[gmx-users] simulation of oligomers/monomers
Justin A. Lemkul
jalemkul at vt.edu
Mon Jul 18 19:42:15 CEST 2011
Kavyashree M wrote:
> Sir,
>
> My aim was to find out the difference between the monomer protein and
> monomer of the dimer. it was for a preliminary analysis of the dynamics of
> the structure and not a detailed study. But whatever the aim is, if the
> protein is
> stable during the simulation then can a comparison be made for the dynamics
> of protein from different sources.
>
If stability is not an issue, then maybe you can do some assessment. Perhaps
dimerization (or higher oligomerization) is needed to impart coordinated motion
for catalysis; there are many such examples. This will require a fairly
detailed approach like PCA to uncover, rather than some cursory examination of
dynamics. What you need is a well-defined question that you can answer with the
tools available to you.
-Justin
> Thank you
> With Regards
> M. Kavyashree
>
> On Mon, Jul 18, 2011 at 6:22 PM, Ragothaman Yennamalli
> <ragothaman at gmail.com <mailto:ragothaman at gmail.com>> wrote:
>
> With regards to run a monomeric simulation as resonable or not, I
> would agree with Mark that it depends what you wish to learn, and
> depends on what your hypothesis is.
> Ragothaman
>
> On Mon, Jul 18, 2011 at 7:49 AM, Kavyashree M <hmkvsri at gmail.com
> <mailto:hmkvsri at gmail.com>> wrote:
>
> Thank you Sir,
>
> The interface is connected by salt bridges and hydrogen bonding
> interactions and not severely
> hydrophobic. I tried simulating the monomers it stayed quite
> stable without unfolding till 50ns.
> Even the other structure which are reported to be dimer is a
> reported as a trimer in solution.
> Another one is a part of a bifunctional protein which is an
> octamer. So Because of all these
> confusions I through some information could be obtained from a
> monomeric simulation..
> Is it reasonable?
>
>
> Thanking you
> With Regards
> M. Kavyashree
>
> On Mon, Jul 18, 2011 at 6:02 PM, Ragothaman Yennamalli
> <ragothaman at gmail.com <mailto:ragothaman at gmail.com>> wrote:
>
> Look at this paper where the simulation was done on a
> protein dimer:
> http://www.ncbi.nlm.nih.gov/pubmed/17027497
>
> On Mon, Jul 18, 2011 at 2:50 AM, Mark Abraham
> <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>>
> wrote:
>
> On 18/07/2011 3:08 PM, Kavyashree M wrote:
>
> Dear users,
>
> I am working on a protein which is a dimer (in the
> crystal structure), predicted according top PISA.
> and some of the homologous proteins are dimers
> (covalent /non-covalent) some are monomers.
> There has not been any literature regarding the fact
> that the functional unit is a dimer, ie the enzyme
> is not functional when the dimeric interface is
> disturbed due to mutations. Also the active sites
> are not
> shared among the dimeric partners. In this situation
> is it meningful to do a simulation of monomers alone
> and try to get some information.
>
>
> The dimeric interface might be so hydrophobic the
> protein would unfold - but unlikely given the homology
> evidence. It could certainly perturb the structure
> significantly, and perhaps such perturbations connect
> with the activity. Only detailed understanding of the
> structure and function can help you decide about this.
>
>
> In general is it necessary to simulate only the
> functional oligomers or monomer also can be done ?
>
>
> Depends on the system, and depends what you wish to learn.
>
> Mark
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--
========================================
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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