A Database of Outer Membrane Protein Simulations, Dr Syma Khalid & Prof Mark S.P. Sansom

The outer membrane proteins (OMPs) of Gram-negative bacteria play a key role in the function and structural integrity of the outer membrane. The OMPs cover a number of different functions, including membrane pores, passive and active transporters, recognition proteins, and membrane-bound enzymes. Currently ~20 high-resolution structures of OMPs are known, revealing them all to be based on a transmembrane (TM) beta-barrel architecture, with sizes ranging from 8 to 22 strands in the barrel. From a biomedical perspective, OMPs are of some interest as potential targets for novel antimicrobial drugs and vaccines.

To aid the development of novel antibiotics targeted against these proteins, we must first understand and characterise their dynamics. Thus, we have generated a database of OMP molecular dynamics simulations. The database provides simulation data for a wide range of OMPs. One of the advantages of MD simulations is the relative ease with which protein-environment interactions can be explored. Such data is available for each simultion in the databse, for comparative analyses. The following protocols have been used to populate the databse:

» Embed protein in bilayer/water with neutralising counterions
» Carry out minimum of 10 ns of atomistic MD using GROMACS
» Perform analyses to (RMSD, RMSF, lipid-protein interactions)
» Submit to database: simulation properties/snapshots, final system coordinates, and analysis of lipid-protein interactions

This work has been supported by:

» Dr Kathryn Scott, Dr Peter J Bond and Anthony Ivetac (analysis of lipid-protein interaction, database design)



Dr Syma Khalid, Structural Bioinformatics & Computational Biochemistry, University of Oxford.

Now RCUK Fellow, University of Southampton. For more information email S.Khalid@soton.ac.uk