Sandbox Reserved 1456

From Proteopedia

(Difference between revisions)

Revision as of 18:31, 16 November 2018

This Sandbox is Reserved from October 22, 2018 through April 30, 2019 for use in the course Biochemistry taught by Bonnie Hall at the Grand View University, Des Moines, IA USA. This reservation includes Sandbox Reserved 1456 through Sandbox Reserved 1470.

To get started:

Click the edit this page tab at the top. Save the page after each step, then edit it again.
Click the 3D button (when editing, above the wikitext box) to insert Jmol.
show the Scene authoring tools, create a molecular scene, and save it. Copy the green link into the page.
Add a description of your scene. Use the buttons above the wikitext box for bold, italics, links, headlines, etc.

More help: Help:Editing

Structure and Mechanism of Cysteine Peptidase Gingipain K (Kgp), a Major Virulence Factor of Porphyromonas gingivalis in Periodontitis

This is a default text for your page '. Click above on edit this page' to modify. Be careful with the < and > signs.

You may include any references to papers as in: the use of JSmol in Proteopedia ^[1] or to the article describing Jmol ^[2] to the rescue.

1 jmolSetTarget('1');jmolLink('delete $clickGreenLinkEcho; refresh;setL = \"setLoading();\"; javascript @setL; script /wiki/extensions/Proteopedia/spt/wipeFullLoadButton.spt; ~green = \"Function\"; isosurface DELETE; scn = load(\"/wiki/scripts/79/799584/Rainbow_all_protein/5.spt\"); scn = scn.replace(\'# initialize;\', \'# initialize;\nclearSceneScaleCmd = \"clearSceneScale();\"; javascript @clearSceneScaleCmd;\n\'); scn = scn.replace(\'_setSelectionState;\', \'_setSelectionState; message Scene_finished;\'); scn = scn.replace(\'_setState;\', \'_setState; setButtonsStartingState();\'); scn = scn.replace(\'DORESIZE\', \'\'); script inline scn;','Function','Function');
2 Disease
3 Relevance
4 Structural highlights

The protein, Kgp, is being studied in the bacteria Porphyromonas gingivalis. Kgp is a virulence factor of P. gingivalis that cleaves many constituents of connective tissue, leading to decreased bactericidal activity and chronic inflammation of the gums. Virulence is due to nutrient acquisition, cleavage of host cell surface receptors, signaling via protease activated receptors, and inactivation of cytokines and of the complement system.

Disease

Porphyromonas gingivalis is a Gram-negative oral anaerobe that causes periodontitis. P. gingivalis degrades the immune and inflammatory response, giving them access to the circulatory system, allowing them to start and increase severity of systemic diseases, such as cardiovascular diseases and rheumatoid arthritis.

Relevance

Bacteria usually benefit human health, but if they are a susceptible host, they can become pathogenic and cause infection and disease. This is happening at a faster rate as the pathogens become more resistant to antibiotics as time passes and the pharmaceutical industry neglects to create new antimicrobials that could combat the growing virulence of these resistant pathogens. By studying Kgp, scientists hope to find a suitable inhibitor for this protein.

Structural highlights

The main present in Kgp are alpha helices and antiparallel beta sheets. Alpha helices and beta sheets impact how the protein will fold by allowing for specific amino acid interactions. Alpha helices are tightly wound with a center channel too small for even a hydrogen atom to pass through. Alpha helices and beta sheets cannot have a glycine or proline residue as part of the chain and are only found in beta-turns. By knowing this, you know that glycine and proline would not be found in the primary amino acid sequence where the alpha helices and beta sheets would be found.

This model shows that the atoms that make up Kgp do not leave much room for other molecules to pass through. The surface of the protein is a fairly even distribution of hydrophobic (gray) and hydrophilic (purple) atoms. The red atoms are the solvent, and they are interacting with the hydrophilic atoms present on the surface of Kgp.

The of this molecule is

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

Retrieved from "http://52.214.119.220/wiki/index.php/Sandbox_Reserved_1456"

@@ Line 18: / Line 18: @@
 This <scene name='79/799584/Spacefill_rainbow/1'>space-fill</scene> model shows that the atoms that make up Kgp do not leave much room for other molecules to pass through. The surface of the protein is a fairly even distribution of hydrophobic (gray) and hydrophilic (purple) atoms. The red atoms are the solvent, and they are interacting with the hydrophilic atoms present on the surface of Kgp.
+The <scene name='79/799584/Ligand_ckc/1'>ligand</scene> of this molecule is
+<scene name='79/799584/Active_site/1'>active site</scene>
+<scene name='79/799584/Catalytic_triad/1'>catalytic triad</scene>
 </StructureSection>
 == References ==
 <references/>

Sandbox Reserved 1456

From Proteopedia

Revision as of 18:31, 16 November 2018

Structure and Mechanism of Cysteine Peptidase Gingipain K (Kgp), a Major Virulence Factor of Porphyromonas gingivalis in Periodontitis

Contents

Disease

Relevance

Structural highlights

References

Views

Personal tools

Navigation

Search

Toolbox