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Loop interactions and dynamics tune the enzymatic activity of the human histone deacetylase 8.

Kunze MB, Wright DW, Werbeck ND, Kirkpatrick J, Coveney PV, Hansen DF - J. Am. Chem. Soc. (2013)

Bottom Line: Yet it has remained unclear how the dynamics of the entrance surface tune and influence the catalytic activity of HDAC8.Using long time scale all atom molecular dynamics simulations we have found a mechanism whereby the interactions and dynamics of two loops tune the configuration of functionally important residues of HDAC8 and could therefore influence the activity of the enzyme.Our work delivers detailed insight into the dynamic loop network of HDAC8 and provides an explanation for a number of experimental observations.

View Article: PubMed Central - PubMed

Affiliation: Institute of Structural and Molecular Biology, Division of Biosciences, University College London , Gower Street, London WC1E 6BT, United Kingdom.

ABSTRACT
The human histone deacetylase 8 (HDAC8) is a key hydrolase in gene regulation and has been identified as a drug target for the treatment of several cancers. Previously the HDAC8 enzyme has been extensively studied using biochemical techniques, X-ray crystallography, and computational methods. Those investigations have yielded detailed information about the active site and have demonstrated that the substrate entrance surface is highly dynamic. Yet it has remained unclear how the dynamics of the entrance surface tune and influence the catalytic activity of HDAC8. Using long time scale all atom molecular dynamics simulations we have found a mechanism whereby the interactions and dynamics of two loops tune the configuration of functionally important residues of HDAC8 and could therefore influence the activity of the enzyme. We subsequently investigated this hypothesis using a well-established fluorescence activity assay and a noninvasive real-time progression assay, where deacetylation of a p53 based peptide was observed by nuclear magnetic resonance spectroscopy. Our work delivers detailed insight into the dynamic loop network of HDAC8 and provides an explanation for a number of experimental observations.

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Related in: MedlinePlus

States of the L1 and L2 loop conformations when interacting withSAHA (chemical structure shown in the insert). (a): HDAC8:SAHA complexsnapshot of the simulation with SAHA (licorice) and HDAC8 (gray cartoon)where the binding rail is in its ‘out’ conformation.Positions of Lys33, Asp87–89, Tyr100, and Asp101 are illustratedwith colored spheres. (b): Microkinetic processes over the simulationtime as defined in Figure 2: (i) Φ angleof Tyr100, indicating binding-rail conformation; (ii) L1:L2 salt bridgepresence between Lys33 and Asp87–89; (iii) presence of an α-helixat residues 93–97.
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fig3: States of the L1 and L2 loop conformations when interacting withSAHA (chemical structure shown in the insert). (a): HDAC8:SAHA complexsnapshot of the simulation with SAHA (licorice) and HDAC8 (gray cartoon)where the binding rail is in its ‘out’ conformation.Positions of Lys33, Asp87–89, Tyr100, and Asp101 are illustratedwith colored spheres. (b): Microkinetic processes over the simulationtime as defined in Figure 2: (i) Φ angleof Tyr100, indicating binding-rail conformation; (ii) L1:L2 salt bridgepresence between Lys33 and Asp87–89; (iii) presence of an α-helixat residues 93–97.

Mentions: The structureof the HDAC8:SAHA complex is shown in Figure 3a. Flexible behavior of the ligand and the loops at the entrancesurface in the HDAC8:SAHA complex is expected, since crystallographicB-factors are large in these regions, while high R values are also observed for this ligand (VideoS2).


Loop interactions and dynamics tune the enzymatic activity of the human histone deacetylase 8.

Kunze MB, Wright DW, Werbeck ND, Kirkpatrick J, Coveney PV, Hansen DF - J. Am. Chem. Soc. (2013)

States of the L1 and L2 loop conformations when interacting withSAHA (chemical structure shown in the insert). (a): HDAC8:SAHA complexsnapshot of the simulation with SAHA (licorice) and HDAC8 (gray cartoon)where the binding rail is in its ‘out’ conformation.Positions of Lys33, Asp87–89, Tyr100, and Asp101 are illustratedwith colored spheres. (b): Microkinetic processes over the simulationtime as defined in Figure 2: (i) Φ angleof Tyr100, indicating binding-rail conformation; (ii) L1:L2 salt bridgepresence between Lys33 and Asp87–89; (iii) presence of an α-helixat residues 93–97.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3926704&req=5

fig3: States of the L1 and L2 loop conformations when interacting withSAHA (chemical structure shown in the insert). (a): HDAC8:SAHA complexsnapshot of the simulation with SAHA (licorice) and HDAC8 (gray cartoon)where the binding rail is in its ‘out’ conformation.Positions of Lys33, Asp87–89, Tyr100, and Asp101 are illustratedwith colored spheres. (b): Microkinetic processes over the simulationtime as defined in Figure 2: (i) Φ angleof Tyr100, indicating binding-rail conformation; (ii) L1:L2 salt bridgepresence between Lys33 and Asp87–89; (iii) presence of an α-helixat residues 93–97.
Mentions: The structureof the HDAC8:SAHA complex is shown in Figure 3a. Flexible behavior of the ligand and the loops at the entrancesurface in the HDAC8:SAHA complex is expected, since crystallographicB-factors are large in these regions, while high R values are also observed for this ligand (VideoS2).

Bottom Line: Yet it has remained unclear how the dynamics of the entrance surface tune and influence the catalytic activity of HDAC8.Using long time scale all atom molecular dynamics simulations we have found a mechanism whereby the interactions and dynamics of two loops tune the configuration of functionally important residues of HDAC8 and could therefore influence the activity of the enzyme.Our work delivers detailed insight into the dynamic loop network of HDAC8 and provides an explanation for a number of experimental observations.

View Article: PubMed Central - PubMed

Affiliation: Institute of Structural and Molecular Biology, Division of Biosciences, University College London , Gower Street, London WC1E 6BT, United Kingdom.

ABSTRACT
The human histone deacetylase 8 (HDAC8) is a key hydrolase in gene regulation and has been identified as a drug target for the treatment of several cancers. Previously the HDAC8 enzyme has been extensively studied using biochemical techniques, X-ray crystallography, and computational methods. Those investigations have yielded detailed information about the active site and have demonstrated that the substrate entrance surface is highly dynamic. Yet it has remained unclear how the dynamics of the entrance surface tune and influence the catalytic activity of HDAC8. Using long time scale all atom molecular dynamics simulations we have found a mechanism whereby the interactions and dynamics of two loops tune the configuration of functionally important residues of HDAC8 and could therefore influence the activity of the enzyme. We subsequently investigated this hypothesis using a well-established fluorescence activity assay and a noninvasive real-time progression assay, where deacetylation of a p53 based peptide was observed by nuclear magnetic resonance spectroscopy. Our work delivers detailed insight into the dynamic loop network of HDAC8 and provides an explanation for a number of experimental observations.

Show MeSH
Related in: MedlinePlus