This integrate multi-institutional Program Project in Structural Biology of DNA Repair (SBDR) addresses the challenge of understanding at the molecular level the pathways controlling genetic integrity. SBDR will a) produce biologically relevant DNA repair protein structures, b) identify fundamental structural principles for repair proteins, and c) provide the structural framework for a unified understanding of the biochemistry, genetics and biology needed for this field. SBDR will leverage and integrate the existing biological and structural research strengths and programs of the investigators and their institutions to develop, test, and promote a new paradigm for optimizing inter-disciplinary scientific collaborations in the post-genomic era. The structural biology of individual proteins is linked to complexes and pathways through five interconnecting Projects investigating key DNA repair processes: 1) base excision repair, 2) transcription-coupled and replication-associated base excision repair, 3) double-strand break detection and rejoining, 4) homozygous recombinatorial repair, and 5) mismatch repair. The resulting biologically driven determinations of repair protein structures will apply the comparative knowledge of the sequenced bacterial, archael, yeast, and human genomes to an understanding of the structural cell biology of DNA repair in man. LBNL will provide the center for unified research efforts by SBDR through three Cores: Expression and Molecular Biology, Structural Cell Biology, and Administrative. Together, these Cores will insure efficient application and coordination of methodological, technical, and scientific advances by the five component Projects. Quantitative characterization of dynamic conformations plus coupled high and low-resolution X-ray diffraction studies at the new SIBYLS synchrotron beamline at LBNL will integrate DNA repair biology with structure at escalating levels of complexity from domains to multi-protein molecular machines. As an integrated whole, SBDR addresses three unifying hypotheses: 1) DNA repair proteins function as a chemo-mechanical devices that detect and repair damage via protein and DNA conformational switching; 2) DNA repair proteins interact dynamically to form multi-protein macromolecular machines that utilize cooperatively and allostery to coordinate and regulate function; and 3) structurally-encoded interactions and pathway connections are as important as chemistry for biological function of repair proteins. The large macromolecular recognition interfaces thus identified are likely to contain more sequence polymorphisms than smaller, functionally, critical , active site regions. SBDR Program results will therefore be fundamental to rational deign of epidemiological studies and will provide the logical next step to fully utilizing the information on individual polymorphisms in DNA repair proteins developed by the DOE and NIH Environmental and Human Genome Project.
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