MINOS will develop new methods and techniques to test the hypothesis that changes in conformation and/or assembly determine biological outcomes. The staff and scientists of the SIBYLS beamline provide comprehensive expertise in the targeted areas of nucleic acid binding proteins. High Throughput (HT) Small Angle X-ray Scattering (SAXS), Macromolecular Crystallography (MX), and hybrid computational methods. MINOS builds upon our results developing and employing SAXS to define accurate conformations and assemblies in solution in combination with PSI high-resolution crystal structures for detail. Biological information involves changes in shape as well as active site chemistry. SAXS provides robust analyses of shape and conformational change in solution whereas crystallography provides precise information on structural chemistry. Leveraging our existing SAXS and molecular biology expertise, we will innovate new methods and technologies to integrate and advance PSI and community characterizations of key human proteins and their complexes (with partner proteins, DNA, and RNA). MINOS will work closely with PSI centers and individual researchers to identify promising targets and constructs, optimize solution conditions, and provide solution conformation and assembly results that complement PSI high resolution crystal structures. MINOS will provide new methods, tools, and strategies to characterize key human and higher eukaryotes proteins and their complexes for structural biology and medicine, which have been challenging for current PSI and community efforts. Technical goals include identifying and optimizing SAXS data collection strategies for human proteins and their complexes in concert with high resolution structural studies within the PSI centers, rescuing stalled protein targets, and developing hybrid methods and techniques for easing the bottlenecks that currently place real limits on overall PSI productivity.
The Specific Aims will endeavor to 1) develop and apply innovative HT SAXS methods to solve solution structures of PSLBiology defined targets, and 2) use solution scattering technologies to link PSI and community structures to biology. Structures determined by PSI and community collaborations will direct SAXS experiments, test functional implications from SAXS structures,, and provide critical details for defining conformational trajectories in solution. Collectively the proposesd Aims provide a clear path to leverage PSI 'and research community strengths and technologies for imaging human and higher eukaryote proteins and their complexes with major impacts on biological understanding.

Public Health Relevance

Preventing and treating human disease ultimately relies on an understanding of how proteins, DNA, and RNA control key cellular functions. A major aspect of understanding these key macromolecules is a detailed picture of their shape, flexibility, and dynamic nature.
MINOS aims to provide new technologies and methods to study dynamic human macromolecules for structural biology and medicine, and will test the hypothesis that changes in the shape and assembly of dynamic macromolecules control biological outcomes in predictable ways, thereby aiding our ability to predict and treat human disease.

Agency
National Institute of Health (NIH)
Type
Research Project (R01)
Project #
5R01GM105404-03
Application #
8656719
Study Section
Special Emphasis Panel (ZRG1)
Program Officer
Edmonds, Charles G
Project Start
Project End
Budget Start
Budget End
Support Year
3
Fiscal Year
2014
Total Cost
Indirect Cost
Name
Lawrence Berkeley National Laboratory
Department
Biochemistry
Type
Organized Research Units
DUNS #
City
Berkeley
State
CA
Country
United States
Zip Code
94720
Deshpande, Rajashree A; Williams, Gareth J; Limbo, Oliver et al. (2014) ATP-driven Rad50 conformations regulate DNA tethering, end resection, and ATM checkpoint signaling. EMBO J 33:482-500
Jones, Christopher P; Cantara, William A; Olson, Erik D et al. (2014) Small-angle X-ray scattering-derived structure of the HIV-1 5' UTR reveals 3D tRNA mimicry. Proc Natl Acad Sci U S A 111:3395-400
Boucher, Jeffrey I; Jacobowitz, Joseph R; Beckett, Brian C et al. (2014) An atomic-resolution view of neofunctionalization in the evolution of apicomplexan lactate dehydrogenases. Elife 3:
Holton, James M; Classen, Scott; Frankel, Kenneth A et al. (2014) The R-factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures. FEBS J 281:4046-60
Pieper, Ursula; Webb, Benjamin M; Dong, Guang Qiang et al. (2014) ModBase, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res 42:D336-46
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
Singh, Harkewal; Arentson, Benjamin W; Becker, Donald F et al. (2014) Structures of the PutA peripheral membrane flavoenzyme reveal a dynamic substrate-channeling tunnel and the quinone-binding site. Proc Natl Acad Sci U S A 111:3389-94
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
Schumacher, Maria A; Tonthat, Nam K; Kwong, Stephen M et al. (2014) Mechanism of staphylococcal multiresistance plasmid replication origin assembly by the RepA protein. Proc Natl Acad Sci U S A 111:9121-6
Dyer, Kevin N; Hammel, Michal; Rambo, Robert P et al. (2014) High-throughput SAXS for the characterization of biomolecules in solution: a practical approach. Methods Mol Biol 1091:245-58

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