The SCB Core will provide to all six SBDR Projects the following: 1) Macromolecular Crystallography and Small Angle X-ray Scattering data collection at the SIBYLS beamline located at beamline 12.3.1 of the Advanced Light Source synchrotron at LBNL. The SIBYLS beamline is a unique synchrotron resource that provides tunable wavelength X-rays for both MX and SAXS experiments. 2) Collaboration on SBDR targets with SCB staff for both MX and SAXS studies. 3) Development and application of SAXS analysis software to address current limitations and beamline hardware to optimize data quality for SBDR targets. This includes software that will combine results from high and low resolution techniques through the systematic and objective fitting of X-ray crystal structures that are consistent with the experimental SAXS data. 4) Analysis by Multi-angle Light Scattering (MALS) System in line with Size Exclusion Chromatography (SEC) in the SIBYLS wet lab. MALS with its 1% molecular mass accuracy is critical for validating complexes for SAXS analysis. 5) In silico and in vitro screening services to identify small molecule inhibitors for selected SBDR targets that control biological outcome and coordination of inhibitor studies with Joe Gray. The results from the SCB Core will be applied to the understanding of cancer etiology and potential cancer therapy through interactions with collaborators. These services are central to the goal of each Project to structurally characterize DNA repair complexes. MX provides atomic resolution information, while SAXS provides structural information on the conformations of DNA repair proteins and complexes in solution. The Core is centralized at the ALS because of the need for high flux, tunable wavelength X-rays for MX and SAXS studies. The Core also provides a critical mass of expertise needed for the difficult structural studies of flexible and modular proteins and complexes. The SCB Core, in collaboration with all six SBDR Projects, will generate insights into dynamic and coordinated assembly of large protein complexes involved in DNA repair processes.

Public Health Relevance

The SCB Core will provide to SBDR Projects expertise and facilities to structurally characterize DNA repair complexes by macromolecular crystallography, small angle X-ray scattering, and multi-angle light scattering. High resolution structures and structural analysis in solution are central to achieve the SBDR goal of mechanistic, predictive biology for improved cancer interventions that will be highly relevant to public health.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Research Program Projects (P01)
Project #
5P01CA092584-13
Application #
8567649
Study Section
Special Emphasis Panel (ZCA1-RPRB-0)
Project Start
Project End
Budget Start
2013-09-01
Budget End
2014-08-31
Support Year
13
Fiscal Year
2013
Total Cost
$672,748
Indirect Cost
$205,632
Name
Lawrence Berkeley National Laboratory
Department
Type
DUNS #
078576738
City
Berkeley
State
CA
Country
United States
Zip Code
94720
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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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