Abstract

The goal of this project is to develop and apply computational methods to reproduce, understand and predict structural and thermodynamical aspects of molecular recognition in the EcoRV enzyme-DNA and the small ligand-DNA complexes. We will use this methodology with a protein (EcoRV) interacting with DNA and small ligands: actinomycin, acridine, netropsin, furimidazoline. We will use the available experimental data on these systems as a critical guideline to evaluate the theory. Understanding recognition in the systems proposed here, especially in the EcoRV-DNA complex, will further the long term goal of the parent NIH grant, which is to make the computer approaches reliable and truly predictive in order to use them as an important tool in understanding molecular interactions as well as in the drug design process.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
Fogarty International Center (FIC)
Type
Small Research Grants (R03)
Project #
5R03TW001234-03
Application #
6499506
Study Section
International and Cooperative Projects 1 Study Section (ICP)
Program Officer
Katz, Flora N
Project Start
2000-02-01
Project End
2004-01-31
Budget Start
2002-02-01
Budget End
2004-01-31
Support Year
3
Fiscal Year
2002
Total Cost
$35,640
Indirect Cost

  Institution

Name
University of California San Francisco
Department
Pharmacology
Type
Schools of Pharmacy
DUNS #
073133571
City
San Francisco
State
CA
Country
United States
Zip Code
94143

  Publications

Queiroz, Daniel Barboza Cava; Porto, Catarina S; Grossman, Gail et al. (2008) Immunolocalization of alpha(1A)-adrenoceptors in rat and human epididymis. Cell Tissue Res 332:509-22
He, Bin; Gampe Jr, Robert T; Hnat, Andrew T et al. (2006) Probing the functional link between androgen receptor coactivator and ligand-binding sites in prostate cancer and androgen insensitivity. J Biol Chem 281:6648-63
Queiroz, Daniel B C; Silva, Adilson M da; Gutierrez-Ospina, Gabriel et al. (2006) Cells positive for microtubule-associated protein 1B (MAP 1B) are present along rat and human efferent ductules and epididymis. Cell Tissue Res 325:125-33
Bai, Suxia; He, Bin; Wilson, Elizabeth M (2005) Melanoma antigen gene protein MAGE-11 regulates androgen receptor function by modulating the interdomain interaction. Mol Cell Biol 25:1238-57
He, Bin; Gampe Jr, Robert T; Kole, Adam J et al. (2004) Structural basis for androgen receptor interdomain and coactivator interactions suggests a transition in nuclear receptor activation function dominance. Mol Cell 16:425-38
Huo, Shuanghong; Wang, Junmei; Cieplak, Piotr et al. (2002) Molecular dynamics and free energy analyses of cathepsin D-inhibitor interactions: insight into structure-based ligand design. J Med Chem 45:1412-9