Dataset Information

Aromatic side-chain flips orchestrate the conformational sampling of functional loops in human histone deacetylase 8.

ABSTRACT: Human histone deacetylase 8 (HDAC8) is a key hydrolase in gene regulation and an important drug-target. High-resolution structures of HDAC8 in complex with substrates or inhibitors are available, which have provided insights into the bound state of HDAC8 and its function. Here, using long all-atom unbiased molecular dynamics simulations and Markov state modelling, we show a strong correlation between the conformation of aromatic side chains near the active site and opening and closing of the surrounding functional loops of HDAC8. We also investigated two mutants known to allosterically downregulate the enzymatic activity of HDAC8. Based on experimental data, we hypothesise that I19S-HDAC8 is unable to release the product, whereas both product release and substrate binding are impaired in the S39E-HDAC8 mutant. The presented results deliver detailed insights into the functional dynamics of HDAC8 and provide a mechanism for the substantial downregulation caused by allosteric mutations, including a disease causing one.

SUBMITTER: Shukla VK

PROVIDER: S-EPMC8278956 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature

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Aromatic side-chain flips orchestrate the conformational sampling of functional loops in human histone deacetylase 8.

Shukla Vaibhav Kumar VK Siemons Lucas L Gervasio Francesco L FL Hansen D Flemming DF

Chemical science 20210527 27

Human histone deacetylase 8 (HDAC8) is a key hydrolase in gene regulation and an important drug-target. High-resolution structures of HDAC8 in complex with substrates or inhibitors are available, which have provided insights into the bound state of HDAC8 and its function. Here, using long all-atom unbiased molecular dynamics simulations and Markov state modelling, we show a strong correlation between the conformation of aromatic side chains near the active site and opening and closing of the sur ...[more]

PMID: 34349901

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Project description:The three-dimensional structures of the dihydrofolate reductase enzymes from Escherichia coli (ecDHFR or ecE) and Homo sapiens (hDHFR or hE) are very similar, despite a rather low level of sequence identity. Whereas the active site loops of ecDHFR undergo major conformational rearrangements during progression through the reaction cycle, hDHFR remains fixed in a closed loop conformation in all of its catalytic intermediates. To elucidate the structural and dynamic differences between the human and E. coli enzymes, we conducted a comprehensive analysis of side chain flexibility and dynamics in complexes of hDHFR that represent intermediates in the major catalytic cycle. Nuclear magnetic resonance relaxation dispersion experiments show that, in marked contrast to the functionally important motions that feature prominently in the catalytic intermediates of ecDHFR, millisecond time scale fluctuations cannot be detected for hDHFR side chains. Ligand flux in hDHFR is thought to be mediated by conformational changes between a hinge-open state when the substrate/product-binding pocket is vacant and a hinge-closed state when this pocket is occupied. Comparison of X-ray structures of hinge-open and hinge-closed states shows that helix αF changes position by sliding between the two states. Analysis of χ1 rotamer populations derived from measurements of (3)JCγCO and (3)JCγN couplings indicates that many of the side chains that contact helix αF exhibit rotamer averaging that may facilitate the conformational change. The χ1 rotamer adopted by the Phe31 side chain depends upon whether the active site contains the substrate or product. In the holoenzyme (the binary complex of hDHFR with reduced nicotinamide adenine dinucleotide phosphate), a combination of hinge opening and a change in the Phe31 χ1 rotamer opens the active site to facilitate entry of the substrate. Overall, the data suggest that, unlike ecDHFR, hDHFR requires minimal backbone conformational rearrangement as it proceeds through its enzymatic cycle, but that ligand flux is brokered by more subtle conformational changes that depend on the side chain motions of critical residues.

Dataset Information

Aromatic side-chain flips orchestrate the conformational sampling of functional loops in human histone deacetylase 8.

Publications

Aromatic side-chain flips orchestrate the conformational sampling of functional loops in human histone deacetylase 8.

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