Talk:Ssutton: PTL Logic

What you call protein-DNA logic, I actually call transcription-based logic. The reason is that I think that what is more important is the signal carrier (i.e. transcription or PoPS) than how it is implemented (i.e. proteins binding to DNA). But that's just my two cents. --RS

I agree 125% with you, Reshma. Take this one up with Drew. We have gone around and around on this issue, and he insists that it should be PDL logic. I assumed that he spoke for everyone, so I used PDL in this document out of respect. But now that I see it is a Drew-ism, I'm switching it back to Transcription-based logic. Thanks for the note, and keep 'em coming! -- SS

Below is a wikified version of the text that you have in image file. Doing this to all the text should make editing much easier. There's probably something than can be done about other formatting (like if you want the text in a narrower column).

• In this system, each device is essentially a MAP Kinase. Each device shown here contains the following parts:
  • Kinase Scaffold
  • Docking Site
  • PO₄ Site
  • Docking Groove
  • PO₄ Groove
  • Catalytic Domain
• The above parts are needed so that one MAP Kinase can recognize another. MAP Kinases recognize their substrates in two ways:
  • The Docking Groove of the upstream kinase (e.g. Device1) binds to the Docking Site of the downstream kinase (e.g. Device2).
  • The PO₄ Groove of the upstream kinase binds to the PO₄ Site of the downstream kinase.
• Once a MAP Kinase PO₄ Site has been phosphorylated, the MAP Kinase undergoes a conformational change which positions the Catalytic Domain into its active conformation with catalytic activity parameter k_cat.
• Devices can be linearly arranges so as to form a cascade:
  • Device1 phosphorylates and activates Device2.
  • Device2 phosphorylates and activates Device3, etc.
• The signal passed between devices is some sort of catalytic activity of one kinase for another.

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