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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

Center for Genomic Experimentation and Computation

Orna Resnekov

Molecular Sciences Institute

Berkeley, CA

slide2

Goal: To combine genomic and computational research

in order to make predictive models of biological systems.

molecular sciences institute

Magritte

slide3

The mating pathway

a factor

a

a

a factor

molecular sciences institute

zygote

a/a

slide4

The Alpha Project

a factor

a

a

a factor

molecular sciences institute

zygote

a/a

slide5

Pathway after pheromone

molecular sciences institute

We are trying to both model and simulate the pathway

slide6

Simplified view of pathway

molecular sciences institute

slide7

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

slide8

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

slide9

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.

slide10

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

slide11

Resources needed

  • RO1 level funding for 3-5 people

molecular sciences institute

slide12

Response to pheromone

molecular sciences institute

slide13

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