Pilot Centers
NIGMS supports the following pilot research centers in its Protein Structure Initiative:
Berkeley Structural Genomics Center (BSGC) |
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Like many of the NIGMS-funded structural genomics centers, this one aims to speed up structure determination by X-ray crystallography. It will focus on two bacteria with extremely small genomes to study proteins essential for independent life. The bacteria, Mycoplasma genitalium and Mycoplasma pneumoniae, are closely related. The former contains the smallest genome of any free-living organism and infects the human genital and respiratory tracts. The latter causes a form of pneumonia. Organizations: Lawrence Berkeley National Laboratory, University of North Carolina, Stanford University Principal investigator: Sung-Hou Kim, Lawrence Berkeley National Laboratory Targets: minimal genomes -- M. genitalium, M. pneumoniae Technology: robotic cloning; miniexpression screening; crystallization screening; automatic crystal changing and centering robots; computational filtering methods for target selection Web site: http://www.strgen.org/ |
Center for Eukaryotic Structural Genomics (CESG) |
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This Wisconsin-based center seeks to develop high-throughput methods for protein production, characterization and structure determination from Arabidopsis thaliana, a plant that is frequently used in laboratory research and that has many genes in common with humans and animals, including genes linked to disease. Organizations: University of Wisconsin, Medical College of Wisconsin (Milwaukee), Tokyo Metropolitan University, Molecular Kinetics, Inc., Hebrew University, Ehime University, CellFree Sciences (Yokohama), European Bioinformatics Institute-Hinxton Principal investigator: John L. Markley, University of Wisconsin, Madison Targets: Arabidopsis thaliana Technology: comprehensive LIMS for structural genomics; maskless array gene chip to screen cDNA libraries for presence of target genes; predictions of protein disorder for target selection; cell-free protein production; stereo-array isotope labeling for NMR Web site: http://www.uwstructuralgenomics.org/ |
The Joint Center for Structural Genomics (JCSG) |
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This California-based center is developing high-throughput methods for protein production, crystallization, and structure determination. It will initially focus on novel structures from the roundworm Caenorhabditis elegans and on human proteins thought to be involved in cell signaling. It will also determine the structures of similar proteins from other organisms to ensure the inclusion of the greatest number of different protein folds. Organizations: The Scripps Research Institute, University of California at San Diego, Stanford University, Stanford Synchrotron Radiation Labs, Genomics Institute of the Novartis Research Foundation Principal investigator: Ian Wilson, The Scripps Research Institute Targets: Thermotoga maritima, mouse Technology: crystallome screen of T. Maritima proteome; beamline automation; data centric informatics platform; nanovolume crystallization Web site: http://www.jcsg.org |
The Midwest Center for Structural Genomics |
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This consortium of seven institutions is working to reduce the average cost of a protein structure from $100,000 to $20,000. The group will select protein targets from all three kingdoms of life (Eukarya, Archaea, and Bacteria), with an emphasis on previously unknown folds and on proteins from disease-causing organisms. Organizations: Argonne National Laboratory, Northwestern University, Washington University School of Medicine, University College London, University of Texas Southwestern Medical Center, University of Toronto, University of Virginia Principal investigator: Andrzej Joachimiak, Argonne National Laboratory Targets: microorganisms, especially pathogens Technology: HTP target selection; automated gene cloning, protein expression, and solubility evaluation; low cost and high density fermentation; automated purification, crystallization, and structure determination; computational methods for fold analysis and function prediction; databases and LIMS Web site: http://www.mcsg.anl.gov |
New York-Structural GenomiX Research Center (NYSGXRC) |
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Five institutions in and around New York City and San Diego, Calif., will develop techniques to streamline every step of structural genomics. The consortium expects to solve several hundred protein structures from humans and model organisms. Organizations: Structural GenomiX, Inc., Albert Einstein College of Medicine, Brookhaven National Laboratory, Columbia University, Rockefeller University, University of California at San Francisco, Weill Medical College of Cornell Principal investigator: Stephen K. Burley, Structural GenomiX, Inc., San Diego, Calif. Targets: disease related proteins from eukaryotes and bacteria Technology: auto inducing media; His6-Smt3 protein expression vector; automation in protein production; automation in protein crystallization; automation in structure determination Web site: http://www.nysgrc.org |
Northeast Structural Genomics Consortium (NESGC) |
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Researchers in New Jersey, New York, Connecticut, Washington State, and Ontario, Canada will target proteins from various model organisms--including the fruit fly, yeast, and the roundworm--and related human proteins. This consortium will use both X-ray crystallography and NMR spectroscopy to determine protein structures. Organizations: Rutgers University, Columbia University, Hauptman-Woodward Medical Research Institute, Ontario Cancer Institute, Pacific Northwest National Laboratory, State University of New York Buffalo, University of Toronto, Yale University, Weill Medical College of Cornell, Mt. Sinai School of Medicine Principal investigator: Gaetano Montelione, Rutgers University Targets: model eukaryotes -- D. melanogaster, S. cerevisiae, C. elegans, mouse, human Technology: systemic bioinformatics on domain families; crystallization image analysis; NMR reduced dimensionality data collection; automated analysis of NMR structures Web site: http://www.nesg.org |
Southeast Collaboratory for Structural Genomics (SECSG) |
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Researchers will analyze part of the human genome and the entire genomes of two representative organisms--the roundworm Caenorhabditis elegans and its more primitive microbial ancestor, Pyrococcus furiosus. The group emphasizes technology development, especially for automated crystallography and NMR techniques. Organizations: University of Georgia, University of Alabama-Birmingham, University of Alabama-Huntsville, Harvard Medical School, Duke University, Georgia State University Principal investigator: Bi-Cheng Wang, University of Georgia Targets: P. furiosus, C. elegans, human Technology: direct crystallography; NMR direct determination of backbone structures; self-learning crystallization system Web site: http://www.secsg.org |
Structural Genomics of Pathogenic Protozoa (SGPP) |
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This group aims to develop new ways to solve protein structures from organisms known as protozoans, many species of which cause deadly diseases such as sleeping sickness, malaria, and Chagas' disease. Organizations: University of Washington, Seattle Biomedical Research Institute, University of Rochester, Hauptman-Woodward Medical Research Institute, Lawrence Berkeley National Laboratory, Stanford University Principal investigator: Wim G. J. Hol, University of Washington Targets: disease related proteins from Leishmania species, Trypanosoma species, Plasmodium falciparum Technology: computational domain parsing; high throughput protein-pair discovery; new robots for crystallization in capillaries Web site: http://www.sgpp.org/ *co-funded by the National Institute of Allergy and Infectious Diseases |
TB Structural Genomics Consortium (TBSGC) |
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A collaboration of scientists in six countries formed to determine and analyze the structures of about 400 proteins from Mycobacterium tuberculosis. The group seeks to optimize the technical and managerial underpinnings of high-throughput structure determination and will develop a database of structures and functions. NIH's National Institute of Allergy and Infectious Diseases, which is co-funding this project with NIGMS, anticipates that this information also will lead to the design of new and improved drugs and vaccines for tuberculosis. Organizations: Los Alamos National Laboratory, Albert Einstein College of Medicine, Texas A&M University, University of California Los Angeles, University of California Berkeley, Lawrence Livermore National Laboratory Principal investigator: Thomas Terwilliger, Los Alamos National Laboratory Targets: disease related proteins from M. tuberculosis Technology: engineering proteins for solubility with GFP reporter; automation of crystallography structure determination Web site: http://www.doe-mbi.ucla.edu/TB *co-funded by the National Institute of Allergy and Infectious Diseases |
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