Rationale and Motivation
The mammalian mitochondrial proteome consists of ~1,200 proteins, including hundreds with no biological characterization. Mitochondrial dysfunction is at the heart of more than 50 human diseases ranging from neonatal fatalities to adult-onset neurodegeneration, and is a likely contributor to type II diabetes, cancer, metabolic syndrome, obesity, and the aging process. Thus, mitochondrial proteomes represent a ripe focus area for high-throughput assisted structure-function investigations by the National Institutes of Health (NIH) Protein Structure Initiative (PSI) Network.
NESG: MPP’s Partner Among the PSI Centers for High-Throughput Structure Determination
The Northeast Structural Genomics (NESG) Consortium is partnering with the MPP as its engine for high-throughput structure determination. NESG developed into a highly successful large-scale structural genomics center during phase-two of the Protein Structure Initiative (PSI-2, 2005-2010). Structural targets nominated by the MPP are fed into the NESG pipeline with the goal of protein production from E. coli cells followed by structure determination by X-ray crystallography or NMR spectroscopy. Any targets found not to be amenable to production from E. coli cells, but shown to be produced in good yield by MPP’s cell-free protein production platform, will be produced by the latter platform for structure determination.
Definition of the Roles of the MPP and NESG
The MPP, with assistance from its biological collaborators, develops prioritized lists of mitochondrial proteins for structure determination. The NESG takes this list and utilizes its high-throughput pipeline to produce proteins and solve structures. Full information is shared between MPP and NESG. Once a structure is determined, the MPP and its biological collaborators bring to bear known functional information and, as appropriate, design functional follow-up studies to complete a structure-function story on the target suitable for publication. All manuscripts are vetted by the parties involved so that proper author attributions are made and all are in agreement prior to submission for publication.
Rules of the Protein Structure Initiative (PSI)
The MPP, NESG, and MPP collaborators are subject to the rules of the funding agency (PSI). The MPP interfaces with the PSI Network by providing full information to the PSI Knowledgebase (TargetDB and PepcDB) and by transferring all clones and plasmids to the PSI Materials Repository. Structures are deposited in the Protein Data Bank (PDB) upon completion for immediate release, and NMR data are deposited in the BioMagResBank (BMRB).