[gmx-users] flexibility

[Thomas Evangelidis]

Hi Tsjerk,

thanks for nice the reference. If I have understood correctly, the authors
have applied their technique to characterize the residues and the respective
motions that confer thermal stability to a thermophilic enzyme compared to a
mesophilic homologue. In my case I want to study the effects of a point
mutation on the dynamics of an enzyme, in order to explain the increased
catalytic activity that is observed* in vitro* and* in vivo*. The difference
here is that I know exactly which part of the protein is implicated for the
gain of function (the mutation site). Do you reckon I could gain more from
doing the afore-mentioned statistical analysis instead of just comparing the
RMSF between the wt and the mutant?


thanks in advance,
Thomas


On 1 June 2011 15:43, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi,
>
> The usual (statistical) way to compare fluctuations (variances) is by
> taking the ratio (i.e. of the MSFs, not the RMSFs). Maragliano e.a.
> (BiophysJ 2004) wrote on such comparison of fluctuations, using a
> variance ratio test.
> In your case, you'd have to combine it with a structure alignment to
> find which numbers should be compared with which.
>
> Cheers,
>
> Tsjerk
>
> On Wed, Jun 1, 2011 at 1:24 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> >
> >
> > shiva birgani wrote:
> >>
> >>    Message: 1
> >>    Date: Tue, 31 May 2011 06:56:16 -0400
> >>    From: "Justin A. Lemkul" <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> >>    Subject: Re: [gmx-users] flexiblity
> >>    To: Discussion list for GROMACS users <gmx-users at gromacs.org
> >>    <mailto:gmx-users at gromacs.org>>
> >>    Message-ID: <4DE4C950.70704 at vt.edu <mailto:4DE4C950.70704 at vt.edu>>
> >>    Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >>
> >>
> >>
> >>    shiva birgani wrote:
> >>     > Dear all
> >>     > I have simulated two different proteins (A and B). I need to
> compare
> >>     > their flexibility. RMSF help to examine their flexibilty
> >>    individually,
> >>     > but I want to campare them with each other.
> >>     > Do anybody know a solution to this? Would you please help me in
> >>    this regard?
> >>     >
> >>
> >>    Is it not just a matter of comparing the RMSF between the two
> proteins?
> >>
> >>    -Justin
> >>
> >>    --
> >>    ========================================
> >>
> >> Dear Justin
> >>
> >> Yes I want to compare them, but I am not sure that RMSF is appropriate
> >> test to comparison, because two proteins are completely different in
> their
> >> amino acid contents and numbers.
> >>
> >
> > RMSF is the correct metric for measuring the flexibility of your
> proteins.
> >  How you then interpret the data in light of what's known about your
> system
> > and the goals of your study is up to you.  All part of good experimental
> > design.
> >
> > -Justin
> >
> > --
> > ========================================
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
> > --
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
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-- 

======================================================================

Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: tevang at bioacademy.gr

          tevang3 at gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/
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