[gmx-users] membrane protein simulation
javaheri.gromacs at gmail.com
Fri Apr 24 16:36:48 CEST 2015
Yes, it would be very helpful. thanks for your help.
On Thu, Apr 23, 2015 at 9:40 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> Hi Mostafa,
> We have a complete simulation system of bacteriorhodopsin in the purple
> membrane, which you can use as basis for your simulations if you want.
> On Apr 22, 2015 10:08 PM, "Mostafa Javaheri" <javaheri.gromacs at gmail.com>
> > Dear Justin
> > I am going to simulate a homo trimer trans-membrane protein; Base on the
> > crystallographic structures there is 7 phosphatidyl glycerol phosphate
> > (PGP) per each monomer and also 3 glycolipid molecules (S-TGA-1, or
> 3-HSO 3
> > -Galpβ1-6ManpR1-2GlcpR-1-archeol) located inside the trimer on the
> > extracellular side of membrane. In the membrane protein tutorial of
> > 1,2-dipalmitoyl-*sn*-glycero-3-phosphatidylcholine (DPPC) is introduced
> > the standard lipids, so should I treat PGPs and glycolipids as ligands
> > going through protein ligand complex tutorial?
> > Or treat glycolipids as ligands, continue the membrane protein tutorial
> > use DPPCs instead of PGPs?
> > Is it OK if I replace PGP with DPPC from the standpoint of simulation?
> > Sincerely
> > --
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