[gmx-users] simulation of oligomers/monomers

[Ragothaman Yennamalli]

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> 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> 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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>>
>>
>>
>>
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