[gmx-users] simulation of oligomers/monomers

Mark Abraham Mark.Abraham at anu.edu.au
Mon Jul 18 09:50:23 CEST 2011

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.


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