title: Histone Deacetylase 8: Characterization of Physiological Divalent Metal Catalysis.
abstract: Histone deacetylases (HDACs) are responsible for the removal of acetyl groups from histones, resulting in gene silencing. Overexpression of HDACs is associated with cancer, and their inhibitors are of particular interest as chemotherapeutics. However, HDACs remain a target of mechanistic debate. HDAC class 8 is the most studied HDAC, and of particular importance due to its human oncological relevance. HDAC8 has traditionally been considered to be a Zn-dependent enzyme. However, recent experimental assays have challenged this assumption and shown that HDAC8 is catalytically active with a variety of different metals, and that it may be a Fe-dependent enzyme in vivo. We studied two opposing mechanisms utilizing a series of divalent metal ions in physiological abundance (Zn(2+), Fe(2+), Co(2+), Mn(2+), Ni(2+), and Mg(2+)). Extensive sampling of the entire protein with different bound metals was done with the mixed quantum-classical QM/DMD method. Density functional theory (DFT) on an unusually large cluster model was used to describe the active site and reaction mechanism. We have found that the reaction profile of HDAC8 is similar among all metals tested, and follows one of the previously published mechanisms, but the rate-determining step is different from the one previously claimed. We further provide a scheme for estimating the metal binding affinities to the protein. We use the quantum theory of atoms in molecules (QTAIM) to understand the different binding affinities for each metal in HDAC8 as well as the ability of each metal to bind and properly orient the substrate for deacetylation. The combination of this data with the catalytic rate constants is required to reproduce the experimentally observed trend in metal-depending performance. We predict Co(2+) and Zn(2+) to be the most active metals in HDAC8, followed by Fe(2+), and Mn(2+) and Mg(2+) to be the least active.
authors.affiliation: Department of Chemistry and Biochemistry, University of California, Los Angeles , Los Angeles, California 90095, United States.
authors.forename: Michael R
authors.initials: MR
authors.lastname: Nechay
authors.affiliation: Department of Chemistry and Biochemistry, University of California, Los Angeles , Los Angeles, California 90095, United States.
authors.forename: Nathan M
authors.initials: NM
authors.lastname: Gallup
authors.affiliation: Molecular Theory Group, Colorado School of Mines , Golden, Colorado 80401, United States.
authors.forename: Amanda
authors.initials: A
authors.lastname: Morgenstern
authors.affiliation: Department of Chemistry and Biochemistry, University of California, Los Angeles , Los Angeles, California 90095, United States.
authors.forename: Quentin A
authors.initials: QA
authors.lastname: Smith
authors.affiliation: Molecular Theory Group, Colorado School of Mines , Golden, Colorado 80401, United States.
authors.forename: Mark E
authors.initials: ME
authors.lastname: Eberhart
authors.affiliation: Department of Chemistry and Biochemistry, University of California, Los Angeles , Los Angeles, California 90095, United States.|California NanoSystems Institute , Los Angeles, California 90095, United States.
authors.forename: Anastassia N
authors.initials: AN
authors.lastname: Alexandrova
mesh_terms: D055162:Biocatalysis; D020134:Catalytic Domain; D002413:Cations, Divalent; D003035:Cobalt / Q000737:chemistry*; D018360:Crystallography, X-Ray; D006655:Histone Deacetylases / Q000737:chemistry*; D006801:Humans; D007501:Iron / Q000737:chemistry*; D007700:Kinetics; D008274:Magnesium / Q000737:chemistry*; D008345:Manganese / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D011789:Quantum Theory; D012097:Repressor Proteins / Q000737:chemistry*; D055672:Static Electricity; D013816:Thermodynamics; D015032:Zinc / Q000737:chemistry*
chemical_list: D002413:Cations, Divalent; D012097:Repressor Proteins; D003035:Cobalt; D008345:Manganese; D007501:Iron; C409470:HDAC8 protein, human; D006655:Histone Deacetylases; D008274:Magnesium; D015032:Zinc