Center for Genomic Experimentation and Computation

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Center for Genomic Experimentation and
Computation

• Orna Resnekov
• Molecular Sciences Institute
• Berkeley, CA

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Goal To combine genomic and computational
research in order to make predictive models of
biological systems.
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Magritte
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The mating pathway
a factor
a
a
a factor
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zygote a/a
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The Alpha Project
a factor
a
a
a factor
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zygote a/a
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Pathway after pheromone
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We are trying to both model and simulate the
pathway
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Simplified view of pathway
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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
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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?

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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)

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We have polyclonal abs, we are identifying
posttranslational modifications (MS), we are
making monoclonal abs to modified proteins, we
have fluorescently tagged proteins.
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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

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Resources needed

• RO1 level funding for 3-5 people

molecular sciences institute
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Response to pheromone
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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
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