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.<br>Ragothaman<br><br><div class="gmail_quote">On Mon, Jul 18, 2011 at 7:49 AM, Kavyashree M <span dir="ltr"><<a href="mailto:hmkvsri@gmail.com">hmkvsri@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Thank you Sir, <br><br>The interface is connected by salt bridges and hydrogen bonding interactions and not severely<br>
hydrophobic. I tried simulating the monomers it stayed quite stable without unfolding till 50ns. <br>Even the other structure which are reported to be dimer is a reported as a trimer in solution. <br>
Another one is a part of a bifunctional protein which is an octamer. So Because of all these<br>confusions I through some information could be obtained from a monomeric simulation..<br>Is it reasonable?<div class="im"><br>
<br>Thanking you<br>
With Regards<br>M. Kavyashree<br><br></div><div class="gmail_quote"><div><div></div><div class="h5">On Mon, Jul 18, 2011 at 6:02 PM, Ragothaman Yennamalli <span dir="ltr"><<a href="mailto:ragothaman@gmail.com" target="_blank">ragothaman@gmail.com</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div></div><div class="h5">Look at this paper where the simulation was done on a protein dimer:<br><a href="http://www.ncbi.nlm.nih.gov/pubmed/17027497" target="_blank">http://www.ncbi.nlm.nih.gov/pubmed/17027497</a><br>
<br><div class="gmail_quote">On Mon, Jul 18, 2011 at 2:50 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div>On 18/07/2011 3:08 PM, Kavyashree M wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear users,<br>
<br>
I am working on a protein which is a dimer (in the crystal structure), predicted according top PISA.<br>
and some of the homologous proteins are dimers (covalent /non-covalent) some are monomers.<br>
There has not been any literature regarding the fact that the functional unit is a dimer, ie the enzyme<br>
is not functional when the dimeric interface is disturbed due to mutations. Also the active sites are not<br>
shared among the dimeric partners. In this situation is it meningful to do a simulation of monomers alone<br>
and try to get some information.<br>
</blockquote>
<br></div></div>
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.<div>
<div>
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
In general is it necessary to simulate only the functional oligomers or monomer also can be done ?<br>
</blockquote>
<br></div></div>
Depends on the system, and depends what you wish to learn.<br>
<br>
Mark<br><font color="#888888">
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