[gmx-users] PDBs for mixed lipid bilayer/membrane

[Justin A. Lemkul]

Volker Wirth wrote:
> Hello list,
>
> first of all, my question in short: Does anyone know a source for
> PDB-files of mixed membranes (such as DMPC/DMPS or so)?
>
> And here more info:
> Within my diploma thesis I want to simulate a protein (ca. 20
> residues) interacting with a lipid bilayer (not a transmembrane
> protein). Besides the probably normal challanges in starting up with
> GROMACS, I need your help with a special problem:
>
> As a source for one-component bilayer pdb's (containing DOPC, SDPC,
> DMPC, DPPC and POPC) I found
>    http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies
>    http://persweb.wabash.edu/facstaff/fellers/
>    http://www.lrz-muenchen.de/~heller/membrane/membrane.html
>    http://www.apmaths.uwo.ca/~mkarttu//downloads.shtml
> and maybe one could do fancy (protein insertion-) things using the
> membrane builder of
>    http://www.charmm-gui.org/
> but to get closer to reality (and to be able to compare simulation
> results with experiments) one might prefer a mix of different lipids
> (e.g. DMPC, DMPS, DMPG, at least anything like **PC, **PS, **PG or
> anything like that). Here is my problem, because I can't find any
> sites that offer such pdb files.
>   

Right, I don't know of any either!  One place to check would be Mikko 
Karttunen's site:

http://www.apmaths.uwo.ca/~mkarttu/downloads.shtml

The site advertises a raft configuration, but it is not online.  Perhaps 
contacting the corresponding author of the related paper might be useful.

The only report of a simple binary mixture of lipids is the following 
reference:

Leekumjorn, S. and Sum, A.K. (2006) Biophys. J. 90: 3951-3965.

They might also make their DPPC/DPPE configuration available.

As far as anything more complex, I haven't seen it, although that 
doesn't mean it's not out there.  I (and probably others on this list) 
would also be interested in hearing back if you come across any other 
mixtures.

-Justin

> Is there someone out there who knows more or even has experience in
> simulations like that? A similar example would help me with this, too.
>
> Thanks a lot in advance, I hope I can share my knowledge some other time, too
>
> Volker
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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