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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