Rate Law from Kd for a weak and transient PPI

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Hikmet Emre Kaya

May 25, 2023, 4:54:33 AM5/25/23
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Hello everyone,

This might be a silly question so bear with me as I try to revive my undergrad physical chemistry knowledge :)

Can one write a rate law in COPASI for a weak and transient interaction between two proteins for which Kd is given? Or does one need more information? 

Thanks in advance.

Scampicchio Matteo Mario

May 25, 2023, 5:36:52 AM5/25/23
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Minimal info are:

  1. your mechanism (like, A + B -> C for an irreversible step or A + B = C for a reversible step).
  2. The initial concentration of reactants and products.

Time units can be second, days, weeks or else, no problem. Copasi can handle units.

Regards, Matteo


From: copasi-u...@googlegroups.com <copasi-u...@googlegroups.com> On Behalf Of Hikmet Emre Kaya
Sent: Thursday, May 25, 2023 10:55 AM
To: COPASI User Forum <copasi-u...@googlegroups.com>
Subject: [copasi-user-forum] Rate Law from Kd for a weak and transient PPI


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Hikmet Emre Kaya

May 30, 2023, 10:06:13 AM5/30/23
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Thank you for your response! I guess I am just stuck because I am trying to construct a model with a protein that interacts with a bunch of other proteins involved in cancerous signaling, but there is very little kinetics information to populate such a model. Has anyone struggled with similar problems, and how did you go about solving it?

Scampicchio Matteo Mario

May 30, 2023, 10:39:15 AM5/30/23
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I am afraid your question is more about experimental works in cancerous signaling rather than about Copasi. Consider redirecting your question to a forum more specialized to your field of study. Once you have a model and some kinetic data, we can help with Copasi.

Kind regards and good luck

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