On 18/10/10 13:12, Chen wrote:
At 2010-10-18 16:38:30??"David van der Spoel"<[email protected]> wrote:
On 2010-10-18 06.56, [email protected] 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.
I thought about the unfolding state space is huge. I just wonder
whether the relative low radius of gyration value space sampled by us is caused
by some error setting in MD parameters. If no one here finds there's problem in
my MD parameters, then I can keep going. Thanks!
In theory, you should be able to calculate the expected gyration radius
of a purely non-interacting random chain (which one can take as the
limit of an unfolded protein). given the distance between monomeric
units (i.e. C-alpha for example here). It is a three-dimensional random
walk.
http://en.wikipedia.org/wiki/Radius_of_gyration#Molecular_applications
Doing the calculation for the equation of the three-dimensional random
walk of your 54 aa protein, with N=54 and a=0.35 nm, it turns out that
the expected gyration radius is:
>>> (np.sqrt(54) * 0.35) * (1/np.sqrt(6))
1.0500000000000003 nm
So, yes, your average protein gyration radius is consistent with the
protein being a random coil -that is, unfolded.
In truth your random coil ball should be a bit larger because in the
calculation we ignore the chain self-avoidance, but on the other hand we
have that a protein chain is not completely non-self-interacting, for
obvious reasons. Therefore it seems you can conclude that your protein
is reasonably close to being unfolded.
Hope it helps,
Massimo
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