User:Cassandra Marsh/Sandbox 2 - Revision history

Cassandra Marsh at 01:49, 7 April 2019

Cassandra Marsh — Sun, 07 Apr 2019 01:49:26 GMT

←Older revision		Revision as of 01:49, 7 April 2019
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	===Potassium Binding Site===		===Potassium Binding Site===
-	There are two potassium ions in HDAC8. While their exact function is unknown, these ions do increase the catalytic activity and stability of the enzyme overall. The potassium ion closest to the active site becomes a <scene name='81/812841/Potassium_binding_site/4'>Potassium Binding Site</scene>. The potassium ion octahedrally coordinates with the side chain oxygen of S199 and D176 and the backbone oxygen of D176, D178, H180 and L200 <ref name="Chen">PMID:25060069</ref>. Because the second potassium ion is about 20 Å from the catalytic center, this only regulates the enzymatic activity by an allosteric effect <ref name="Chen" />.	+	There are two potassium ions in HDAC8. While their exact function is unknown, these ions do increase the catalytic activity and stability of the enzyme overall. The potassium ion closest to the active site becomes a <scene name='81/812841/Potassium_binding_site/5'>Potassium Binding Site</scene>. The potassium ion octahedrally coordinates with the side chain oxygen of S199 and D176 and the backbone oxygen of D176, D178, H180 and L200 <ref name="Chen">PMID:25060069</ref>. Because the second potassium ion is about 20 Å from the catalytic center, this only regulates the enzymatic activity by an allosteric effect <ref name="Chen" />.

Cassandra Marsh at 01:26, 7 April 2019

Cassandra Marsh — Sun, 07 Apr 2019 01:26:39 GMT

←Older revision		Revision as of 01:26, 7 April 2019
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	===Potassium Binding Site===		===Potassium Binding Site===
-	There are two potassium ions in HDAC8. While their exact function is unknown, these ions do increase the catalytic activity of the enzyme overall. The potassium ion closest to the active site becomes a <scene name='81/812841/Potassium_binding_site/4'>Potassium Binding Site</scene>	+	There are two potassium ions in HDAC8. While their exact function is unknown, these ions do increase the catalytic activity and stability of the enzyme overall. The potassium ion closest to the active site becomes a <scene name='81/812841/Potassium_binding_site/4'>Potassium Binding Site</scene>. The potassium ion octahedrally coordinates with the side chain oxygen of S199 and D176 and the backbone oxygen of D176, D178, H180 and L200 <ref name="Chen">PMID:25060069</ref>. Because the second potassium ion is about 20 Å from the catalytic center, this only regulates the enzymatic activity by an allosteric effect <ref name="Chen" />.
		+
		+
	==Deacetylation==		==Deacetylation==

Cassandra Marsh at 22:49, 6 April 2019

Cassandra Marsh — Sat, 06 Apr 2019 22:49:13 GMT

←Older revision		Revision as of 22:49, 6 April 2019
Line 33:		Line 33:

	===Potassium Binding Site===		===Potassium Binding Site===
-	<scene name='81/812841/Potassium_binding_site/4'>Potassium Binding Site</scene>	+	There are two potassium ions in HDAC8. While their exact function is unknown, these ions do increase the catalytic activity of the enzyme overall. The potassium ion closest to the active site becomes a <scene name='81/812841/Potassium_binding_site/4'>Potassium Binding Site</scene>
	==Deacetylation==		==Deacetylation==

Cassandra Marsh at 22:29, 6 April 2019

Cassandra Marsh — Sat, 06 Apr 2019 22:29:21 GMT

←Older revision		Revision as of 22:29, 6 April 2019
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	===Potassium Binding Site===		===Potassium Binding Site===
-	<scene name='81/812841/Potassium_binding_site/1'>Potassium Binding Site</scene>	+	<scene name='81/812841/Potassium_binding_site/4'>Potassium Binding Site</scene>
	==Deacetylation==		==Deacetylation==

Cassandra Marsh at 22:09, 6 April 2019

Cassandra Marsh — Sat, 06 Apr 2019 22:09:14 GMT

←Older revision		Revision as of 22:09, 6 April 2019
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	===Potassium Binding Site===		===Potassium Binding Site===
-		+	<scene name='81/812841/Potassium_binding_site/1'>Potassium Binding Site</scene>
	==Deacetylation==		==Deacetylation==

Cassandra Marsh at 18:46, 6 April 2019

Cassandra Marsh — Sat, 06 Apr 2019 18:46:50 GMT

←Older revision		Revision as of 18:46, 6 April 2019
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	==Introduction==		==Introduction==
	===Histones===		===Histones===
-	[https://en.wikipedia.org/wiki/Histone Histones] are a family of basic, positively charged proteins that associate with DNA inside the nucleus to help condense the DNA into [https://en.wikipedia.org/wiki/Chromatin chromatin] <ref name="Histones"> Histones \| Learn Science at Scitable https://www.nature.com/scitable/definition/histone-histones-57</ref>. The nuclear DNA is wrapped around the histone in order to fit in the nucleus. [https://en.wikipedia.org/wiki/Nucleosome Nucleosomes] are chromatin beads made up of DNA wrapped around eight histone proteins, or a [https://en.wikipedia.org/wiki/Histone_octamer histone octamer] <ref name="Histones" />. The modification of histones are a type of [https://en.wikipedia.org/wiki/Epigenetics ~~Epigenetics~~] where changes are made in gene expression without altering the DNA sequence. Four different examples of modifying histones including [https://en.wikipedia.org/wiki/Histone_acetylation_and_deacetylation Histone acetylation, Histone deacetylation], [https://en.wikipedia.org/wiki/Histone_methylation Histone methylation] and [https://en.wikipedia.org/wiki/Demethylase Histone demethylation] <ref name="Histones" />.	+	[https://en.wikipedia.org/wiki/Histone Histones] are a family of basic, positively charged proteins that associate with DNA inside the nucleus to help condense the DNA into [https://en.wikipedia.org/wiki/Chromatin chromatin] <ref name="Histones"> Histones \| Learn Science at Scitable https://www.nature.com/scitable/definition/histone-histones-57</ref>. The nuclear DNA is wrapped around the histone in order to fit in the nucleus. [https://en.wikipedia.org/wiki/Nucleosome Nucleosomes] are chromatin beads made up of DNA wrapped around eight histone proteins, or a [https://en.wikipedia.org/wiki/Histone_octamer histone octamer] <ref name="Histones" />. The modification of histones are a type of [https://en.wikipedia.org/wiki/Epigenetics epigenetics], where changes are made in gene expression without altering the DNA sequence. Four different examples of modifying histones including [https://en.wikipedia.org/wiki/Histone_acetylation_and_deacetylation Histone acetylation, Histone deacetylation], [https://en.wikipedia.org/wiki/Histone_methylation Histone methylation] and [https://en.wikipedia.org/wiki/Demethylase Histone demethylation] <ref name="Histones" />.

	===Histone Deacetylases (HDACs)===		===Histone Deacetylases (HDACs)===

Cassandra Marsh at 18:43, 6 April 2019

Cassandra Marsh — Sat, 06 Apr 2019 18:43:57 GMT

←Older revision		Revision as of 18:43, 6 April 2019
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	====HDAC8====		====HDAC8====
-	[https://en.wikipedia.org/wiki/HDAC8 Histone Deacetylase 8] is an enzyme found in ''[https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]''.	+	[https://en.wikipedia.org/wiki/HDAC8 Histone Deacetylase 8] is an enzyme found in ''[https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]''. HDAC8 is 388 residues long and consists of eight-stranded parallel β-sheets surrounded by 11 α-helices <ref name="Vanninni" />. HDAC8 is the only functional HDAC that is found to be a single polypeptide instead of being high-molecular-weight multi-protein complexes <ref name="Vanninni" />. The substrate bound to the HDAC8 includes an acetyl group, one arginine, one histidine, two lysines and MCM, a Coumarin fluorescence tag.
		+
		+

Cassandra Marsh at 18:33, 6 April 2019

Cassandra Marsh — Sat, 06 Apr 2019 18:33:09 GMT

←Older revision		Revision as of 18:33, 6 April 2019
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-	=Histone Deacetylase 8 (HDAC 8), ''H. ~~sapians~~''=	+	=Histone Deacetylase 8 (HDAC 8), ''H. sapiens''=
	<StructureSection load='2v5w' size='350' frame='true' side='right' caption='HDAC 8 (PDB:2v5w)' scene=''>		<StructureSection load='2v5w' size='350' frame='true' side='right' caption='HDAC 8 (PDB:2v5w)' scene=''>

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	====HDAC8====		====HDAC8====
-	[https://en.wikipedia.org/wiki/HDAC8 Histone Deacetylase 8] is	+	[https://en.wikipedia.org/wiki/HDAC8 Histone Deacetylase 8] is an enzyme found in ''[https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]''.

Cassandra Marsh at 18:27, 6 April 2019

Cassandra Marsh — Sat, 06 Apr 2019 18:27:16 GMT

←Older revision		Revision as of 18:27, 6 April 2019
Line 5:		Line 5:
	==Introduction==		==Introduction==
	===Histones===		===Histones===
-	[https://en.wikipedia.org/wiki/Histone Histones] are a family of basic, positively charged proteins that associate with DNA inside the nucleus to help condense the DNA into [https://en.wikipedia.org/wiki/Chromatin chromatin] <ref name="Histones"> Histones \| Learn Science at Scitable https://www.nature.com/scitable/definition/histone-histones-57</ref>. The nuclear DNA is wrapped around the histone in order to fit in the nucleus. [https://en.wikipedia.org/wiki/Nucleosome Nucleosomes] are chromatin beads made up of DNA wrapped around eight histone proteins, or a [https://en.wikipedia.org/wiki/Histone_octamer histone octamer] <ref name="Histones" />. Four different examples of modifying histones including [https://en.wikipedia.org/wiki/Histone_acetylation_and_deacetylation Histone acetylation, Histone deacetylation], [https://en.wikipedia.org/wiki/Histone_methylation Histone methylation] and [https://en.wikipedia.org/wiki/Demethylase Histone demethylation] <ref name="Histones" />.	+	[https://en.wikipedia.org/wiki/Histone Histones] are a family of basic, positively charged proteins that associate with DNA inside the nucleus to help condense the DNA into [https://en.wikipedia.org/wiki/Chromatin chromatin] <ref name="Histones"> Histones \| Learn Science at Scitable https://www.nature.com/scitable/definition/histone-histones-57</ref>. The nuclear DNA is wrapped around the histone in order to fit in the nucleus. [https://en.wikipedia.org/wiki/Nucleosome Nucleosomes] are chromatin beads made up of DNA wrapped around eight histone proteins, or a [https://en.wikipedia.org/wiki/Histone_octamer histone octamer] <ref name="Histones" />. The modification of histones are a type of [https://en.wikipedia.org/wiki/Epigenetics Epigenetics] where changes are made in gene expression without altering the DNA sequence. Four different examples of modifying histones including [https://en.wikipedia.org/wiki/Histone_acetylation_and_deacetylation Histone acetylation, Histone deacetylation], [https://en.wikipedia.org/wiki/Histone_methylation Histone methylation] and [https://en.wikipedia.org/wiki/Demethylase Histone demethylation] <ref name="Histones" />.

	===Histone Deacetylases (HDACs)===		===Histone Deacetylases (HDACs)===

Cassandra Marsh at 18:17, 6 April 2019

Cassandra Marsh — Sat, 06 Apr 2019 18:17:55 GMT

←Older revision		Revision as of 18:17, 6 April 2019
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	===Histone Deacetylases (HDACs)===		===Histone Deacetylases (HDACs)===
-	ε-Amino-lysine acetylation is a type of histone modification that controls the stability of proteins and biological function in eukaryotic cells <ref name="Vanninni">~~doi~~:~~:10.1038/sj.embor.7401047~~</ref>. Histone Deacetylation is the reversal process for this acetylation modification. There are different classes of HDACs based on phylogenetic analysis:	+	ε-Amino-lysine acetylation is a type of histone modification that controls the stability of proteins and biological function in eukaryotic cells <ref name="Vanninni">PMID:17721440</ref>. Histone Deacetylation is the reversal process for this acetylation modification. There are different classes of HDACs based on phylogenetic analysis:

	•Class I - HDACs 1-3 and 8, which are homologous to yeast Rpd3		•Class I - HDACs 1-3 and 8, which are homologous to yeast Rpd3