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 <[email protected]> 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 <[email protected]> wrote: > > > > > > shiva birgani wrote: > >> > >> Message: 1 > >> Date: Tue, 31 May 2011 06:56:16 -0400 > >> From: "Justin A. Lemkul" <[email protected] <mailto:[email protected]>> > >> Subject: Re: [gmx-users] flexiblity > >> To: Discussion list for GROMACS users <[email protected] > >> <mailto:[email protected]>> > >> Message-ID: <[email protected] <mailto:[email protected]>> > >> 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 > > > > ======================================== > > -- > > gmx-users mailing list [email protected] > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > Please don't post (un)subscribe requests to the list. Use the www > interface > > or send it to [email protected]. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > 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 > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- ====================================================================== Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: [email protected] [email protected] website: https://sites.google.com/site/thomasevangelidishomepage/
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