Hello, welcome to my MEMBRANE page!
As part of my PhD-work I constructed and simulated a molecular dynamics model of a POPC double layer membrane. These results have been published in my thesis [HELL93] and a paper [HELL92] (you can find the bibliography in the README file). If you have the public domain viewer RasMol installed, you should download this gnuzipped tar file and view the membrane movies made by Eric Martz using my membrane files.
As a service to the community I also made available the coordinates of my membrane in different phases:
|crystal.pdb.Z||contains a very early coordinate set shortly|
after construction of the membrane
|gel.pdb.Z||is a taken after the gel phase simulation|
|fluid.pdb.Z||is taken at the end of the fluid phase simulation.|
The corresponding files with -H in their name contain all hydrogen atoms explicitly:
I also embedded Bacteriorhodopsin into this membrane:
|popc-br.pdb.Z||Br incorporated into membrane, starting structure.|
|popc-br-equi.pdb.Z||is the equilibrated structure of bR in a POPC membrane|
after about 80ps of molecular dynamics.
For analysis of simulation runs and preparation of .psf-files I use X-PLOR from Axel Brünger at Yale. For those who are not already X-PLOR wizards I include a compilation of a few X-PLOR input files for inspiration. If you create some input files which you are willing to share, please send them to me and I will include them here.
The simulations which led to the above mentioned files have been carried out in the Theoretical Biophysics group of Prof. Klaus Schulten, Beckman Institute, University of Illinois at Urbana-Champaign, U.S.A., and were then continued in the Theoretical Biophysics group of Prof. Paul Tavan, University of Munich, Munich, Germany. Now I am at the Leibniz-Rechenzentrum where I am still continuing my membrane work and, of course, my involvement with the latest high performance parallel computers.
All I ask for is that you reference my membrane paper and my PhD-thesis if you make use of the coordinates of the membrane, and also that you send to me preprints/reprints of papers that you might write which make use of said coordinate sets. The distribution of the data is governed by the GNU copyleft.
Also I would appreciate it if you could send me a short e-mail notice why you downloaded the coordinate sets, which sets, and what you want to do with it. Perhaps some useful collaborations could evolve this way.
On July 26th, 1999, I uploaded a movie (61MBytes! There is also a smaller version with only 18MBytes available.) of my recent simulation of cholesterol in a DPPC membrane. This is a collaboration with Prof. Thomas Bayerl,University of Würzburg, Germany, and Dr. Christine Gliss. We are currently preparing a publication of this project, so I can't say much here yet, but more files will appear in the near future.
Using RenderMan from Pixar on my NeXTSTEP workstation and the EGO interface ego2rib I made a few nice renderings of this membrane/cholesterol setup:
DPPC/cholesterol system at 20oC after 739ps simulation time. All molecules belonging to the boundary layer, i.e., those which are bound to reference positions, are displayed semitransparent. Cholesterol molecules are shown in green, lipid carbons in grey, phosphorus atoms are yellow, nitrogen is blue, oxygen red, and hydrogen white. To better view the interior of the membrane and of the head group region, a part of the membrane has been cut away.
...which view do you like better? Ideas for improving the picture? Email them to me!
Eric Martz made some nice visualizations of my lipids with RasMol.
Thank you very much and good luck with your simulations,
s-mail: Helmut Heller
Leibniz-Rechenzentrum der Bayerischen Akademie der Wissenschaften
Distributed Resources Group
P.S.: For the benefit of DOS/WINDOZE users I included a DOS binary, uncomp.exe, which allows to uncompress UNIX .Z files on a DOS computer.