AMBER Archive (2006)

Subject: Re: AMBER: RMSD: is it related to flexibility?

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Thu Oct 05 2006 - 11:08:05 CDT

Ann,

If all you want is to compare flexibilities, it may be a beter idea to
define a couple of characteristic internal distances and monitor them
in time. For a better description of the method, take a look at:

"Sulfide Binding Hemoglobins: Effects of Mutations on Active Site Flexibility"
Fernandez-Alberti et al. Biophys. J. vol. 91, p.1698 (2006)

Best wishes,

Gustavo Seabra.

On 10/5/06, a a <patd_2_at_hotmail.com> wrote:
> Dear David,
>
> Thank you very much for your comments. The following is the experimental
> work done previously. Both the wild type and mutated proteins form a
> covalent complex with a drug. They both modified the drug to a metabolite.
> Experimentally, we measured the metabolite concentration over the time,
> and found mutant one produce metabolite ten times faster than the wild type.
> We originally expected that it is due to different binding affinity of the
> drug, but finally we found the binding affinities for these two proteins to
> the drug are the same both experimentally and theoretically (docking). As
> it is well documented that the rate for these protein to release the
> metabolite is a function of a flexibility of a loop on these proteins (the
> loop is mutated). Thus, we try to see if the mutation change the
> flexibility of the loop theoretically, so as to explain the increased rate.
>
> Follow the tutorial on the web, I carried out minimization, equilibrium and
> a production 1-ns MD with sander for these two proteins, and double checked
> that the potential energies are stable at the production period. This is
> the preliminary result that we got. The RMSD (reference to a PDB file) of
> the loop of the wild type protein in average is 2.0, but 3.0 for the mutant
> one. The RMSD vs time plot shown that the RMSD increase from zero and
> reach stable (~ 4 A) at ~300 ps for the wild type and ~200 ps for the
> mutant. Is the difference in terms of RMSD (1-2 A) and time to reach stable
> (100 ps) significant enough for drawing any conclusions?
>
> If not, could you mind to suggest the best way to model the release rate of
> metabolite B from these two proteins?
>
> I am new to MD calculations, just learn it several months ago from the
> websites, your professional suggestions are valuable to me. Many thanks in
> advanced.
>
> Best regards,
>
> Ann
>
> >From: "David A. Case" <case_at_scripps.edu>
> >Reply-To: amber_at_scripps.edu
> >To: amber_at_scripps.edu
> >Subject: Re: AMBER: RMSD: is it related to flexibility?
> >Date: Wed, 4 Oct 2006 08:08:32 -0700
> >
> >On Wed, Oct 04, 2006, a a wrote:
> > >
> > > I got two protein structures with different performance on the loop
> > > mobilitiy, one of them move very fast, another one is about 10 time less
> > > flexible, based on our experimental data.
> >
> >The answer probably depends on what kind of experimental data one is
> >talking
> >about here; that will effectively determine what is being measured and
> >represented as "flexibility". And that, in turn, will help decide what
> >sorts
> >of calculations might be relevant.
> >
> >...regards...dac
> >
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