NMR data management for structural genomics: Applications in the structure determination and functional characterization of iron-sulfur cluster bioassembly proteins

Modern protein NMR spectroscopy laboratories have a rapidly growing need for an easily queried local archival system of raw experimental NMR datasets. SPINS (Standardized ProteIn Nmr Storage) is an object-oriented relational database that provides facilities for high-volume NMR data archival, organization of analyses, and dissemination of results to the public domain by automatic preparation of the header files required for submission of data to the BioMagResBank (BMRB). The current version of SPINS coordinates the process from data collection to BMRB deposition of raw NMR data by standardizing and integrating the storage and retrieval of these data in a local laboratory file system. The software integrates various stand-alone software components used in the NMR data analysis, allowing users to archive the complete structure determination process. This thesis provides an overview of the data model underlying the SPINS database system, a description of its implementation in Oracle, and its implementation in a structural genomics project.; Iron-sulfur cluster proteins are found to play a role in a number of cellular processes. These include electron transport, transcriptional regulation, and a number of catalytic and regulatory processes. Three bacterial operons have been characterized which code for Fe-S proteins. Homologous proteins can be found in both prokaryotic as well as eukaroyotic organisms. Recently the Northeast Structural Genomics Consortium (NESG) has structurally characterized a number of proteins showing homology to the Fe-S cluster proteins. Here we present the structures of S.aureus protein SAV1430 (ZR18) and S. epidermis protein SE0630 (SeR8) which represent the middle and C-terminus of the NifU protein. Taking this structural data together with other high throughput data one can put together a bio-network of interacting Fe-S cluster bioassembly proteins. Interestingly, SAV1430 and SE0609 represent domains of a eukaryotic protein family represented by the homo sapien protein HIRIP5. HIRIP5 has been shown to bind Laforin, a protein involved in the lethal neurodegenerative disorder Lafora disease.