Notes

Final Snapshot
Snapshots are shown of the final frame in simulation. Water, ion and lipid tail particles are excluded for clarity. The backbone trace of the protein is shown in blue.
The particle colours are:
Phosphate in lipid/detergent headgroups - red
Glycerol linker in lipid - yellow
Choline in PC headgroups - blue
Ethanolamine in PE headgroups - navy
Glycerol in PG headgroups - cyan
The coordinates of the protein and lipid in the final frame are available for download

Simulation Properties
The C-alpha RMSD relative to the starting structure is shown for the last 100 ns of the simulation. Data are shown for all residues and for residues that are in regular secondary structure in the starting pdb. The secondary structural assignments were made using DSSP.
The C-alpha RMSF is shown for the last 100 ns of the simulation
The RMSD and RMSF data files can be downloaded in xvg format.

Bilayer Analysis
The protein is aligned in the x-y plane and the properties of the bilayer analysed over the last 100 ns of the simulation. The bilayer is divided into 5 x 5 Angstrom bins and the mean position of phosphate particles relative to the bilayer centre of mass is calculated for each bin. The data for the upper and lower leaflet are displayed as contour plots on the website, along with a picture showing the phosphate particles from the first and last frames superposed with the protein as a ribbon diagram. The ribbon is coloured from blue at the N-terminus to red at the C-terminus. The data files are downloadable in matrix format with the centre coordinates of the bins as column and row headings. Rows represent the x-dimension, columns the y-dimension. A pdb file with the protein oriented as for the bilayer analysis is also available for download.

Contact Analysis
The surface of the protein is shown coloured according to the fraction of the last 100 ns of simulation each residue makes contact with a lipid/detergent headgroup. Particles are considered to make a contact when they are separated by a distance of no more than 6 Angstrom. Headgroups include the particles representing the glycerol linker. Residues are coloured blue-green-red from 0-50-100% of time contact is made between the protein and lipid headgroup.
A table of simulation properities is available for download.


Structural Bioinformatics & Computational Biochemistry, University of Oxford.