Sandbox Reserved 1668
From Proteopedia
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{{Sandbox_Reserved_BHall_Sp21}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --> | {{Sandbox_Reserved_BHall_Sp21}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --> | ||
| - | == | + | ==Structure of human PYCR1 complexed with THFA== |
<StructureSection load='6XOZ' size='340' side='right' caption='Caption for this structure' scene=''> | <StructureSection load='6XOZ' size='340' side='right' caption='Caption for this structure' scene=''> | ||
This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the < and > signs. | This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the < and > signs. | ||
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== Function of your protein == | == Function of your protein == | ||
| - | + | PYCR1 is a protein involved in proline biosynthesis. THFA is a ligand that can bind to the active site on the PYCR1 protein. This inhibits PYCR1's ability to bind to proline-5-carboxylate to synthesize proline. | |
| + | Here is a view with the protein at 50% transparency and the ligands colored <scene name='87/873230/Protein_view_2/2'>black</scene>. | ||
== Biological relevance and broader implications == | == Biological relevance and broader implications == | ||
| + | PYRC1 is the target for potential cancer therapy. THFA binds to the active site on the protein and inhibits it's ability to synthesize proline from proline-5-carboxylate. Cancer cells require more proline than a regular human cell, so finding a ligand to bind to the active site of PYCR1 and inhibit the synthesis of proline could potentially work to stop cancer cells growth and division. Unfortunately, THFA is not as good of an inhibitor than other ligands mentioned in the article, so further research is needed to find a better inhibitor. | ||
== Important amino acids== | == Important amino acids== | ||
| + | Here is a <scene name='87/873230/Ligands/1'>ligands</scene> view, with all of the ligands visible. This is a <scene name='87/873230/Ligands_zoomed/1'>zoomed in</scene> picture of one of the THFA ligands on the PYCR1 protein. THFA interacts with the amino acids Serine 233, Valine 231, Threonine 238, and Alanine 237 from the PYCR1 protein. <scene name='87/873230/Amino_acid_view/1'>This view</scene> highlights all of those amino acids in magenta, with the protein transparency set to 90%. | ||
== Structural highlights == | == Structural highlights == | ||
| - | There are 5 domains. Among all of them, there is about 50% alpha helices, 40% beta sheets, and about 10% other structures. Alpha helices, beta sheets, and some of the other structures all are bonded to the different ligands. Some of the ligands bond to H2O “outside of the loop” | + | There are 5 domains. Among all of them, there is about 50% alpha helices, 40% beta sheets, and about 10% other structures. Alpha helices, beta sheets, and some of the other structures all are bonded to the different ligands. Some of the ligands bond to H2O “outside of the loop”. |
| + | Here is a view of the <scene name='87/873230/Alpha_helices/1'>alpha helices</scene> highlighted in green, and this is a view of the <scene name='87/873230/Beta_sheets/1'>beta sheets</scene> highlighted in pink. | ||
| + | This is a view of domain E's <scene name='87/873230/Tertiary_structure/2'>tertiary structure</scene>. | ||
| + | This is a <scene name='87/873230/Spacefill_view/2'>space-filling</scene> view of 6XOZ. | ||
| - | == Other important features == | ||
| + | == Other important features == | ||
| + | <scene name='87/873230/Hydrophobic_vs_polar/1'>This view</scene> shows us the hydrophobic areas in the protein in comparison with the polar areas. Looking <scene name='87/873230/Hydrophobic_vs_polar_closer/1'>closer</scene>, we can see that the ligands are located in hydrophobic areas. Proline is hydrophobic, meaning in order to bind, the binding site would need to be located in a hydrophobic region on the protein. In this <scene name='87/873230/Proline/1'>next image</scene>, you can see the locations of all the prolines. In <scene name='87/873230/Hydrophobic_vs_polar_vs_pro/1'>one more view</scene>, you can see the hydrophobic areas in grey, polar in pink, and proline in blue. This shows that prolines are located in the hydrophobic areas. | ||
| - | This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes. | ||
</StructureSection> | </StructureSection> | ||
Current revision
| This Sandbox is Reserved from 01/25/2021 through 04/30/2021 for use in Biochemistry taught by Bonnie Hall at Grand View University, Des Moines, USA. This reservation includes Sandbox Reserved 1665 through Sandbox Reserved 1682. |
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Structure of human PYCR1 complexed with THFA
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References
- ↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
- ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644
