[gmx-users] membrane protein simulation

Arneh Babakhani ababakha at mccammon.ucsd.edu
Fri Oct 27 02:05:30 CEST 2006


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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