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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