[gmx-users] simulation of oligomers/monomers

[Kavyashree M]

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.

Thank you
With Regards
M. Kavyashree

On Mon, Jul 18, 2011 at 6:22 PM, Ragothaman Yennamalli <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> 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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