This proposal describes a research program that aims to develop and apply peptide arrays to elucidate specificity and reactivity patterns of histone deacetylase (HDAC) activity. This process, which plays a fundamental role in chromatin modeling and gene regulation, is mediated by a network of enzymes and histone substrates. Biochemical studies of the relevant enzyme-substrate activities are very limited, owing primarily to a lack of methods to monitor and define patterns of enzyme activity. The applicants have developed self-assembled monolayers (SAMs) of alkanethiolates on gold as a platform for biochips that provide for quantitative assays and label-free detection when used with conventional matrix assisted laser desorption ionization -time of flight mass spectrometry (MALDI-ToF-MS), a technique termed SAMDI (self-assembled monolayers for MALDI-MS). The proposed work will develop a route to prepare peptide arrays and use these arrays to characterize the substrate specificities of HDAC enzymes and characterize the regulation of histone activity by additional post-translational modifications in the peptide substrate.

Public Health Relevance

Gene expression is regulated by a network of histone deacetylase enzymes and histone substrates in which deviations can lead towards several cancers and aging. Biochemical studies of the relevant enzyme-substrate activities are very limited, owing primarily to a lack of methods to monitor and define patterns of enzyme activity. The proposed work will develop a route to prepare peptide arrays and use these arrays to characterize the substrate specificities of HDAC enzymes and characterize the regulation of histone activity by additional posttranslational modifications in the peptide substrate.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM084188-03
Application #
7778335
Study Section
Enabling Bioanalytical and Biophysical Technologies Study Section (EBT)
Program Officer
Edmonds, Charles G
Project Start
2008-04-01
Project End
2012-02-29
Budget Start
2010-03-01
Budget End
2011-02-28
Support Year
3
Fiscal Year
2010
Total Cost
$297,810
Indirect Cost
Name
University of Chicago
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
005421136
City
Chicago
State
IL
Country
United States
Zip Code
60637
Kornacki, James R; Stuparu, Andreea D; Mrksich, Milan (2015) Acetyltransferase p300/CBP associated Factor (PCAF) regulates crosstalk-dependent acetylation of histone H3 by distal site recognition. ACS Chem Biol 10:157-64
Sodji, Quaovi H; Kornacki, James R; McDonald, John F et al. (2015) Design and structure activity relationship of tumor-homing histone deacetylase inhibitors conjugated to folic and pteroic acids. Eur J Med Chem 96:340-59
Patil, Vishal; Sodji, Quaovi H; Kornacki, James R et al. (2013) 3-Hydroxypyridin-2-thione as novel zinc binding group for selective histone deacetylase inhibition. J Med Chem 56:3492-506
Kuo, Hsin-Yu; DeLuca, Teresa A; Miller, William M et al. (2013) Profiling deacetylase activities in cell lysates with peptide arrays and SAMDI mass spectrometry. Anal Chem 85:10635-10642
Sodji, Quaovi H; Patil, Vishal; Kornacki, James R et al. (2013) Synthesis and structure-activity relationship of 3-hydroxypyridine-2-thione-based histone deacetylase inhibitors. J Med Chem 56:9969-81
Li, Shuheng; Liao, Xiaoli; Mrksich, Milan (2013) Steady-state of an enzymatic reaction is dependent on the density of reactant. Langmuir 29:294-8
Gurard-Levin, Zachary A; Scholle, Michael D; Eisenberg, Adam H et al. (2011) High-throughput screening of small molecule libraries using SAMDI mass spectrometry. ACS Comb Sci 13:347-50
Mwakwari, Sandra C; Guerrant, William; Patil, Vishal et al. (2010) Non-peptide macrocyclic histone deacetylase inhibitors derived from tricyclic ketolide skeleton. J Med Chem 53:6100-11
Gurard-Levin, Zachary A; Kilian, Kristopher A; Kim, Joohoon et al. (2010) Peptide arrays identify isoform-selective substrates for profiling endogenous lysine deacetylase activity. ACS Chem Biol 5:863-73
Gurard-Levin, Zachary A; Kim, Joohoon; Mrksich, Milan (2009) Combining mass spectrometry and peptide arrays to profile the specificities of histone deacetylases. Chembiochem 10:2159-61

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