User:Asif Hossain/Sandbox 1: Difference between revisions
Asif Hossain (talk | contribs) No edit summary |
Asif Hossain (talk | contribs) No edit summary |
||
| Line 7: | Line 7: | ||
==HDAC Enzymes and Homology== | ==HDAC Enzymes and Homology== | ||
There are four major classes of HDAC proteins (I,II, III, and IV). Other than the Class III “[https://en.wikipedia.org/wiki/Sirtuin sirtuins]” that utilize a [https://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/2016/bichaw.2016.55.issue-11/acs.biochem.5b01210/20160316/images/medium/bi-2015-01210h_0006.gif NAD<sup>+</sup> cofactor-dependent mechanism], all other HDAC classes use Zn<sup>2+</sup>-assisted catalysis through mechanisms (Figure | There are four major classes of HDAC proteins (I,II, III, and IV). Other than the Class III “[https://en.wikipedia.org/wiki/Sirtuin sirtuins]” that utilize a [https://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/2016/bichaw.2016.55.issue-11/acs.biochem.5b01210/20160316/images/medium/bi-2015-01210h_0006.gif NAD<sup>+</sup> cofactor-dependent mechanism], all other HDAC classes use Zn<sup>2+</sup>-assisted catalysis through mechanisms (Figure 2) reminiscent of a typical [https://en.wikipedia.org/wiki/Serine_protease serine protease].<ref name="DesJarlais, R., & Tummino, P. J.">DesJarlais, R., & Tummino, P. J. (2016). Role of histone-modifying enzymes and their complexes in regulation of chromatin biology. Biochemistry, 55(11), 1584-1599. https://doi.org/10.1021/acs.biochem.5b01210 </ref> While Classes I, II, and IV do have some major distinctions such as size of the protein, in general, they share homology at the catalytic site. HDAC 8 is classified as a Class I HDAC alongside HDACs 1-3. In fact, within Class I HDACs, there are many invariant residues involved in the catalytic site (such as His-Asp dyads), Zn-binding, and ligand binding pocket (such as Asp101) (Figure 1). <ref name="Vannini, A., Volpari, C., Gallinari, P.">Vannini, A., Volpari, C., Gallinari, P., Jones, P., Mattu, M., Carfí, A., ... & Di Marco, S. (2007). Substrate binding to histone deacetylases as shown by the crystal structure of the HDAC8–substrate complex. EMBO reports, 8(9), 879-884. https://doi.org/10.1038/sj.embor.7401047 </ref> | ||
[[Image:Conserved residues.PNG|600px||center||thumb|Figure 1: Weblogo representation comparing conservation of residues (143-182 in HDAC8) to homologous sequences in all class I HDACs. Nearly all active site residues (asterisk), zinc binding (dollar), and binding pocket residues (caret) are conserved across all class I HDACs. Other conserved residues not shown include active site residue Tyr306, zinc binding residue Asp267, and binding pocket residue Asp101. Nonconserved residues from 158 to l70 are part of an α-helix that moves outward from the active side before looping back around to the active site.]] | [[Image:Conserved residues.PNG|600px||center||thumb|Figure 1: Weblogo representation comparing conservation of residues (143-182 in HDAC8) to homologous sequences in all class I HDACs. Nearly all active site residues (asterisk), zinc binding (dollar), and binding pocket residues (caret) are conserved across all class I HDACs. Other conserved residues not shown include active site residue Tyr306, zinc binding residue Asp267, and binding pocket residue Asp101. Nonconserved residues from 158 to l70 are part of an α-helix that moves outward from the active side before looping back around to the active site.]] | ||
| Line 19: | Line 19: | ||
===Key Residues=== | ===Key Residues=== | ||
The <scene name='81/811085/Active_site/13'>active site</scene> of HDAC8 is composed of 2 catalytic dyads: <scene name='81/811085/Dyads/5'>His143/Asp183 and His142/Asp176</scene>, which | The <scene name='81/811085/Active_site/13'>active site</scene> of HDAC8 is composed of 2 catalytic dyads: <scene name='81/811085/Dyads/5'>His143/Asp183 and His142/Asp176</scene>, which activates the catalytic water nucleophile. A Tyr306, through mutation to Phe in the pdb file 2v5w (modeled in the overall view) was observed to render the protein mostly inactive. Thus, it has been hypothesized that this residue is critical for stabilization of the transition state with the Zn<sup>2+</sup> ion. This mutation allowed the determination of the crystal structure of HDAC8 interacting with the ligand. <ref name="Vannini, A., Volpari, C., Gallinari, P.">Vannini, A., Volpari, C., Gallinari, P., Jones, P., Mattu, M., Carfí, A., ... & Di Marco, S. (2007). Substrate binding to histone deacetylases as shown by the crystal structure of the HDAC8–substrate complex. EMBO reports, 8(9), 879-884. https://doi.org/10.1038/sj.embor.7401047 </ref> | ||
===Binding Pocket=== | ===Binding Pocket=== | ||
By encasing the nonpolar, four-carbon side-chain of the | By encasing the nonpolar, four-carbon side-chain of the lysine residue on the ligand, Phe152 and Phe208 engage in hydrophobic Van der Waals interactions with the ligand at different ends of the <scene name='81/811085/Binding_pocket_surface/3'>binding pocket</scene>. Trp141 and Met274 contribute to the overall shape through general hydrophobic interactions.<ref name="Whitehead">Whitehead, L., Dobler, M. R., Radetich, B., Zhu, Y., Atadja, P. W., Claiborne, T., ... & Shao, W. (2011). Human HDAC isoform selectivity achieved via exploitation of the acetate release channel with structurally unique small molecule inhibitors. Bioorganic & medicinal chemistry, 19(15), 4626-4634. https://doi.org/10.1016/j.bmc.2011.06.030 </ref> Finally, the carbonyl oxygen of <scene name='81/811085/Binding_pocket_glycine/2'>Gly151</scene> hydrogen bonds with the amide hydrogen of the acetylated lysine to further interact with the ligand in the relatively hydrophobic tunnel.<ref name="Vannini, A., Volpari, C., Gallinari, P.">Vannini, A., Volpari, C., Gallinari, P., Jones, P., Mattu, M., Carfí, A., ... & Di Marco, S. (2007). Substrate binding to histone deacetylases as shown by the crystal structure of the HDAC8–substrate complex. EMBO reports, 8(9), 879-884. https://doi.org/10.1038/sj.embor.7401047 </ref> | ||
At the rim of the active site, <scene name='81/811087/Ligand_interaction/5'>Asp101</scene> is involved in two hydrogen bonds between its own carbonyl oxygens and two consecutive amide hydrogens of incoming peptide derived ligand. This forces the ligand to assume a cis-conformation. In addition, extensive interactions among many other polar atoms near the rim of the active site help keep the ligand lodged in the hydrophobic tunnel.<ref name="Vannini, A., Volpari, C., Gallinari, P.">Vannini, A., Volpari, C., Gallinari, P., Jones, P., Mattu, M., Carfí, A., ... & Di Marco, S. (2007). Substrate binding to histone deacetylases as shown by the crystal structure of the HDAC8–substrate complex. EMBO reports, 8(9), 879-884. https://doi.org/10.1038/sj.embor.7401047 </ref> | At the rim of the active site, <scene name='81/811087/Ligand_interaction/5'>Asp101</scene> is involved in two hydrogen bonds between its own carbonyl oxygens and two consecutive amide hydrogens of the incoming peptide derived ligand. This forces the ligand to assume a cis-conformation. In addition, extensive interactions among many other polar atoms near the rim of the active site help keep the ligand lodged in the hydrophobic tunnel.<ref name="Vannini, A., Volpari, C., Gallinari, P.">Vannini, A., Volpari, C., Gallinari, P., Jones, P., Mattu, M., Carfí, A., ... & Di Marco, S. (2007). Substrate binding to histone deacetylases as shown by the crystal structure of the HDAC8–substrate complex. EMBO reports, 8(9), 879-884. https://doi.org/10.1038/sj.embor.7401047 </ref> | ||
===Additional Features=== | ===Additional Features=== | ||