Re: [AMBER] protein-protein complex dissociation

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Thu, 16 Apr 2020 09:21:13 -0400

Have you done a control on the wild type to see that it is more stable?
Then you can have more confidence that the observation is due to the
mutation.

On Thu, Apr 16, 2020, 9:18 AM Núbia Toman <nnubiaits.hotmail.com> wrote:

> Dear Amber users,
>
> I performed 1 us MD simulation of a protein-protein complex. After about
> 200ns the complex seemed to start to disassociate and continued partially
> dissociated 70% of the simulation after that it returns to its initial
> position (bound).
>
> This system has a mutation that drastically decreases the binding affinity
> and the simulation results seemed to agree with experimental data. But I am
> wondering if this partial dissociation is a random thing or could be due to
> the effect of the mutation.
>
> Can anyone help me with that?
>
> Best,
>
> Nubia P. Toman
> PhD student, Bioinformatics
> Universidade Federal de Minas Gerais
>
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Received on Thu Apr 16 2020 - 06:30:02 PDT