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Center for Genomic Experimentation and Computation

Center for Genomic Experimentation and Computation. Orna Resnekov Molecular Sciences Institute Berkeley, CA. Goal: To combine genomic and computational research in order to make predictive models of biological systems. molecular sciences institute. Magritte. The mating pathway. a factor.

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Center for Genomic Experimentation and Computation

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  1. Center for Genomic Experimentation and Computation Orna Resnekov Molecular Sciences Institute Berkeley, CA

  2. Goal: To combine genomic and computational research in order to make predictive models of biological systems. molecular sciences institute Magritte

  3. The mating pathway a factor a a a factor molecular sciences institute zygote a/a

  4. The Alpha Project a factor a a a factor molecular sciences institute zygote a/a

  5. Pathway after pheromone molecular sciences institute We are trying to both model and simulate the pathway

  6. Simplified view of pathway molecular sciences institute

  7. To simulate we need numbers… • Abundance (Ste5 ~500, Fus3 ~20,000) • Reaction rates • Affinities of proteins for one another • Structural information (not covered in our current Center grant) molecular sciences institute

  8. Key questions • What is the oligomerization state(s) of purified active Ste5? • What is the stoichiometry of the different multiprotein complexes that have kinase activity? • Which of the structures are biologically relevant Ste5 complexes? molecular sciences institute

  9. Complexity of the sample and purification status • Ste5, Ste11, Ste7, Fus3 • We have expression constructs to make individual proteins and reconstitute the pathway • We are also purifying complexes from cells using affinity tagged proteins (TAP) molecular sciences institute We have polyclonal abs, we are identifying posttranslational modifications (MS), we are making monoclonal abs to modified proteins, we have fluorescently tagged proteins.

  10. Hurdles to overcome • Need a good partner for structural studies • We would like to be doing both cryo-EM and crystallography • Sufficient material for these studies molecular sciences institute

  11. Resources needed • RO1 level funding for 3-5 people molecular sciences institute

  12. Response to pheromone molecular sciences institute

  13. PNNL Richard Smith (Chem) Robert Maxwell SBML Andrew Finney U. WA. Dee Dee Meldrum Mark Holl The Team: MIT Drew Endy (ex MSI) Ty Thomson (BioEng) Caltech Shuki Bruck (CS) Mark Reidel Matt Cook Kirsten Benjamin Roger Brent-DIRECTOR Ian Burbulis Tina Chin Alejandro Colman-Lerner Andrew Gordon (P) Larry Lok (Math) Joyce Maccabea Gustavo Pesce David Pincus Orna Resnekov Dan Rockwell Eduard Serra David Soergel (CS) Kouichi Takahashi Kumiko Yamaguchi Richard Yu (Struct. Bio.) Myron Williams molecular sciences institute

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