Membrane proteins

Porin

Porins are large holes that sit in the outer membrane of certain classes of bacteria. They form a barrier against pathogens but allow small molecules such as ions, sugars, water and amino-acids to flow in and out of the cell. They are of interest for a number of reasons, but one of the main reasons for me to study them was that they are probably the simplest and best studied membrane protein that we know the structure of, in great detail.

Cool computer graphics of a porin protein with water
A porin monomer filled with water, taken from (D.P. Tieleman, H.J.C. Berendsen. 1998. A molecular dynamics study of the pores formed by E. coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylethanolamine bilayer, Biophys. J. 74, pp. 2786-2801. (see also New and Notable, same issue))
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This picture is based on a crystal structure, but we have also done simulations of the whole trimer in a lipid bilayer. This is quite a complicated system, with hundreds of lipids, ca. 13000 water molecules and several dozens of sodium ions.

Cool computer graphics of a porin protein in a bilayer
The OmpF trimer seen from "above". There are three holes running through the proteins, but they appear closed because they are at an angle with the normal. Picture taken from (D.P. Tieleman, H.J.C. Berendsen. 1998. A molecular dynamics study of the pores formed by E. coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylethanolamine bilayer, Biophys. J. 74, pp. 2786-2801. (see also New and Notable, same issue))

Porin occurs as a trimer, a protein made up of three identical units. These units are colored differently in the picture. The green spheres are the headgroups of the lipids, the thin green wires their tails. Also highlighted are the aromatic amino acids in the protein, which form a clear band marking the boundaries of the protein inside the lipid bilayer. We analysed their behaviour in more detail, described in ref. (D.P. Tieleman, L. Forrest, M.S.P. Sansom, H.J.C. Berendsen. 1998. Lipid properties and the orientation of aromatic residues in OmpF, Influenza M2 and Alamethicin systems: Molecular dynamics simulations, Biochemistry 37, pp. 17554-17561)

Cool computer graphics of a porin trimer in a lipid bilayer
The same trimer, seen from the side.

Courtesy of Biocomputing dept., University of Calgary