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C P F M Chemical Proteomics Facility at Marquette

Internet2: Enabling Post-Genomic Technology at Marquette. C P F M Chemical Proteomics Facility at Marquette. The post-genomic challenge Exploring function across protein families using chemical probes. Basic research. Applied research.

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C P F M Chemical Proteomics Facility at Marquette

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  1. Internet2: Enabling Post-Genomic Technology at Marquette C P F M Chemical Proteomics Facility at Marquette The post-genomic challenge Exploring function across protein families using chemical probes Basic research Applied research • The CPFM is in early stages of development • Projects focus on studies of protein function (applied genomics) • Participants from: - MCW - Marquette (Biology & Chemistry) - UW-Milwaukee (MFBSC) - UW-Madison (NMRFAM) Long term goal: “Science in Service to Society”

  2. Internet2: Turning the CPFM into a Collaboratorium

  3. The Promise of Genomics: not yet realized … • Potential Benefits: • Better understanding of biology • Pharmacogenomics & personalized medicine • Treatments for currently untreatable disease • Drugs with fewer side effects • Better understanding of toxicology of pollutants Genes => Proteins “The human genome is data not knowledge, and will be useless until we understand what it means.” attributed to Sydney Brenner

  4. C P F M Chemical Proteomics Facility at Marquette The post-genomic challenge Exploring function across protein families using chemical probes What is the Chemical Proteomics Facility at Marquette? Resources (equipment, software) and people With a mission to: • Enable Chemical Proteomic studies of protein-ligand interactions • Facilitate collaboration across departments and institutions • Provide a better understanding of basic biology • Use science to address social needs • Train scientists and entrepreneurs with social conscience S3 = Biotechnology with social conscience: science, business, law and engineering

  5. C P F M Chemical Proteomics Facility at Marquette The post-genomic challenge Exploring function across protein families using chemical probes Beowulf/Linux cluster facility Modelling lab: remote access to NMRFAM Fluorescence assay lab NMR spectrometer lab CPFM Resources at Marquette: Equipment

  6. Internet2: The CPFM as a Collaboratorium I2 Chemistry Biology I2 I2

  7. 1) Need High Speed (I2) Connection to MFBSC CPFM Client I2 Viewing of microscopy results at CPFM (imaging)

  8. Fluorescence imaging as a window to: • Zebrafish developmental biology • Drug transport

  9. Estrogen receptor Zebrafish Estrogen Receptors (endocrine disruptor targets) Computationally derived with homology modeling … is a protein targeted by endocrine disruptor pollutants (EPA regulations)

  10. 2) Need High Speed (I2) Connection to NMRFAM CPFM Client I2

  11. Teleconference to NMRFAM: what is NMRFAM? Milo Westler, Ph.D. Operations Director NMRFAM

  12. Can use protein structure to design better drugs • And to avoid drug metabolism: • Toxic side effects • Drug/drug interactions Computational Docking for Drug Design (Dock, Autodock, Caveat & Grid) HIV Protease inhibitor

  13. 3) Need High Speed (I2) Connection to UTA CPFM Client University of Texas at Austin National Partnership for Advanced Computational Infrastructure I2 • Ligand-protein docking • Homology modeling • Chemoinformatic analysis of drug properties IBM Power 4 system Marquette’s Beowulf cluster

  14. Unique enabling of Chemoinformatics at Marquette Molecular Legos?

  15. C P F M Chemical Proteomics Facility at Marquette The post-genomic challenge Exploring function across protein families using chemical probes Summary Internet2: Enabling remote access & collaboration • NMRFAM and MFBSC facilities • Computational resources (UT-Austin; Marquette) • Access to local computational data & tools (chemoinformatics) Databases:endocrine disruptors; optimized drug building blocks S3: better drugs, better pollutant screening, basic Biology

  16. Current CPFM Projects and Participants • Medical College of Wisconsin • Henry Miziorko: Enzymes in the mevalonate biosynthetic pathway: structural and mechanistic studies • Jung-Ja Kim: Structural characterization of molecular motion in NADPH-cytochrome P450 oxidoreducatase • Marquette: Chemistry • - James Kincaid:Complementary use of NMR & Raman studies to probe substrate binding to cytochrome P450 • - Dan Sem: Probing protein-ligand interactions in toxicology and chemical proteomics: methods and application • Marquette: Biology • Pinfen Yang: Mechanism of flagellar radial spoke: ligand binding and structural studies of radial spoke protein 2 • Rosemary Stuart: Role of Su e in oligomerizing the F1-F0 ATP synthase complex: structural and binding studies • Other collaborators and resources: • UW-Milwaukee: Marine and Freshwater Biomedical Sciences Center • UW-Madison: NMR Facility • UT-Austin: Supercomputer Facility (NSF)

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