[gmx-users] simulation of oligomers/monomers

[Kavyashree M]

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
> 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>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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