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
<ragotha...@gmail.com <mailto:ragotha...@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 <hmkv...@gmail.com
<mailto:hmkv...@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
<ragotha...@gmail.com <mailto:ragotha...@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.abra...@anu.edu.au <mailto:mark.abra...@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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