[gmx-users] Which Lipid Bilayer for GPCR Simulations

[Xavier Periole]

Akshay Patny wrote:

> Dear All
>
> I am trying to simulate a class A GPCR model in presence of a lipid 
> bilayer. For that, I am trying to prepare my initial system consisting 
> of Protein + Pre-hydrated Lipid bilayer + Counter-ions.
>
> Since I would be using GROMACS 3.3.1, I am planning to use the 
> pre-hydrated lipid bilayer available through Prof. Peter Tieleman’s 
> website: 
> http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies
>
> I am curious what kind of bilayer should I use out of DPPC, DMPC, POPC 
> available? Does some lipid bilayer provide certain advantages over 
> others for simulation of GPCRs?
>
> I appreciate any suggestions regarding the same.
>
DPPC, DMPC and POPC are different bilayers but in what
conserns GPCR simulations you can use DPPC and POPC
without problem. DMPC would be a bit too short !!

Note that you should consider looking up in the literature and
see wehter there is any info conserning the type of lipid
embedding your GPCR !!

XAvier

-- 
----------------------------------
 Xavier Periole - Ph.D.

 Dept. of Biophysical Chemistry / MD Group   
 Univ. of Groningen
 Nijenborgh 4
 9747 AG Groningen
 The Netherlands
 
 Tel: +31-503634329
 Fax: +31-503634398
 email: x.periole at rug.nl
 web-page: http://md.chem.rug.nl/~periole
----------------------------------