High-throughput strategy to identify inhibitors of histone-binding domains.

PubWeight™: 0.75‹?›

🔗 View Article (PMC 4467374)

Published in Methods Enzymol on January 01, 2012

Authors

Elise K Wagner1, Brittany N Albaugh, John M Denu

Author Affiliations

1: Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA.

Articles cited by this

Translating the histone code. Science (2001) 56.77

Chromatin modifications and their function. Cell (2007) 55.98

A Simple Statistical Parameter for Use in Evaluation and Validation of High Throughput Screening Assays. J Biomol Screen (1999) 32.67

Selective inhibition of BET bromodomains. Nature (2010) 18.79

How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nat Struct Mol Biol (2007) 10.98

Controlling the double helix. Nature (2003) 8.61

The Tudor domain 'Royal Family': Tudor, plant Agenet, Chromo, PWWP and MBT domains. Trends Biochem Sci (2003) 5.19

Structure and acetyl-lysine recognition of the bromodomain. Oncogene (2007) 3.20

Haematopoietic malignancies caused by dysregulation of a chromatin-binding PHD finger. Nature (2009) 3.13

TRIM24 links a non-canonical histone signature to breast cancer. Nature (2010) 2.99

Molecular recognition of histone H3 by the WD40 protein WDR5. Nat Struct Mol Biol (2006) 2.55

PHD fingers in human diseases: disorders arising from misinterpreting epigenetic marks. Mutat Res (2008) 2.31

Isothermal titration calorimetry of protein-protein interactions. Methods (1999) 2.03

Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b. Nature (2010) 2.02

Luminescent oxygen channeling immunoassay: measurement of particle binding kinetics by chemiluminescence. Proc Natl Acad Sci U S A (1994) 2.02

The PHD finger: a versatile epigenome reader. Trends Biochem Sci (2011) 1.81

Recognition of multivalent histone states associated with heterochromatin by UHRF1 protein. J Biol Chem (2011) 1.79

IC50-to-Ki: a web-based tool for converting IC50 to Ki values for inhibitors of enzyme activity and ligand binding. Nucleic Acids Res (2009) 1.60

MBT domain proteins in development and disease. Semin Cell Dev Biol (2009) 1.49

A homogeneous method for investigation of methylation-dependent protein-protein interactions in epigenetics. Nucleic Acids Res (2009) 1.49

Luminescent oxygen channeling assay (LOCI): sensitive, broadly applicable homogeneous immunoassay method. Clin Chem (1996) 1.40

Chemical regulation of epigenetic modifications: opportunities for new cancer therapy. Med Res Rev (2008) 1.32

Screening for inhibitors of low-affinity epigenetic peptide-protein interactions: an AlphaScreen-based assay for antagonists of methyl-lysine binding proteins. J Biomol Screen (2009) 1.27

The expression and clinical significance of DNA methyltransferase proteins in human gastric cancer. Dig Dis Sci (2008) 1.24

UHRF1 is a novel diagnostic marker of lung cancer. Br J Cancer (2010) 1.18

Structure and mechanisms of lysine methylation recognition by the chromodomain in gene transcription. Biochemistry (2011) 1.10

High throughput screening. Methods and protocols, second edition. Preface. Methods Mol Biol (2009) 0.78

Articles by these authors

The human Sir2 ortholog, SIRT2, is an NAD+-dependent tubulin deacetylase. Mol Cell (2003) 8.34

Sirtuins deacetylate and activate mammalian acetyl-CoA synthetases. Proc Natl Acad Sci U S A (2006) 7.00

Sirt3 mediates reduction of oxidative damage and prevention of age-related hearing loss under caloric restriction. Cell (2010) 5.73

Mechanism of human SIRT1 activation by resveratrol. J Biol Chem (2005) 4.86

Histone H3-K56 acetylation is catalyzed by histone chaperone-dependent complexes. Mol Cell (2007) 3.38

SIRT3 deacetylates mitochondrial 3-hydroxy-3-methylglutaryl CoA synthase 2 and regulates ketone body production. Cell Metab (2010) 2.77

Calorie restriction and SIRT3 trigger global reprogramming of the mitochondrial protein acetylome. Mol Cell (2012) 2.54

Circadian clock NAD+ cycle drives mitochondrial oxidative metabolism in mice. Science (2013) 2.49

Essential role for the SANT domain in the functioning of multiple chromatin remodeling enzymes. Mol Cell (2002) 2.33

Sirt3 promotes the urea cycle and fatty acid oxidation during dietary restriction. Mol Cell (2011) 2.29

Substrate specificity and kinetic mechanism of the Sir2 family of NAD+-dependent histone/protein deacetylases. Biochemistry (2004) 2.11

Activation of the protein deacetylase SIRT6 by long-chain fatty acids and widespread deacylation by mammalian sirtuins. J Biol Chem (2013) 2.03

The Sirtuin family: therapeutic targets to treat diseases of aging. Curr Opin Chem Biol (2008) 2.00

Mechanisms and molecular probes of sirtuins. Chem Biol (2008) 1.90

Structural identification of 2'- and 3'-O-acetyl-ADP-ribose as novel metabolites derived from the Sir2 family of beta -NAD+-dependent histone/protein deacetylases. J Biol Chem (2002) 1.88

Mechanism of nicotinamide inhibition and transglycosidation by Sir2 histone/protein deacetylases. J Biol Chem (2003) 1.87

Molecular functions of the histone acetyltransferase chaperone complex Rtt109-Vps75. Nat Struct Mol Biol (2008) 1.78

SIRT3 protein deacetylates isocitrate dehydrogenase 2 (IDH2) and regulates mitochondrial redox status. J Biol Chem (2012) 1.77

Chemical mechanisms of histone lysine and arginine modifications. Biochim Biophys Acta (2008) 1.69

Structure and biochemical functions of SIRT6. J Biol Chem (2011) 1.67

Assays for mechanistic investigations of protein/histone acetyltransferases. Methods (2005) 1.65

Catalysis and substrate selection by histone/protein lysine acetyltransferases. Curr Opin Struct Biol (2008) 1.64

Conserved enzymatic production and biological effect of O-acetyl-ADP-ribose by silent information regulator 2-like NAD+-dependent deacetylases. J Biol Chem (2002) 1.62

Binding of the CHD4 PHD2 finger to histone H3 is modulated by covalent modifications. Biochem J (2009) 1.59

Catalytic mechanism of a MYST family histone acetyltransferase. Biochemistry (2007) 1.57

Plant homeodomain (PHD) fingers of CHD4 are histone H3-binding modules with preference for unmodified H3K4 and methylated H3K9. J Biol Chem (2011) 1.55

Metabolite of SIR2 reaction modulates TRPM2 ion channel. J Biol Chem (2006) 1.55

A continuous microplate assay for sirtuins and nicotinamide-producing enzymes. Anal Biochem (2009) 1.54

Small molecule regulation of Sir2 protein deacetylases. FEBS J (2005) 1.54

Sir2 protein deacetylases: evidence for chemical intermediates and functions of a conserved histidine. Biochemistry (2006) 1.49

Mechanism-based inhibition of Sir2 deacetylases by thioacetyl-lysine peptide. Biochemistry (2007) 1.44

Coenzyme specificity of Sir2 protein deacetylases: implications for physiological regulation. J Biol Chem (2004) 1.43

Identification of macrodomain proteins as novel O-acetyl-ADP-ribose deacetylases. J Biol Chem (2011) 1.42

Acetyl-lysine analog peptides as mechanistic probes of protein deacetylases. J Biol Chem (2007) 1.41

The deacetylase Sirt6 activates the acetyltransferase GCN5 and suppresses hepatic gluconeogenesis. Mol Cell (2012) 1.39

Combinatorial profiling of chromatin binding modules reveals multisite discrimination. Nat Chem Biol (2010) 1.39

Bivalent recognition of nucleosomes by the tandem PHD fingers of the CHD4 ATPase is required for CHD4-mediated repression. Proc Natl Acad Sci U S A (2012) 1.37

Sirtuin catalysis and regulation. J Biol Chem (2012) 1.35

KAT(ching) metabolism by the tail: insight into the links between lysine acetyltransferases and metabolism. Chembiochem (2010) 1.32

Where in the cell is SIRT3?--functional localization of an NAD+-dependent protein deacetylase. Biochem J (2008) 1.31

Probing the function of conserved residues in the serine/threonine phosphatase PP2Calpha. Biochemistry (2003) 1.28

Function and metabolism of sirtuin metabolite O-acetyl-ADP-ribose. Biochim Biophys Acta (2010) 1.25

Quantitative assays for characterization of the Sir2 family of NAD(+)-dependent deacetylases. Methods Enzymol (2004) 1.23

Quantification of mitochondrial acetylation dynamics highlights prominent sites of metabolic regulation. J Biol Chem (2013) 1.20

SIRT3 substrate specificity determined by peptide arrays and machine learning. ACS Chem Biol (2010) 1.17

Structural basis for the recognition of a bisphosphorylated MAP kinase peptide by human VHR protein Phosphatase. Biochemistry (2002) 1.14

Sir2 deacetylases exhibit nucleophilic participation of acetyl-lysine in NAD+ cleavage. J Am Chem Soc (2007) 1.14

Sirtuin 1 inhibition delays cyst formation in autosomal-dominant polycystic kidney disease. J Clin Invest (2013) 1.14

Nucleosome recognition by the Piccolo NuA4 histone acetyltransferase complex. Biochemistry (2007) 1.14

Hydrolase regulates NAD+ metabolites and modulates cellular redox. J Biol Chem (2009) 1.13

Orphan macrodomain protein (human C6orf130) is an O-acyl-ADP-ribose deacylase: solution structure and catalytic properties. J Biol Chem (2011) 1.12

SIRT1 top 40 hits: use of one-bead, one-compound acetyl-peptide libraries and quantum dots to probe deacetylase specificity. Biochemistry (2006) 1.11

Identification and characterization of small molecule inhibitors of a plant homeodomain finger. Biochemistry (2012) 1.11

Regulation of glycolytic enzyme phosphoglycerate mutase-1 by Sirt1 protein-mediated deacetylation. J Biol Chem (2011) 1.09

Autoacetylation of the histone acetyltransferase Rtt109. J Biol Chem (2011) 1.08

The acetyltransferase activity of CBP is required for wingless activation and H4 acetylation in Drosophila melanogaster. Mol Cell Biol (2002) 1.08

Modulating acetyl-CoA binding in the GCN5 family of histone acetyltransferases. J Biol Chem (2002) 1.08

Dynamic interplay between histone H3 modifications and protein interpreters: emerging evidence for a "histone language". Chembiochem (2010) 1.06

Kinetic mechanism of the Rtt109-Vps75 histone acetyltransferase-chaperone complex. Biochemistry (2010) 1.06

Acetylation-dependent ADP-ribosylation by Trypanosoma brucei Sir2. J Biol Chem (2007) 1.06

Catalytic activation of histone acetyltransferase Rtt109 by a histone chaperone. Proc Natl Acad Sci U S A (2010) 1.03

Analysis of O-acetyl-ADP-ribose as a target for Nudix ADP-ribose hydrolases. J Biol Chem (2002) 1.00

A combinatorial H4 tail library for exploring the histone code. Biochemistry (2008) 0.99

Site-specific reactivity of nonenzymatic lysine acetylation. ACS Chem Biol (2015) 0.99

Nuclear-cytoplasmic localization of acetyl coenzyme a synthetase-1 in the rat brain. J Comp Neurol (2010) 0.98

Multivalent recognition of histone tails by the PHD fingers of CHD5. Biochemistry (2012) 0.97

Metabolic acetate therapy improves phenotype in the tremor rat model of Canavan disease. J Inherit Metab Dis (2010) 0.92

Synthesis and biochemical evaluation of O-acetyl-ADP-ribose and N-acetyl analogs. Org Biomol Chem (2007) 0.92

Quantification of SAHA-Dependent Changes in Histone Modifications Using Data-Independent Acquisition Mass Spectrometry. J Proteome Res (2015) 0.91

Dual-specificity protein tyrosine phosphatase VHR down-regulates c-Jun N-terminal kinase (JNK). Oncogene (2002) 0.91

Quantification of endogenous sirtuin metabolite O-acetyl-ADP-ribose. Anal Biochem (2008) 0.91

Linking SIRT2 to Parkinson's disease. ACS Chem Biol (2007) 0.90

NUP98-PHF23 is a chromatin-modifying oncoprotein that causes a wide array of leukemias sensitive to inhibition of PHD histone reader function. Cancer Discov (2014) 0.89

Catalysis and mechanistic insights into sirtuin activation. Chembiochem (2010) 0.89

Circadian control of fatty acid elongation by SIRT1 protein-mediated deacetylation of acetyl-coenzyme A synthetase 1. J Biol Chem (2014) 0.89

Hydrolysis of O-acetyl-ADP-ribose isomers by ADP-ribosylhydrolase 3. J Biol Chem (2011) 0.88

Metabolic regulation of histone post-translational modifications. ACS Chem Biol (2015) 0.87

Intramolecular dephosphorylation of ERK by MKP3. Biochemistry (2003) 0.86

Processing mechanism and substrate selectivity of the core NuA4 histone acetyltransferase complex. Biochemistry (2011) 0.86

Ure(k)a! Sirtuins Regulate Mitochondria. Cell (2009) 0.83

Sirtuins caught in the act. Structure (2006) 0.81

Probing the transition-state structure of dual-specificity protein phosphatases using a physiological substrate mimic. Biochemistry (2004) 0.81

Disrupting the reader of histone language. Angew Chem Int Ed Engl (2011) 0.80

Structure of Arabidopsis thaliana At1g77540 protein, a minimal acetyltransferase from the COG2388 family. Biochemistry (2006) 0.79

Kinetic mechanism of adenine phosphoribosyltransferase from Leishmania donovani. Biochemistry (2002) 0.78

Structural and kinetic isotope effect studies of nicotinamidase (Pnc1) from Saccharomyces cerevisiae. Biochemistry (2011) 0.78

Methyl magic and HAT tricks. Nat Struct Biol (2002) 0.77

The C-terminus of human nucleotide receptor P2X7 is critical for receptor oligomerization and N-linked glycosylation. PLoS One (2013) 0.75