Diane,
how big is the transmembrane part of your protein?
Diane Fournier wrote:
Hi gmx-users
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. >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 ?
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).
Any help will be apreciated.
Diane
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