User:Luke Edward Severinac/Sandbox 1

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Caspase-6 in Homo sapiens

Found at high concentrations in the brain and bordering tissues, Caspase-6 has been implicated in several neurological diseases including Alzheimer's and dementia[1]^[1]. It's primarily involved in apoptosis through a largely ambiguous mechanism. It is classified as an [2]endopeptidase as it cleaves an internal peptide bond of its substrate. It has relatively low specificity in the binding site which allows for a variety of substrates, including other caspase enzymes and neuronal proteins to bind^[2]. Furthermore, it is a part of the cysteine-aspartate family[3], which have these critical amino acid residues in the active site of the enzyme. Caspase-6 has both an inactive zinc-bound conformation and an active ligand-bound conformation, which are largely regulated by variations in zinc concentration.

Figure Legend

This is the figure legend of the thumbnail

1 Structure
- 1.1 Active Site
- 1.2 Zinc Exosite
2 Activation of Caspase-6
- 2.1 Structural Units involved in autoactivation
3 Inhibition
- 3.1 Zinc Inhibition
- 3.2 Phosphorylation
4 Function
- 4.1 Caspase-6 involvement in Alzheimer's Disease
5 Luke's free space
6 Relevance

Structure

Active Site

In order to function as an endoprotease, Caspase-6 binds a , which can include neuronal proteins and tubulins [4], in its active site. This binding groove contains three critical amino acid residues necessary to perform cleavage of the peptide bonds. Together,, , and form a

Cystine Aspartase mechanism

. In the theorized mechanism, His-121 provides hydrogen bonding to the carbonyl of the peptide ligand. This stabilizes the tetrahedral intermediate formed when Cys-163 nucleuphilically attacks the protein. Glu-123 is used in the catalytic triad to deprotonate Cys-163, increasing the nucleophilicity of the residue.

Zinc Exosite

Caspase-6 function is inhibited by the binding of a zinc ion, which binds to an allosteric site instead of the active site. This allosteric site is located on the outside of the protein and it is distal to the active site. The Zinc ion is bound to three amino acid residues, Lys-36, Glu-244, and His-287, once the ion is bound to the protein it is then stabilized by a single water molecule. The binding of Zinc at the exosite is suggested to cause a conformational change to the protein, which then causes a change in the active site, which inhibits Caspase-6's ability to bind to substrate. Zinc binding to the exosite is tightly regulated, because it inhibits Caspase-6's ability to inititate apoptosis.

Activation of Caspase-6

Structural Units involved in autoactivation

Before Caspase-6 is a functional and active dimer, the enzyme exists as a procaspase. This precursor enzyme is modified by self-processing, a characteristic unique to Caspase-6. The unprocessed enzyme contains a small and large subunit, a pro domain, as well as a intersubunit linker. To become active, the intersubunit linker binds to the active site, where it is then cleaved. Other cleavages must occur as well for the enzyme to become active, specifically at TETD23 of the pro-domain, DVVD179, and TEVD193 amino acid sequences. Cleavage at these sites occurs in a specific sequence. To begin, the site within the pro-domain, TETD23, must be cleaved. This cleavage is then followed by either DVVD179 or TEVD193. It has been proposed that this sequence of cleavage is due to the structure of Caspase-6, which allows the pro-domain to be more readily available to enter the active site. To some extent, the pro-domain inhibits Caspase-6's ability to cleave the intersubunit loop and self-activate, but this also happens in a currently unknown mechanism. The pro-domain is released after the cleavage at TETD23, which then allows the two subunits to interact to form the active dimer.

Caspase-6 can also be activated by other caspases as an alternate to auto-activation.

It has been found that Caspase-6 can undergo activation without any other caspases, so there is a suggested self-cleavage mechanism for Caspase-6. The intramolecular cleavage of TEVD193 is essential for the initiation caspase-6 activation without Caspase-3 present. As mentioned above the pro-domain somehow inhibits the intramolecular cleavage of TEVD193, but currently the mechanism is not known. The TETD23 and TEVD193 cleavage sites are extremly similar to one another, but the TETD23 cleavage site is always cleaved before TEVD193. This indicates that the TETD23 cleavage site is more readily available for cleavage. The result of the TETD23 cleavage site priority is that the prodomain acts as a “suicide protector”, which protects the TEVD193 cleavage site from self-cleavage[5]. This protection is useful when there are low levels of protein it also helps explain why the pro-domain inhibits self-activation.

Inhibition

Zinc Inhibition

Primary inhibition of Caspase-6 occurs when a zinc ion binds to the exosite containing Lys-36, Glu-244, and His-287 of the active dimer. In addition to these residues, the zinc interacts with one water molecule from the cytoplasm. It has been proposed that helices of the active dimer must rotate or move in some other way to provide these ideal interactions with zinc. This subtle shift is most likely the cause for allosteric inhibition. As the helices move to bind zinc, the amino acids of the active site become misaligned. The altered positions of the amino acids no longer provide ideal interactions for incoming substrates. After zinc binds, no new substrates enter the active site. Thus, Caspase-6 is effectively inhibited.

Phosphorylation

The function of Caspase-6 can be inhibited by phosphorylation of Ser-257. The exact mechanism of this reaction remains unidentified at the time of publication, but proceeds when ARK5 kinase is present. This modification can occur before and after zymogen activation or auto-processing. The phosphoryl group inhibits Caspase-6 through steric interference. When Ser-257 is phosphorylated, the amino acid residue interacts with Pro-201, causing a shift in the helices of Caspase-6. The shift misaligns and disrupts residues found in the active site. This conformational difference prevents the inter-subunit loop from entering during zymogen activation and the self-cleaved active dimer cannot be formed. Additionally, no new substrate is able to enter the active site.

Function

Caspase-6 involvement in Alzheimer's Disease

Caspase-6 activity is associated with the formation of lesions within the Alzheimer's Disease (AD) and they can become present very early on during the disease's progression. Proapoptotic protein p53 is present at increased levels within AD brains, which seems to directly increase the transcription of Caspase-6. Treatments of Alzheimer's include targeting active Caspase-6 proteins because staining has found active Caspase-6 within the hippocampus and cortex of the Brain within in mild, moderate, and severe cases of AD, which indicates that Caspase-6 plays a predominate role in the pathophysiology of Alzheimer's. There has been research conducted that shows activation of Caspase-6 in AD could cause disruption of the cytoskeleton network of neurons, which then causes handicapped synaptic plasticity.

Luke's free space

If is , the activity of this protein is inhibited. If binds to the protein, the activity of the active site is inhibited.

Inactive state of caspase 6:

Relevance

References

↑ Wang XJ, Cao Q, Zhang Y, Su XD. Activation and regulation of caspase-6 and its role in neurodegenerative diseases. Annu Rev Pharmacol Toxicol. 2015;55:553-72. doi:, 10.1146/annurev-pharmtox-010814-124414. Epub 2014 Oct 17. PMID:25340928 doi:http://dx.doi.org/10.1146/annurev-pharmtox-010814-124414
↑ Velazquez-Delgado EM, Hardy JA. Zinc-Mediated Allosteric Inhibition of Caspase-6. J Biol Chem. 2012 Aug 13. PMID:22891250 doi:http://dx.doi.org/10.1074/jbc.M112.397752

Wang, Xiao-Jun, Qin Cao, Yan Zhang, and Xiao-Dong Su. "Activation and Regulation of Caspase-6 and Its Role in Neurodegenerative Diseases." Annual Review of Pharmacology and Toxicology 55.1 (2015): 553-72. Web.

Wang XJ, Cao Q, Liu X, Wang KT, Mi W, et al. 2010. Crystal structures of human caspase 6 reveal a new mechanism for intramolecular cleavage self-activation. EMBO Rep. 11: 841–47

(self cleavage article)

http://www.rcsb.org/pdb/explore/explore.do?structureId=2WDP (this is the non-self cleaved protien)

Proteopedia Page Contributors and Editors (what is this?)

Luke Edward Severinac

Retrieved from "http://52.214.119.220/wiki/index.php/User:Luke_Edward_Severinac/Sandbox_1"

@@ Line 2: / Line 2: @@
 <StructureSection load='4FXO' size='340' side='right' caption='Caspase-6' scene=''>
-Found at high concentrations in the brain and bordering tissues, Caspase-6 has been implicated in several neurological diseases including Alzheimer's and dementia[http://www.alz.org/].  It's primarily involved in apoptosis through a largely ambiguous mechanism.  It is classified as an [https://en.wikipedia.org/wiki/Endopeptidase]endopeptidase as it cleaves an internal peptide bond of its substrate.  It has relatively low specificity in the binding site which allows for a variety of substrates, including other caspase enzymes and neuronal proteins to bind<ref name="ZincMediatedCasp6">PMID: 22891250 </ref>.   Furthermore, it is a part of the cysteine-aspartate family[https://en.wikipedia.org/wiki/Caspase], which have these critical amino acid residues in the active site of the enzyme.  Caspase-6 has both an inactive zinc-bound conformation and an active ligand-bound conformation, which are largely regulated by variations in zinc concentration.
+Found at high concentrations in the brain and bordering tissues, Caspase-6 has been implicated in several neurological diseases including Alzheimer's and dementia[http://www.alz.org/]<ref name="ActiveRegofCasp6andNDdisease">PMID: 25340928 </ref>.  It's primarily involved in apoptosis through a largely ambiguous mechanism.  It is classified as an [https://en.wikipedia.org/wiki/Endopeptidase]endopeptidase as it cleaves an internal peptide bond of its substrate.  It has relatively low specificity in the binding site which allows for a variety of substrates, including other caspase enzymes and neuronal proteins to bind<ref name="ZincMediatedCasp6">PMID: 22891250 </ref>.   Furthermore, it is a part of the cysteine-aspartate family[https://en.wikipedia.org/wiki/Caspase], which have these critical amino acid residues in the active site of the enzyme.  Caspase-6 has both an inactive zinc-bound conformation and an active ligand-bound conformation, which are largely regulated by variations in zinc concentration.
 [[Image:Caspase-6 protein.jpg|100 px|left|thumb|Figure Legend]]
@@ Line 12: / Line 12: @@
 ===Zinc Exosite===
-Caspase-6 function is inhibited by the binding of a zinc ion, which binds to an allosteric site instead of the active site. This allosteric site is located on the outside of the protein and it is distal to the active site. The Zinc ion is bound to three amino acid residues, Lysine-36, Glutamate-244, and Histidine-287, once the ion is bound to the protein it is then stabilized by a single water molecule. The binding of Zinc at the exosite is suggested to cause a conformational change to the protein, which then causes a change in the active site, which inhibits Caspase-6's ability to bind to substrate. Zinc binding to the exosite is tightly regulated, because it inhibits Caspase-6's ability to inititate apoptosis.
+Caspase-6 function is inhibited by the binding of a zinc ion, which binds to an allosteric site instead of the active site. This allosteric site is located on the outside of the protein and it is distal to the active site. The Zinc ion is bound to three amino acid residues, Lys-36, Glu-244, and His-287, once the ion is bound to the protein it is then stabilized by a single water molecule. The binding of Zinc at the exosite is suggested to cause a conformational change to the protein, which then causes a change in the active site, which inhibits Caspase-6's ability to bind to substrate. Zinc binding to the exosite is tightly regulated, because it inhibits Caspase-6's ability to inititate apoptosis.
 =='''Activation of Caspase-6'''==