LEGO May 18, 2015: Difference between revisions

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* Continue to work on LEGO model for the April consistency exercise - http://www.ncbi.nlm.nih.gov/pubmed/24349431
* Continue to work on LEGO model for the April consistency exercise - http://www.ncbi.nlm.nih.gov/pubmed/24349431


===March Paper - Modeling the Mitotic Exit Network===
===March Paper - Modeling the Mitotic Exit Network (G protein- and Hippo kinase-based signaling pathways)===
* Additional reading:  [http://www.ncbi.nlm.nih.gov/pubmed/24594661 The Mitotic Exit Network: new turns on old pathways.] and references cited therein.  Also: [http://www.ncbi.nlm.nih.gov/pubmed/25658911 Asymmetry of the budding yeast Tem1 GTPase at spindle poles is required for spindle positioning but not for mitotic exit.]
* Additional reading:  [http://www.ncbi.nlm.nih.gov/pubmed/24594661 The Mitotic Exit Network: new turns on old pathways.] and references cited therein.  Also: [http://www.ncbi.nlm.nih.gov/pubmed/25658911 Asymmetry of the budding yeast Tem1 GTPase at spindle poles is required for spindle positioning but not for mitotic exit.]
* Steps/functions to model:
* Steps/functions to model:

Revision as of 10:26, 18 May 2015

Action Items from May 4, 2015 Call

  • Make a github ticket for adding IntAct protein complexes to Noctua. [DONE]
  • Heiko will let Seth know that curators may add feature requests, but these are not immediate needs.
  • David, Kimberly, and Rama will review their March paper models to compare with Paul's version.
  • Continue to work on LEGO model for the April consistency exercise - http://www.ncbi.nlm.nih.gov/pubmed/24349431

March Paper - Modeling the Mitotic Exit Network (G protein- and Hippo kinase-based signaling pathways)

  • Additional reading: The Mitotic Exit Network: new turns on old pathways. and references cited therein. Also: Asymmetry of the budding yeast Tem1 GTPase at spindle poles is required for spindle positioning but not for mitotic exit.
  • Steps/functions to model:
    • Tem1 localizes to the spindle pole body - asymmetrically to the bud-directed SPB
    • Tem1 and Cdc15 physically interact in a manner dependent on Tem1's GTP-binding domain
    • Bfa1 physically interacts with Bub2 and with Tem1 (different papers)
    • Bub2 executes the GAP activity - evidence for this?
    • Bfa1/Bub2 complex positively regulates Tem1 GTPase activity, resulting in decreased GTP binding
    • Lte1 is required for localization of Bfa1 to the daughter-bound spindle pole body
    • Tem1 is required for Cdc15 localization to the spindle pole body during late anaphase
    • Cdc15 phosphorylates Dbf2 only when Dbf2 is present with Mob1
    • Dbf2 phosphorylates Kar9
    • Cdc14 dephosphorylates Kar9
    • Kar9 localizes asymmetrically to spindle pole bodies and interacts with the Type V myosin Myo2
  • Questions
    • How would we represent asymmetric spindle pole body localization, i.e. mother- vs daughter-destined spindle pole body?
    • Tem1 has GTPase activity, but its active form in this pathway is as a GTP-bound protein. How could we represent this? Use a PRO ID for 'GTP-bound Tem1' and use that to annotate to Cdc15 binding and regulation of protein localization to spindle pole body?
  • Other organisms
    • C. elegans does not appear to have Tem1, Bfa1, or Cdc15
    • Closest C. elegans Bub2 is TBCK-1, but that appears to only be in the TBC domain, and there is no data about this protein
    • Dbf2 and Mbo1 homologues?
    • C. elegans does have a Cdc14 phosphatase