[AMBER] Transcription factor DNA binding - Gibbs of activation

From: <charalamm.cheng.auth.gr>
Date: Thu, 08 Aug 2019 09:58:27 +0300

Dear AMBER community,

I am a member of iGEM Thessaloniki team, an undergraduate research
team of Aristotle University of Thessaloniki, Greece and I am sending
you this e-mail in order to ask you some questions regarding the
computational model of our project.

My team and I are working on designing a DNA computer system in a cell
free environment, based on a DNA Strand Displacement mechanism. We are
planning on using our toolkit in order to measure the binding affinity
of a Transcription Factor with a DNA sequence. At this point of our
project, we are studying the binding sites of NF-κB, as a proof of

In an effort to create a complete model, we are trying to calculate
the exact time that will be needed in order for the TF to bind to the
DNA and the duration of this binding. Thus, we are thinking on
calculating the kinetic rates of the binding reaction and that's why
we are considering using the Eyering equation or the Collision theory.
However, both methods need ΔG of activation for the calculations. It
is important to be stated, that we do not have any experimental data
concerning the binding reaction.

Therefore, I would like to address you the following questions.
1) Do you think that is possible to predict the free energy of
activation for this reaction?
2) Do you think that AMBERTools18 is suitable for our purposes?

We would really appreciate your help in the matter. Any feedback could
be useful for our project.

Thank you very much for your time.

My best regards,
Charalampos Malathounis

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Received on Thu Aug 08 2019 - 00:00:03 PDT
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