Core B is a synthesis, analysis and biochemical core that will provide indispensable services for all three projects. The synthetic component of Core B will carry out scaled-up synthesis, purification and analysis of """"""""tool-kit"""""""" and other nucleotide analogs for use in Projects 1 and 3. The biochemical component of Core B is designed to carry out protein purifications and to synthesize specialized DNA constructs required for Projects 1 and 3. The analysis component will be responsible for acquiring and performing global analysis on kinetic data, including presteady state stopped-flow fluorescence intensity and rotational anisotropy, rapid quench experiments, as well as basic NMR and EPR-ENDOR analysis, to be used in support of Projects 2 and 3. Core B will also serve as a primary vehicle for training graduate and postdoctoral students in chemical synthesis and protein purification techniques, the principles and practice of enzyme kinetic analysis, and techniques in experimental NMR and EPR spectroscopy.

Public Health Relevance

Core B provides essential chemical probes, biochemical assays and spectroscopic analysis in support of the three component projects of this Program Project. This work will lead to better understanding of the structure, fidelity and catalytic mechanism of DNA polymerases, and also includes synthesis of compounds to develop a new approach to selective inhibition of cancer-related DNA repair by DNA polymerase beta.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Research Program--Cooperative Agreements (U19)
Project #
5U19CA177547-02
Application #
8754984
Study Section
Special Emphasis Panel (ZCA1)
Project Start
Project End
Budget Start
2014-09-01
Budget End
2015-08-31
Support Year
2
Fiscal Year
2014
Total Cost
Indirect Cost
Name
University of Southern California
Department
Type
DUNS #
City
Los Angeles
State
CA
Country
United States
Zip Code
90089
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Ni, Feng; Kung, Alvin; Duan, Yankun et al. (2017) Remarkably Stereospecific Utilization of ATP ?,?-Halomethylene Analogues by Protein Kinases. J Am Chem Soc 139:7701-7704
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Yoon, Hanwool; Warshel, Arieh (2017) Simulating the fidelity and the three Mg mechanism of pol ? and clarifying the validity of transition state theory in enzyme catalysis. Proteins 85:1446-1453
Maximoff, Sergey N; Kamerlin, Shina Caroline Lynn; Florián, Jan (2017) DNA Polymerase ? Active Site Favors a Mutagenic Mispair between the Enol Form of Deoxyguanosine Triphosphate Substrate and the Keto Form of Thymidine Template: A Free Energy Perturbation Study. J Phys Chem B 121:7813-7822
Yoon, Hanwool; Warshel, Arieh (2016) The control of the discrimination between dNTP and rNTP in DNA and RNA polymerase. Proteins 84:1616-1624
Vorobyov, Igor; Kim, Ilsoo; Chu, Zhen T et al. (2016) Refining the treatment of membrane proteins by coarse-grained models. Proteins 84:92-117
Hwang, Candy S; Xu, Liang; Wang, Wei et al. (2016) Functional interplay between NTP leaving group and base pair recognition during RNA polymerase II nucleotide incorporation revealed by methylene substitution. Nucleic Acids Res 44:3820-8

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