User:Oluwapeluwa Sangoseni/Sandbox 1
From Proteopedia
(Difference between revisions)
Line 6: | Line 6: | ||
<table><tr><td colspan='2'> '''6P9U''' is an 8 chain structure with sequences from [http://en.wikipedia.org/wiki/Human humans]. The full crystallographic information is available at [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P9U 6P9U]. For a <b>guided tour on the structure components</b>, use [https://proteopedia.org/wiki/fgij/fg.htm?mol=6P9U FirstGlance]. <br> | <table><tr><td colspan='2'> '''6P9U''' is an 8 chain structure with sequences from [http://en.wikipedia.org/wiki/Human humans]. The full crystallographic information is available at [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P9U 6P9U]. For a <b>guided tour on the structure components</b>, use [https://proteopedia.org/wiki/fgij/fg.htm?mol=6P9U FirstGlance]. <br> | ||
- | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat">, |
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">F2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr> | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">F2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thrombin Thrombin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.5 3.4.21.5] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thrombin Thrombin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.5 3.4.21.5] </span></td></tr> | ||
Line 14: | Line 14: | ||
== Overview == | == Overview == | ||
- | Thrombin is one of the many essential molecules that our body produces and uses to consistently maintain homeostasis. It is a serine protease that acts as both a procoagulant and an anticoagulant, and is essential for blood clot formation, among other functions, such as causing inflammation, repairing tissue, and forming new blood vessels <ref name="first">Le Bonniec, B. F., &Walenga, J. M. (n.d.). Thrombin. Retrieved March 22, 2020, from https://www.sciencedirect.com/topics/medicine-and-dentistry/thrombin</ref>.As a procoagulant, in order to promote blood clotting, thrombin cleaves fibrinogen, a soluble protein that can be found in blood plasma, to produce fibrin. Fibrin is an insoluble protein that can be used, with the addition of aggregated platelets (which are also activated by thrombin), to form blood clots by creating | + | Thrombin is one of the many essential molecules that our body produces and uses to consistently maintain homeostasis. It is a serine protease that acts as both a procoagulant and an anticoagulant, and is essential for blood clot formation, among other functions, such as causing inflammation, repairing tissue, and forming new blood vessels <ref name="first">Le Bonniec, B. F., &Walenga, J. M. (n.d.). Thrombin. Retrieved March 22, 2020, from https://www.sciencedirect.com/topics/medicine-and-dentistry/thrombin</ref>.As a procoagulant, in order to promote blood clotting, thrombin cleaves fibrinogen, a soluble protein that can be found in blood plasma, to produce fibrin. Fibrin is an insoluble protein that can be used, with the addition of aggregated platelets (which are also activated by thrombin), to form blood clots by creating meshes that stop the flow of blood. This is important to prevent the loss of too much blood in the event of an injury that ruptures or damages blood vessels. Thrombin can also induce the coagulation pathway to produce more thrombin by activation of factor XI, and cofactors V and VIII <ref name="first" />. As said before, it also acts as a regulatory anticoagulant by binding to thrombomodulin. Thrombomodulin is a receptor glycoprotein found on the surface of the membranes of endothelial cells, and when thrombin binds to it, it activates the protein C pathway to start a process known as fibrinolysis, which breaks down fibrin and destroys blood clots <ref> Narayanan S., Multifunctional roles of thrombin., Ann Clin Lab Sci., 1999; 29: 275-280 </ref>.This is required to prevent excessive blood clotting, which would be problematic as required blood flow may be impeded. Thrombin also regulates fibrinolysis by activating carboxypeptidase B2, also known as thrombin activatable fibrinolysis inhibitor. With this wide array of necessary functions, thrombin is a very important enzyme for maintenance of our bodies. |
== Function and Structure == | == Function and Structure == | ||
- | Thrombin alone does not cleave fibrinogen, however, and the process is far more complex than one would initially be led to believe. Several molecules also participate in the process, including 6P9U. Most research and data for this molecule has only been conducted and compiled very recently, as the protein data was only deposited in the PDB in mid-late 2019, so, compared to other well-known molecules, there is still quite a bit of work that can be done to learn more about it <ref name="third">Pelc, L.a., et al. “Crystal Structure of Human Thrombin Mutant W215A.” 2019, doi:10.2210/pdb6p9u/pdb.</ref>. 6P9U is the crystallized structure of the human thrombin mutant, W215A. Data about this molecule’s structure was compiled using X-ray diffraction, at a resolution of 3.3 Å. It is found in humans, and features an 8-carbon chain structure. It has a cyclic C2 symmetry, and is a hetero 4 mer with the stoichiometry equation A2B2, meaning it has 2 alpha sub units, and 2 beta sub units. In terms of its macromolecular content, it has a total structural weight of 141170.61 Daltons, and features an atom count of 9004. It has a residue count of 1216, with two unique protein chains. These two unique chains consist of two different prothrombin or coagulation factor II macromolecules, with different sequence lengths (31 and 273). Both are expressed by the gene F2. The macromolecule also contains two ligands that bind to it: a Zinc ion (Zn2+), and n-acetyl-D-glucosamine (C8H15NO6). 6P9U/W215A serves as a residue for a hydrolase, facilitating hydrolysis for thrombin, in which a molecule of water is used to break bonds between atoms or molecules. This allows for the required peptide bonds to be cleavedto enable the conversion of fibrinogen to fibrin. 6P9U/W215A’s functionality and uses extend to a wider variety of possibilities than just cleaving peptide bonds, however. | + | Thrombin alone does not cleave fibrinogen, however, and the process is far more complex than one would initially be led to believe. Several molecules also participate in the process, including 6P9U. Most research and data for this molecule has only been conducted and compiled very recently, as the protein data was only deposited in the PDB in mid-late 2019, so, compared to other well-known molecules, there is still quite a bit of work that can be done to learn more about it <ref name="third">Pelc, L.a., et al. “Crystal Structure of Human Thrombin Mutant W215A.” 2019, doi:10.2210/pdb6p9u/pdb.</ref>. 6P9U is the crystallized structure of the human thrombin mutant, W215A. Data about this molecule’s structure was compiled using X-ray diffraction, at a resolution of 3.3 Å. It is found in humans, and features an 8-carbon chain structure. It has a cyclic C2 symmetry, and is a hetero 4 mer with the stoichiometry equation A2B2, meaning it has 2 alpha sub units, and 2 beta sub units. In terms of its macromolecular content, it has a total structural weight of 141170.61 Daltons, and features an atom count of 9004. It has a residue count of 1216, with two unique protein chains. These two unique chains consist of two different prothrombin or coagulation factor II macromolecules, with different sequence lengths (31 and 273). Both are expressed by the gene F2. The macromolecule also contains two ligands that bind to it: a <scene name='84/842972/Zn/3'>Zinc ion (Zn2+)</scene>, and <scene name='84/842972/Nag_scene/4'>n-acetyl-D-glucosamine (C8H15NO6)</scene>. 6P9U/W215A serves as a residue for a hydrolase, facilitating hydrolysis for thrombin, in which a molecule of water is used to break bonds between atoms or molecules. This allows for the required peptide bonds to be cleavedto enable the conversion of fibrinogen to fibrin. 6P9U/W215A’s functionality and uses extend to a wider variety of possibilities than just cleaving peptide bonds, however. |
W215, along with E217 and E192, are residues that work together to regulate thrombin’s activity. Specifically, W215 is responsible for maintaining the allosteric equilibrium of thrombin’s closed and open conformations, which would maintain thrombin’s catalytic activity, bycontrolling the rate of transition between the two forms, if need be <ref name="fourth">Pelc, L. A., Koester, S. K., Chen, Z., Gistover, N. E., & Di Cera, E. (2019). Residues W215, E217 and E192 control the allosteric E*-E equilibrium of thrombin. Scientific reports, 9(1), 12304. https://doi.org/10.1038/s41598-019-48839-1</ref>. It does this by use of hydrophobic interactions with the benzene ring portion of thrombin’s F227 residue. This keeps the enzyme’s active site open, which causes the rate at which the open conformation closes to decrease. This is because thrombin’s zymogen, which is the inactive, immature form of the enzyme, is the more common form of the enzyme when it is in its closed conformation. By opening, the zymogen matures along with it, being converted into the active and mature form. It was discovered that W215A functions similarly to W215, as if you were to replace W215 with W215A, the rate of transition between the two conformations would still be maintained, almost as if it were still W215. If W215 or W215A were to be removed completely, or its hydrophobic interaction with F227 is otherwise disrupted, then the rate at which thrombin’s conformation closes would be increased, and thrombin’s activity would be decreased, as the equilibrium between the closed and open conformations are responsible for the enzyme’s activity <ref name="fourth" />. | W215, along with E217 and E192, are residues that work together to regulate thrombin’s activity. Specifically, W215 is responsible for maintaining the allosteric equilibrium of thrombin’s closed and open conformations, which would maintain thrombin’s catalytic activity, bycontrolling the rate of transition between the two forms, if need be <ref name="fourth">Pelc, L. A., Koester, S. K., Chen, Z., Gistover, N. E., & Di Cera, E. (2019). Residues W215, E217 and E192 control the allosteric E*-E equilibrium of thrombin. Scientific reports, 9(1), 12304. https://doi.org/10.1038/s41598-019-48839-1</ref>. It does this by use of hydrophobic interactions with the benzene ring portion of thrombin’s F227 residue. This keeps the enzyme’s active site open, which causes the rate at which the open conformation closes to decrease. This is because thrombin’s zymogen, which is the inactive, immature form of the enzyme, is the more common form of the enzyme when it is in its closed conformation. By opening, the zymogen matures along with it, being converted into the active and mature form. It was discovered that W215A functions similarly to W215, as if you were to replace W215 with W215A, the rate of transition between the two conformations would still be maintained, almost as if it were still W215. If W215 or W215A were to be removed completely, or its hydrophobic interaction with F227 is otherwise disrupted, then the rate at which thrombin’s conformation closes would be increased, and thrombin’s activity would be decreased, as the equilibrium between the closed and open conformations are responsible for the enzyme’s activity <ref name="fourth" />. |
Revision as of 21:20, 29 April 2020
6P9U, Crystal Structure of Human Thrombin Mutant W215A
|
References
- ↑ 1.0 1.1 Le Bonniec, B. F., &Walenga, J. M. (n.d.). Thrombin. Retrieved March 22, 2020, from https://www.sciencedirect.com/topics/medicine-and-dentistry/thrombin
- ↑ Narayanan S., Multifunctional roles of thrombin., Ann Clin Lab Sci., 1999; 29: 275-280
- ↑ Pelc, L.a., et al. “Crystal Structure of Human Thrombin Mutant W215A.” 2019, doi:10.2210/pdb6p9u/pdb.
- ↑ 4.0 4.1 Pelc, L. A., Koester, S. K., Chen, Z., Gistover, N. E., & Di Cera, E. (2019). Residues W215, E217 and E192 control the allosteric E*-E equilibrium of thrombin. Scientific reports, 9(1), 12304. https://doi.org/10.1038/s41598-019-48839-1
- ↑ Bunce, M. W., Toso, R., &Camire, R. M. (2011). Zymogen-like factor Xa variants restore thrombin generation and effectively bypass the intrinsic pathway in vitro. Blood, 117(1), 290–298. https://doi.org/10.1182/blood-2010-08-300756
- ↑ 6.0 6.1 6.2 6.3 6.4 Berny-Lang, M. A., Hurst, S., Tucker, E. I., Pelc, L. A., Wang, R. K., Hurn, P. D., Di Cera, E., McCarty, O. J., & Gruber, A. (2011). Thrombin mutant W215A/E217A treatment improves neurological outcome and reduces cerebral infarct size in a mouse model of ischemic stroke. Stroke, 42(6), 1736–1741. https://doi.org/10.1161/STROKEAHA.110.603811
- ↑ The Internet Stroke Center. (n.d.). Retrieved March 22, 2020, from http://www.strokecenter.org/patients/about-stroke/ischemic-stroke/
- ↑ Gruber, A., Cantwell, A. M., Cera, E. D., & Hanson, S. R. (2002). The Thrombin Mutant W215A/E217A Shows Safe and Potent Anticoagulant and Antithrombotic Effectsin Vivo. Journal of Biological Chemistry,277(31), 27581-27584. doi:10.1074/jbc.c200237200