User:Sean Callahan/Sandbox 1: Difference between revisions
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<scene name='81/811711/ | <scene name='81/811711/Whole_protein/1'></scene>Lysine Specific Demethylase 1 (''Homo sapiens'') | ||
<StructureSection load='2h94' size='340' frame='true' side='right' caption='LSD1 2h94' scene='81/811711/ | <StructureSection load='2h94' size='340' frame='true' side='right' caption='LSD1 2h94' scene='81/811711/Whole_protein/1'> | ||
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue. | You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue. | ||
==Introduction== | ==Introduction== | ||
Histones are positively charged proteins that help organize DNA into tightly packed chromosomes by acting as a spool for DNA to wrap around. Histones are composed of 4 subunits (H2A, H2B, H3, and H4) and have the capability to loosen or tighten their interactions with DNA to either promote or inhibit transcription. There are a variety of mechanisms that histones achieve these interactions, some examples being the addition or removal of acetyl, methyl, or phosphate groups. These modifications can either increase or decrease the affinity the histone has for the DNA strand. Demethylases are responsible for removing methyl groups from different histone residues. While this is typically associated with increasing histone-DNA interaction, and thus silencing transcription, demethylation has also been associated with the promotion of transcription depending on the residue that is being demethylated.[[Image:HistoneStructure.png | 400px| right| thumb| | Histones are positively charged proteins that help organize DNA into tightly packed chromosomes by acting as a spool for DNA to wrap around. Histones are composed of 4 subunits (H2A, H2B, H3, and H4) and have the capability to loosen or tighten their interactions with DNA to either promote or inhibit transcription. There are a variety of mechanisms that histones achieve these interactions, some examples being the addition or removal of acetyl, methyl, or phosphate groups. These modifications can either increase or decrease the affinity the histone has for the DNA strand. Demethylases are responsible for removing methyl groups from different histone residues. While this is typically associated with increasing histone-DNA interaction, and thus silencing transcription, demethylation has also been associated with the promotion of transcription depending on the residue that is being demethylated.[[Image:HistoneStructure.png | 400px| right| thumb| This is the crystal structure of a histone bound to DNA. Its subunits are color coded.]] | ||
There are two main classes of demethylases, and they are categorized by their co-factors and co-substrates. One class of demethylases uses an FAD co-factor to catalyze the demethylation reaction. The other class of demethylases uses a FE+2 ion and a-ketoglutarate as a co-substrate to catalyze the reaction. Although the co-factors used are different, both classes operate by hydroxylating the target methyl group. Lysine Specific Demethylases 1 is a histone demethylase that uses FAD as a co-factor<ref name="Forneris">PMID: 15811342</ref>. Specifically, LSD1 is responsible for demethylating Lys 4 and Lys 9 on the H3 subunit of the histone. | There are two main classes of demethylases, and they are categorized by their co-factors and co-substrates. One class of demethylases uses an FAD co-factor to catalyze the demethylation reaction. The other class of demethylases uses a FE+2 ion and a-ketoglutarate as a co-substrate to catalyze the reaction. Although the co-factors used are different, both classes operate by hydroxylating the target methyl group. Lysine Specific Demethylases 1 is a histone demethylase that uses FAD as a co-factor<ref name="Forneris">PMID: 15811342</ref>. Specifically, LSD1 is responsible for demethylating Lys 4 and Lys 9 on the H3 subunit of the histone. | ||
