The question really is what is the timescale of the opening. Domain motions
tend to be relatively slow compared to md- perhaps micro or milliseconds.
You most likely would need some enhanced sampling methods for such slow
motions. Another approach may be to look at a different method, perhaps
using a course grain rather than atomic model.
On Jun 27, 2012 7:42 PM, "Acoot Brett" <acootbrett.yahoo.com> wrote:
> 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
