2AR (teal) compared to the LLF motif found in MRGPRX2 (red). Transmembrane helices and residues are numbered and labeled to show how this structural change shifts the orientation of the helices.]] | [[Image:PIF_resized.png|500px|right|thumb|'''Figure 3.''' Conserved PIF motif in 5HT2AR (teal) compared to the LLF motif found in MRGPRX2 (red). Transmembrane helices and residues are numbered and labeled to show how this structural change shifts the orientation of the helices. PDBs: 7s8l and 6wha.]] | ||
Another motif found in most, but not all, A family GPCR’s is the PIF motif. The PIF residues (<scene name='90/904305/Llf_motif/5'>Leu-117, Leu-194, and Phe-232</scene>) are found on transmembrane helices 5, 3, and 6, respectively. In MRGPRX2, the PIF motif is changed to LLF residues. '''Figure 3''' shows the conserved PIF motif on 5HT2AR, <scene name='90/904306/Alignment_llf/1'>compared</scene> to the LLF motif on MRGPRX2. This change to LLF shifts helix 6 towards helix 3, and contributes to the tighter packing of helices <ref name="Cao">PMID: 34789874</ref> <ref name="Yang">PMID: 34789875</ref> and therefore a more surface-level ligand binding site. | Another motif found in most, but not all, A family GPCR’s is the PIF motif. The PIF residues (<scene name='90/904305/Llf_motif/5'>Leu-117, Leu-194, and Phe-232</scene>) are found on transmembrane helices 5, 3, and 6, respectively. In MRGPRX2, the PIF motif is changed to LLF residues. '''Figure 3''' shows the conserved PIF motif on 5HT2AR, <scene name='90/904306/Alignment_llf/1'>compared</scene> to the LLF motif on MRGPRX2. This change to LLF shifts helix 6 towards helix 3, and contributes to the tighter packing of helices <ref name="Cao">PMID: 34789874</ref> <ref name="Yang">PMID: 34789875</ref> and therefore a more surface-level ligand binding site. | ||
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==== DRY/ ERC Motif ==== | ==== DRY/ ERC Motif ==== | ||
[[Image:Screen Shot 2022-03-15 at 10.23.20 AM.png|200px|left|thumb|'''Figure 4.''' ERC Motif]] | [[Image:Screen Shot 2022-03-15 at 10.23.20 AM.png|200px|left|thumb|'''Figure 4.''' ERC Motif of MRGPRX2 with key residues shown as ball and stick. PDB: 7s8l.]] | ||
The E/DRY motif in most class A GPCRs is responsible for forming salt bridges with surrounding residues and TM6<ref name="Rovati">PMID: 17192495</ref>. These salt bridges maintain the inactive conformation of the receptor until ligand binding breaks the ionic "lock" from these interactions. MRGPRX2 has an ERC motif rather than the typically [https://proteopedia.org/wiki/index.php/A_Physical_Model_of_the_%CE%B22-Adrenergic_Receptor#conserved%20DRY%20motif conserved E/DRY Motif]. The amino acid residue shift from TYR-174 to CYS-128 allows compaction of the helices in MRGPRX2 where the standard TYR physically pushes the TMD helices apart('''Figure 4'''). The conserved residues E and R still form salt bridges with nearby residues. This and the closer packing of the helices contribute to a less significant TMD conformational change upon ligand binding ('''Figure 10'''). | The E/DRY motif in most class A GPCRs is responsible for forming salt bridges with surrounding residues and TM6<ref name="Rovati">PMID: 17192495</ref>. These salt bridges maintain the inactive conformation of the receptor until ligand binding breaks the ionic "lock" from these interactions. MRGPRX2 has an ERC motif rather than the typically [https://proteopedia.org/wiki/index.php/A_Physical_Model_of_the_%CE%B22-Adrenergic_Receptor#conserved%20DRY%20motif conserved E/DRY Motif]. The amino acid residue shift from TYR-174 to CYS-128 allows compaction of the helices in MRGPRX2 where the standard TYR physically pushes the TMD helices apart('''Figure 4'''). The conserved residues E and R still form salt bridges with nearby residues. This and the closer packing of the helices contribute to a less significant TMD conformational change upon ligand binding ('''Figure 10'''). | ||
<scene name='90/904306/Alignment_erc/2'>ERC/DRY Alignment</scene> | <scene name='90/904306/Alignment_erc/2'>ERC/DRY Alignment</scene> | ||
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==== Disulfide Bonds ==== | ==== Disulfide Bonds ==== | ||
[[Image:Screen Shot 2022-03-27 at 5.45.52 PM.png|300px|right|thumb|'''Figure 5.''' Overlay of the 5HT2AR and MRGPRX2 TMP for comparison of disulfide bond location.]] | [[Image:Screen Shot 2022-03-27 at 5.45.52 PM.png|300px|right|thumb|'''Figure 5.''' Overlay of the 5HT2AR and MRGPRX2 TMP for comparison of disulfide bond location. PDBs: (MRGPRX2): 7s8l and (5HT2A): 6wha.]] | ||
In a large majority of class A GPCRs, there is a conserved disulfide bond between extracellular loop 2 (ECL2) and transmembrane helix 3 (TM3). This bond has been proposed to have a role in structural stability, expression, and function of GPCRs<ref name="Naranjo">PMID: 25445670</ref>. The MRGPRX2 disulfide bond is between <scene name='90/904305/Disulfide_bond/2'>Cys-168 and Cys-180</scene> on TM helices 5 and 4, respectively. For example, the <scene name='90/904306/5ht2a_disulfide/2'>serotonin GPCR</scene> shows this disulfide bond between the ECL2 and TM3. Although this bond is in a different location than other class A GPCRs, there is evidence to suggest its location is essential for the signaling of the X2 receptor as the ECL2 instead located at the top of TM4 and TM5 allowing for the large, extracellular binding pocket observed in X2<ref name="Cao">PMID: 34789874</ref>. | In a large majority of class A GPCRs, there is a conserved disulfide bond between extracellular loop 2 (ECL2) and transmembrane helix 3 (TM3). This bond has been proposed to have a role in structural stability, expression, and function of GPCRs<ref name="Naranjo">PMID: 25445670</ref>. The MRGPRX2 disulfide bond is between <scene name='90/904305/Disulfide_bond/2'>Cys-168 and Cys-180</scene> on TM helices 5 and 4, respectively. For example, the <scene name='90/904306/5ht2a_disulfide/2'>serotonin GPCR</scene> shows this disulfide bond between the ECL2 and TM3. Although this bond is in a different location than other class A GPCRs, there is evidence to suggest its location is essential for the signaling of the X2 receptor as the ECL2 instead located at the top of TM4 and TM5 allowing for the large, extracellular binding pocket observed in X2<ref name="Cao">PMID: 34789874</ref>. | ||
<scene name='90/904306/Alignment_disulfide/1'>Disulfide Bond Alignment</scene> | <scene name='90/904306/Alignment_disulfide/1'>Disulfide Bond Alignment</scene> | ||
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=== After Activation === | === After Activation === | ||
After ligand binding and transmembrane protein activation, this signal is transmitted to the alpha subunit of the G-protein which undergoes chemical and conformational changes. The alpha subunit is initially bound with GDP which is then physically replaced by GTP leading to conformational changes. These changes can be seen in this [https://youtu.be/k4fjSZV_-OQ video] of a G-protein alpha subunit activation derived from common rats. | After ligand binding and transmembrane protein activation, this signal is transmitted to the alpha subunit of the G-protein which undergoes chemical and conformational changes. The alpha subunit is initially bound with GDP which is then physically replaced by GTP leading to conformational changes. These changes can be seen in this [https://youtu.be/k4fjSZV_-OQ video] of a G-protein alpha subunit activation derived from common rats. This video was constructed by one of the page's authors using PDB files 1bof and 1cip. | ||
[[Image:Screen Shot 2022-03-282 at 6.59.44 PM.png|500px|center|thumb|'''Figure 9.''' Overlay of unbound (transparent) and bound (opaque) transmembrane proteins of both MRGRPX2 (left) and 5-HT2AR (right).]] | [[Image:Screen Shot 2022-03-282 at 6.59.44 PM.png|500px|center|thumb|'''Figure 9.''' Overlay of unbound (transparent) and bound (opaque) transmembrane proteins of both MRGRPX2 (left) and 5-HT2AR (right). PDBs: 7s8l and 6wha.]] | ||
=== Clinical Relevance === | === Clinical Relevance === | ||
