yes i can indeed be an artifact. there is no easy way to know this,
other than to compare to experiment, to use it to make a hypothesis
that is tested by experiment, or to repeat at different pulling rates
or different pulling methods/directions and see how the results are
affected.
others may have more suggestions.
On Thu, Apr 7, 2011 at 12:10 PM, Catein Catherine
<askamber23.hotmail.com> wrote:
>
> Dear Sir/Madam,
>
> I have done a PMF for a protein-drug dissociation process.
>
> Large conformation change in the protein was observed. It opens up the space for the drug to dissociate from the binding site. I tends to interprete that as a conformation change during drug dissociation process.
>
> However, could the large conformational change be only artifacts of fast pulling, because the timescales required for a partial protein unfolding is not consistent with experimental dissociation rates?
>
> Could you mind to comments on how to interprete the conformation change in PMF of drug-dissociation?
>
> Best regards & thanks,
>
> Catherine
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Received on Thu Apr 07 2011 - 09:30:04 PDT
