Tutorial-l Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Aug 11 2008 - 16:28:10 CDT

I'm not so familiar with gramicidin, but let me point out that the
choice of lipids is often made on the basis of ease and familiarity
as much as absolute "correctness". In VMD, since membranes for POPE
and POPC are provided, they are often most convenient. Other
researchers may have more experience with DMPC. One should
definitely try to consider the native environment of the protein, but
depending on what one hopes to learn from the simulations, the choice
of lipid may not (but not always!) be that important.

I hope this helps more than it confuses!

On Aug 11, 2008, at 11:18 AM, Hyundeok Song wrote:

> Hi all
>
> I have a question abut a membrane in Gramicidin channel.
> I studied below site.
>
> Building Gramicidin A
> http://www.ks.uiuc.edu/Research/namd/tutorial/NCSA2002/hands-on/
>
> Tutorial used POPE membrane.
> palmitoyl-oleoyl-phosphatidylethanolamine (POPE)
>
> Also, I saw many papers used DMPC membrane instead of POPE in
> Gramicidin. dimyristoyl-phosphatidylcholine(DMPC)
>
> I drawed the chemical structure of DMPC and POPE and searched the
> difference between DMPC and POPE in Gramicidin. But, I still don't
> know why some use POPE and others use DMPC in Gramicidin. What is
> the difference between them in Gramicidin?
> thanks.
>
> Hyun.
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