I am trying to set up an ED experiment with the low resolution structure of a
membrane protein in the hope of generating NMR-like structures.
By ED do you mean essential dynamics? I haven't done that, but it
seems to me that the system setup should be identical to regular MD.
From what I have read until now, I know that I should either
restrain the transmembrane domain of the enzyme (or simulate without
it), or do the simulation within a bilayer membrane. The choice is
somewhat complicated by the
fact that the active site of the protein (which is of interest to
me) is quite
close to the transmembrane domain. So I think it would be safer to
simulate with the membrane, or is there a simpler solution ?
I would recommend a full membrane. If you don't have time to
explicitly simulate the membrane, you can put harmonic restraints on
the heavy atoms of the side chains of the aromatic residues that would
usually interact with the lipid headgroups and put a water droplet
over the top of the active site. As for how to determine the position
and orientation of your protien in the membrane, see for example 1)
Kandasamy and Larson Biophys. J. Vol 90 April 2006 2326-43; 2) Lomize
et al, Protein Sci. 2006 15:1318-33.
Also, I am quite new to membrane protein simulation and I would like
to know how the bilayer type is chosen ? (My protein is a eukaryotic
enzyme naturally bound to the endoplasmic reticulum).
I determine my bilayer type based on 4 questions, in approximately the
order shown:
A) What would the in vivo situation be?
B) What is the hydrophobic length of the protein?
C) What parameters are available?
D) What starting coordinates are available?
For the Rat liver ER, you're looking at 20% PE, 14% PI/PS, 53% PC, 4%
sphingomyelin, 10% unknown; and Carbon tails between 10-20% populatino
for each of C16:0 C18:0 C18:1 C18:2 C20:4 C22:6 over PC and PE
(Davison & Wills, Biochem. J. 1974, 140, 461-8) and a hydrophobic
length of about 28A (Lomize et al, Protein Sci. 2006 15:1318-33).
Since simulated membranes tend to be too thick according to the
current deconvolution of Xray scattering data, and given the specifics
listed above, I would personally use DPPC as an ER mimetic. You can
get starting coords and parameters for this from Dr. Tieleman's
website: http://moose.bio.ucalgary.ca/
Chris
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