A proton-shuttle reaction mechanism for histone deacetylase 8 and the catalytic role of metal ions (Q41890560)

13 October 2017

A proton-shuttle reaction mechanism for histone deacetylase 8 and the catalytic role of metal ions (English)

1 reference

13 October 2017

Ruibo Wu

1

1 reference

13 October 2017

Shenglong Wang

2

1 reference

13 October 2017

Nengjie Zhou

3

1 reference

13 October 2017

Zexing Cao

4

1 reference

13 October 2017

Yingkai Zhang

5

1 reference

13 October 2017

language of work or name

English

0 references

publication date

1 July 2010

1 reference

Journal of the American Chemical Society

13 October 2017

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13 October 2017

132

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13 October 2017

27

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13 October 2017

9471-9479

1 reference

Chemical phylogenetics of histone deacetylases

13 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908479

Activation and inhibition of histone deacetylase 8 by monovalent cations

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908479

Born-Oppenheimer ab initio QM/MM molecular dynamics simulations of the hydrolysis reaction catalyzed by protein arginine deiminase 4.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908479

Side chain specificity of ADP-ribosylation by a sirtuin

5 June 2018

1 reference

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Discovery of potent and selective histone deacetylase inhibitors via focused combinatorial libraries of cyclic alpha3beta-tetrapeptides

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908479

Quantum mechanical/molecular mechanical and density functional theory studies of a prototypical zinc peptidase (carboxypeptidase A) suggest a general acid-general base mechanism

5 June 2018

1 reference

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Active site cysteine is protonated in the PAD4 Michaelis complex: evidence from Born-Oppenheimer ab initio QM/MM molecular dynamics simulations

5 June 2018

1 reference

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Design, synthesis, and biological activity of boronic acid-based histone deacetylase inhibitors

5 June 2018

1 reference

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Increasing the time step with mass scaling in Born-Oppenheimer ab initio QM/MM molecular dynamics simulations

5 June 2018

1 reference

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Isoform-specific histone deacetylase inhibitors: the next step?

5 June 2018

1 reference

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Interfacing ab initio Quantum Mechanical Method with Classical Drude Osillator Polarizable Model for Molecular Dynamics Simulation of Chemical Reactions

5 June 2018

1 reference

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Molecular dynamics study of the structure, flexibility and dynamics of thermostable l1 lipase at high temperatures.

5 June 2018

1 reference

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The many roles of histone deacetylases in development and physiology: implications for disease and therapy

5 June 2018

1 reference

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Structural Studies of Human Histone Deacetylase 8 and Its Site-Specific Variants Complexed with Substrate and Inhibitors † , ‡

5 June 2018

1 reference

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Therapeutic application of histone deacetylase inhibitors for central nervous system disorders

5 June 2018

1 reference

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Zinc metalloproteins as medicinal targets.

5 June 2018

1 reference

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Chemical mechanisms of histone lysine and arginine modifications

5 June 2018

1 reference

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Combinatorial patterns of histone acetylations and methylations in the human genome

5 June 2018

1 reference

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Comparative molecular dynamics simulations of histone deacetylase-like protein: binding modes and free energy analysis to hydroxamic acid inhibitors

5 June 2018

1 reference

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How do SET-domain protein lysine methyltransferases achieve the methylation state specificity? Revisited by Ab initio QM/MM molecular dynamics simulations

5 June 2018

1 reference

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The Rpd3/Hda1 family of lysine deacetylases: from bacteria and yeast to mice and men

5 June 2018

1 reference

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Histone deacetylase inhibitors: from bench to clinic

5 June 2018

1 reference

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Phenylalanine-containing hydroxamic acids as selective inhibitors of class IIb histone deacetylases (HDACs)

5 June 2018

1 reference

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Substrate binding to histone deacetylases as shown by the crystal structure of the HDAC8-substrate complex

5 June 2018

1 reference

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Chemistry of acetyl transfer by histone modifying enzymes: structure, mechanism and implications for effector design

5 June 2018

1 reference

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HATs and HDACs: from structure, function and regulation to novel strategies for therapy and prevention

5 June 2018

1 reference

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Ab initio quantum mechanical/molecular mechanical molecular dynamics simulation of enzyme catalysis: the case of histone lysine methyltransferase SET7/9.

5 June 2018

1 reference

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HDACs, histone deacetylation and gene transcription: from molecular biology to cancer therapeutics

5 June 2018

1 reference

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Chromatin modifications and their function

5 June 2018

1 reference

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Dimethyl sulfoxide to vorinostat: development of this histone deacetylase inhibitor as an anticancer drug

5 June 2018

1 reference

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Comparison of multiple Amber force fields and development of improved protein backbone parameters

5 June 2018

1 reference

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Anticancer activities of histone deacetylase inhibitors

5 June 2018

1 reference

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Catalytic activity and inhibition of human histone deacetylase 8 is dependent on the identity of the active site metal ion.

5 June 2018

1 reference

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H++: a server for estimating pKas and adding missing hydrogens to macromolecules

5 June 2018

1 reference

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Farnesyltransferase--new insights into the zinc-coordination sphere paradigm: evidence for a carboxylate-shift mechanism

5 June 2018

1 reference

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Crystal structure of a eukaryotic zinc-dependent histone deacetylase, human HDAC8, complexed with a hydroxamic acid inhibitor

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908479

Development and testing of a general amber force field

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908479

Histone deacetylases (HDACs): characterization of the classical HDAC family

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908479

Cloning and characterization of a novel human class I histone deacetylase that functions as a transcription repressor

5 June 2018

1 reference

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Structures of a histone deacetylase homologue bound to the TSA and SAHA inhibitors

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2908479

SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling

5 June 2018

1 reference

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Binding of substrate CO2 to the active site of human carbonic anhydrase II: a molecular dynamics study

5 June 2018

1 reference

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Flexibility of Catalytic Zinc Coordination in Thermolysin and HDAC8: A Born-Oppenheimer ab initio QM/MM Molecular Dynamics Study

5 June 2018

1 reference

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Highly dissociative and concerted mechanism for the nicotinamide cleavage reaction in Sir2Tm enzyme suggested by ab initio QM/MM molecular dynamics simulations

18 August 2018

1 reference

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Structural origin of selectivity in class II-selective histone deacetylase inhibitors

18 August 2018

1 reference

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Design and synthesis of a potent histone deacetylase inhibitor

18 August 2018

1 reference

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The carboxylate shift in zinc enzymes: a computational study.

18 August 2018

1 reference

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Crystal structure of a bacterial class 2 histone deacetylase homologue

18 August 2018

1 reference

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Theoretical study revealing the functioning of a novel combination of catalytic motifs in histone deacetylase

18 August 2018

1 reference

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Structural snapshots of human HDAC8 provide insights into the class I histone deacetylases

18 August 2018

1 reference

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18 August 2018

1 reference

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18 August 2018

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18 August 2018

1 reference

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Theoretical studies on farnesyltransferase: The distances paradox explained

18 August 2018

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2 December 2018

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Unexpected deacetylation mechanism suggested by a density functional theory QM/MM study of histone-deacetylase-like protein

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Identifiers

DOI

10.1021/JA103932D

1 reference

13 October 2017

1 reference

13 October 2017

1 reference