We are studying the structural organization of DNA repair complexes that excise DNA damage and the functional consequences of disrupting these protein-protein interactions by mutation and small molecule inhibitors. Alternative pathways of repair are available for many types of DNA damage, and posttranslational modifications generated in response to DNA damage control the differential assembly of repair complexes, providing a mechanism for regulating pathway choice. Cancer-associated defects in DNA maintenance activities can be exploited therapeutically by targeting the remaining repair activities with mechanism-based inhibitors. Our work focuses on the mechanisms of repairing DNA single strand breaks generated by the base excision and nucleotide excision repair pathways. We are studying the physical assembly of DNA damage excision complexes in vitro and in cultured cells, and the mechanism of coupling DNA cleavage to end processing and ligation. Small angle x-ray scattering of purified DNA repair complexes reveals dynamic conformational states that we propose are important for handoffs of DNA repair intermediates to successive enzymes in a pathway. High resolution crystal structures and small molecule screening experiments are being used to predict and identify inhibitors of repair protein interactions, which are candidates for anti-tumor therapies and serve as reversible chemical probes of cellular physiology during DNA damage responses. This integrated approach takes advantage of the broad expertise of investigators in Projects 1, 2, and 6 for assays and biological materials, as well as the unique capabilities of the Expression and Molecular Biology Core and the Structural Cell Biology Core of the SBDR Program to produce proteins and structurally evaluate repair complexes.

Public Health Relevance

The Achilles'heel of all cancer cells is their defect in DNA repair and cell cycle checkpoints that can kill tumor cells by causing them to enter cell division before repair is complete. Thus, many cancers are treated by radiation and chemotherapies to overload repair in tumor cells but not in normal cells, which are better protected by redundant repair pathways and functioning cell cycle checkpoints. SBDR will comprehensively characterize DNA repair circuits to reveal tumor vulnerabilities that are key to short-circuiting DNA repair and specifically killing cancer cells while not harming better-protected normal cells.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Research Program Projects (P01)
Project #
5P01CA092584-13
Application #
8543539
Study Section
Special Emphasis Panel (ZCA1-RPRB-0 (M1))
Program Officer
Pelroy, Richard
Project Start
2001-09-27
Project End
2016-08-31
Budget Start
2013-09-01
Budget End
2014-08-31
Support Year
13
Fiscal Year
2013
Total Cost
$2,808,109
Indirect Cost
$858,328
Name
Lawrence Berkeley National Laboratory
Department
Biology
Type
Organized Research Units
DUNS #
078576738
City
Berkeley
State
CA
Country
United States
Zip Code
94720
Feldkamp, Michael D; Mason, Aaron C; Eichman, Brandt F et al. (2014) Structural analysis of replication protein A recruitment of the DNA damage response protein SMARCAL1. Biochemistry 53:3052-61
Groocock, Lynda M; Nie, Minghua; Prudden, John et al. (2014) RNF4 interacts with both SUMO and nucleosomes to promote the DNA damage response. EMBO Rep 15:601-8
Paull, Tanya T; Deshpande, Rajashree A (2014) The Mre11/Rad50/Nbs1 complex: recent insights into catalytic activities and ATP-driven conformational changes. Exp Cell Res 329:139-47
Shibata, Atsushi; Moiani, Davide; Arvai, Andrew S et al. (2014) DNA double-strand break repair pathway choice is directed by distinct MRE11 nuclease activities. Mol Cell 53:7-18
Mahaney, Brandi L; Lees-Miller, Susan P; Cobb, Jennifer A (2014) The C-terminus of Nej1 is critical for nuclear localization and non-homologous end-joining. DNA Repair (Amst) 14:9-16
Frank, Andreas O; Vangamudi, Bhavatarini; Feldkamp, Michael D et al. (2014) Discovery of a potent stapled helix peptide that binds to the 70N domain of replication protein A. J Med Chem 57:2455-61
Wu, Ching-Shyi; Ouyang, Jian; Mori, Eiichiro et al. (2014) SUMOylation of ATRIP potentiates DNA damage signaling by boosting multiple protein interactions in the ATR pathway. Genes Dev 28:1472-84
Davis, Anthony J; Chen, Benjamin P C; Chen, David J (2014) DNA-PK: a dynamic enzyme in a versatile DSB repair pathway. DNA Repair (Amst) 17:21-9
Zhao, Weixing; Saro, Dorina; Hammel, Michal et al. (2014) Mechanistic insights into the role of Hop2-Mnd1 in meiotic homologous DNA pairing. Nucleic Acids Res 42:906-17
Longerich, Simonne; Kwon, Youngho; Tsai, Miaw-Sheue et al. (2014) Regulation of FANCD2 and FANCI monoubiquitination by their interaction and by DNA. Nucleic Acids Res 42:5657-70

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