[gmx-users] simulation of oligomers/monomers

Ragothaman Yennamalli ragothaman at gmail.com
Mon Jul 18 14:32:34 CEST 2011

Look at this paper where the simulation was done on a protein dimer:

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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