Thanks David. I think that we're saying the same thing, but there is
indeed a 'correct' denatured state at a given temperature and pressure
and protein concentration and salt concentration, etc. It was this to
which I was referring.
Chris.
On 2010-10-18 06.56, chris.neale at utoronto.ca wrote:
Generally, forcefields are not parameterized for temperatures other than
298K, so simulations are not expected to reproduce the expected
properties (like boiling water and the correct temperature denaturation
of proteins).
There's almost certainly other issues here (including the fact that I'm
entirely sure that you can get a lot more than 24 ns of simulation on a
54 aa protein; and 26 atom of pressure seems pretty arbitrary) but it
will come down to this eventually.
Just because you found a paper in which they get a denatured state does
not imply that they got the correct denatured state.
There is no correct denatured state. There are infinitely many. Check
out recent work on NMR of "unfolded" proteins.
Chris.
-- original message --
Hi All,
I met a problem when I try to unfold a protein using Gromacs, It seemed
the protein cannot be totally unfolded!
The simulated system has one Engrailed Homeodomain (En) protein (a three
helix bundle protein with 54 residues, 629 atoms), total 4848 spce
waters, and 7 Cl- used to neutralize the system in a 5.752(nm)^3 water
BOX. I use the NTP ensemble with T=498K and P=26atm. The system has 1nm
thick water in each side of the En protein, and the density of the
system has been adjusted to0.829 g/cm3.
The simulation lasted 24ns. The helixes disappeared at about 4ns. And
after that some beta sheet formed in the N terminal of the protein.
However, the protein kept in a compact state during the 24ns simulation.
The radius of gyration of the protein fluctuated around 1.1nm during the
simulation.
I've also noticed similar simulation done by others. For example, David
Becka and Valerie Daggett reviewed their En protein unfolding in paper
"Methods for molecular dynamics simulations of protein folding/unfolding
in solution. Methods 34 (2004) 112¨C120". The simulations were performed
with ENCAD and ilmm, and used an 0.8nm cutoff range. And the ensemble
they used is NVE as I know. A stretched unfolding state occurred at
about 5ns in their 60ns simulation in 498K, with little helix structure.
I was wondering whether the difference is caused by using different MD
software and force field, or by some wrong parameters in my .mdp file.
I've also conducted another 18ns simulation, and the result is almost
the same. I list he mdp file below. Any comment is appreciated!
--
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