Dear All,
There is a protein with 3-D crystal structure known (about
800 amino acids). It contains 2 domains. In one domain, it has a key Lys
residue. In the other domain, it contains a key Asp residue, and it is also
know that the direct interaction between this Lys and this Asp plays a key role
for the interacting of the 2 domains and keeps the compactness of the whole molecule.
Further research demonstrates mutation of either this Lys residue or this Asp
residue would make the protein in a open-conformation demonstrated by FRET and
SAXS.
However if I want to do the molecular dynamics simulation of
the protein based on the protein model
got by homology modelling with either this Lys or this Asp mutated to Ala, I
seems it is rather difficult or impossible to get the mutated protein with the
open conformation.
Can you make some comment on why the open conformation
cannot be got by molecular dynamics simulation, or do you think whether the
open conformation could be got by molecular dynamics simulation?
Cheers,
Acoot
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Received on Wed Jun 27 2012 - 17:00:03 PDT
