Abstract

Our long term goal is to develop and apply state-of-the-art computational methods to provide theoretical underpinnings of the histone code. Histone proteins that form the nucleosome core are subject to a variety of post-translational transformations. These histone modifications make up the histone code which extends the information in the genetic code and is emerging as an essential mechanism to regulate gene expression. Failure of appropriate histone modifications can lead to aberrant gene regulation and is implicated in human diseases, notably cancer. In spite of a current flurry of significant advances in experimental studies, there has been little theoretical understanding regarding how the histone code is written, i.e., how enzymes generate or remove these modifications. In this proposal, we mainly focus on two such important histone-modifying enzyme families: Class I and II histone deacetylases (HDACs), and histone lysine methyltransferases (HKMTs). The former are among the most promising targets for the development of anti-tumor drugs, while histone lysine methylation has been addressed in studies of age-related neurodegenerative disorders as well as cancer. Our theoretical approaches will center on the combined ab initio quantum mechanical and molecular mechanical (QM/MM) methods, which allow for accurate modeling of the chemistry at the enzyme active site while properly .including the effects of protein environment.
In aim 1, we will characterize the catalytic mechanism for class I and II histone deacetylases.
In aim 2, we will investigate HKMTs to provide detailed insights into how the product specificity of histone lysine methylation is achieved.
In aim 3, new ab initio QM/MM methods will be developed to further improve its accuracy, efficiency and capability. These proposed studies will not only make fundamental contributions to this new and important area of molecular biology, but also should facilitate the design of novel mechanism-based drugs for diseases stemming from aberrant histone modifications.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM079223-03
Application #
7577372
Study Section
Special Emphasis Panel (ZRG1-BCMB-Q (90))
Program Officer
Preusch, Peter C
Project Start
2007-02-01
Project End
2012-01-31
Budget Start
2009-02-01
Budget End
2010-01-31
Support Year
3
Fiscal Year
2009
Total Cost
$252,431
Indirect Cost

  Institution

Name
New York University
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
041968306
City
New York
State
NY
Country
United States
Zip Code
10012

  Publications

Cai, Yuqin; Fu, Iwen; Geacintov, Nicholas E et al. (2018) Synergistic effects of H3 and H4 nucleosome tails on structure and dynamics of a lesion-containing DNA: Binding of a displaced lesion partner base to the H3 tail for GG-NER recognition. DNA Repair (Amst) 65:73-78
Wang, Cheng; Zhang, Yingkai (2017) Improving scoring-docking-screening powers of protein-ligand scoring functions using random forest. J Comput Chem 38:169-177
Fu, Iwen; Cai, Yuqin; Geacintov, Nicholas E et al. (2017) Nucleosome Histone Tail Conformation and Dynamics: Impacts of Lysine Acetylation and a Nearby Minor Groove Benzo[a]pyrene-Derived Lesion. Biochemistry 56:1963-1973
Mu, Hong; Geacintov, Nicholas E; Min, Jung-Hyun et al. (2017) Nucleotide Excision Repair Lesion-Recognition Protein Rad4 Captures a Pre-Flipped Partner Base in a Benzo[a]pyrene-Derived DNA Lesion: How Structure Impacts the Binding Pathway. Chem Res Toxicol 30:1344-1354
Hou, Xuben; Rooklin, David; Fang, Hao et al. (2016) Resveratrol serves as a protein-substrate interaction stabilizer in human SIRT1 activation. Sci Rep 6:38186
Zhou, Y; Wang, S; Li, Y et al. (2016) Born-Oppenheimer Ab Initio QM/MM Molecular Dynamics Simulations of Enzyme Reactions. Methods Enzymol 577:105-18
Fu, Iwen; Cai, Yuqin; Zhang, Yingkai et al. (2016) Entrapment of a Histone Tail by a DNA Lesion in a Nucleosome Suggests the Lesion Impacts Epigenetic Marking: A Molecular Dynamics Study. Biochemistry 55:239-42
Zhou, Yanzi; Xie, Daiqian; Zhang, Yingkai (2016) Amide Rotation Hindrance Predicts Proteolytic Resistance of Cystine-Knot Peptides. J Phys Chem Lett 7:1138-42
Lei, Jinping; Zhou, Yanzi; Xie, Daiqian et al. (2015) Mechanistic insights into a classic wonder drug--aspirin. J Am Chem Soc 137:70-3
Gong, Wenjing; Wu, Ruibo; Zhang, Yingkai (2015) Thiol versus hydroxamate as zinc binding group in HDAC inhibition: An ab initio QM/MM molecular dynamics study. J Comput Chem 36:2228-35

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