Loop Interactions and Dynamics Tune the Enzymatic Activity of the Human Histone Deacetylase 8

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• 作者：Micha B. A. Kunze ; David W. Wright ; Nicolas D. Werbeck ; John Kirkpatrick ; Peter V. Coveney ; D. Flemming Hansen
• 刊名：Journal of the American Chemical Society
• 出版年：2013
• 出版时间：November 27, 2013
• 年：2013
• 卷：135
• 期：47
• 页码：17862-17868
• 全文大小：371K
• 年卷期：v.135,no.47(November 27, 2013)
• ISSN：1520-5126

文摘

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.