Hi there,
On Wed, Aug 7, 2019 at 11:58 PM <charalamm.cheng.auth.gr> wrote:
> 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
> principle.
>
> 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?
>
In principle yes. In practice, you have 3D diffusion coupled with 2D
diffusion along the DNA (sliding across sequences and doing so with
non-digital displacement). Now that your TF is on the DNA and moving along
it, it'll undergo conformational changes when it recognizes its target
cognate sequence.
Take a look at this publication on how we approached the 2D component of
diffusion using Amber and check the references for 3D diffusion
https://academic.oup.com/nar/article/44/1/63/2499624
Take a look at this publication on how Haoquan approached the kinetics of
sequence recognition using Amber:
http://dx.doi.org/10.1021/jacs.6b11433
> 2) Do you think that AMBERTools18 is suitable for our purposes?
>
AmberTools is probably not suitable for getting diffusion/binding kinetics
of highly charged systems in which solvent structure is important, dynamics
are key but often "slow" and you don't have a lot of experimental data. The
good news is that Amber is relatively cheap for
Academic/non-profit/government entities.
>
> We would really appreciate your help in the matter. Any feedback could
> be useful for our project.
>
If Amber is on the table for you, check out publications from Carlos
Simmerling's group, Modesto Orozco's group, and David Case's group.
> Thank you very much for your time.
>
> My best regards,
> Charalampos Malathounis
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
Hope that helped,
Kevin
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 08 2019 - 08:00:03 PDT
