Hi Tsjerk,<br><br>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<i> in vitro</i> and<i> in vivo</i>. 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?<br>
<br><br>thanks in advance,<br>Thomas<br> <br><br><div class="gmail_quote">On 1 June 2011 15:43, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi,<br>
<br>
The usual (statistical) way to compare fluctuations (variances) is by<br>
taking the ratio (i.e. of the MSFs, not the RMSFs). Maragliano e.a.<br>
(BiophysJ 2004) wrote on such comparison of fluctuations, using a<br>
variance ratio test.<br>
In your case, you'd have to combine it with a structure alignment to<br>
find which numbers should be compared with which.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<div><div></div><div class="h5"><br>
On Wed, Jun 1, 2011 at 1:24 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br>
><br>
><br>
> shiva birgani wrote:<br>
>><br>
>> Message: 1<br>
>> Date: Tue, 31 May 2011 06:56:16 -0400<br>
>> From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>>><br>
>> Subject: Re: [gmx-users] flexiblity<br>
>> To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
>> <mailto:<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>>><br>
>> Message-ID: <<a href="mailto:4DE4C950.70704@vt.edu">4DE4C950.70704@vt.edu</a> <mailto:<a href="mailto:4DE4C950.70704@vt.edu">4DE4C950.70704@vt.edu</a>>><br>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
>><br>
>><br>
>><br>
>> shiva birgani wrote:<br>
>> > Dear all<br>
>> > I have simulated two different proteins (A and B). I need to compare<br>
>> > their flexibility. RMSF help to examine their flexibilty<br>
>> individually,<br>
>> > but I want to campare them with each other.<br>
>> > Do anybody know a solution to this? Would you please help me in<br>
>> this regard?<br>
>> ><br>
>><br>
>> Is it not just a matter of comparing the RMSF between the two proteins?<br>
>><br>
>> -Justin<br>
>><br>
>> --<br>
>> ========================================<br>
>><br>
>> Dear Justin<br>
>><br>
>> Yes I want to compare them, but I am not sure that RMSF is appropriate<br>
>> test to comparison, because two proteins are completely different in their<br>
>> amino acid contents and numbers.<br>
>><br>
><br>
> RMSF is the correct metric for measuring the flexibility of your proteins.<br>
> How you then interpret the data in light of what's known about your system<br>
> and the goals of your study is up to you. All part of good experimental<br>
> design.<br>
><br>
> -Justin<br>
><br>
> --<br>
> ========================================<br>
><br>
> Justin A. Lemkul<br>
> Ph.D. Candidate<br>
> ICTAS Doctoral Scholar<br>
> MILES-IGERT Trainee<br>
> Department of Biochemistry<br>
> Virginia Tech<br>
> Blacksburg, VA<br>
> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
><br>
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<br>
<br>
<br>
</div></div>--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
post-doctoral researcher<br>
Molecular Dynamics Group<br>
* Groningen Institute for Biomolecular Research and Biotechnology<br>
* Zernike Institute for Advanced Materials<br>
University of Groningen<br>
The Netherlands<br>
<div><div></div><div class="h5">--<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>
<p style="margin-bottom: 0cm;" align="LEFT">======================================================================</p>
<p style="margin-bottom: 0cm;" align="LEFT">Thomas Evangelidis</p>
<p style="margin-bottom: 0cm;" align="LEFT">PhD student</p>
<p style="margin-bottom: 0cm;" align="LEFT">Biomedical Research
Foundation, Academy of Athens</p>
<p style="margin-bottom: 0cm;" align="LEFT">4 Soranou Ephessiou , 115 27
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<p style="margin-bottom: 0cm;" align="LEFT"><br>
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<br>