Simulation of ion conduction in the ompF porin channel using BioMOCA

We report on recent BioMOCA simulations of K/sup +/ and Cl/sup $/transport through the ompF porin channel. OmpF porin is a highly charged (net charge on the entire porin molecule is /spl sim/-30|e|) trimeric protein channel found in the outer membrane of the E. coli bacterium. It has an unusually stable arrangement that maintains its structural integrity well beyond the normal physiological range of salt concentrations, temperatures, and applied voltages. High-resolution molecular structures for ompF and several of its mutants are well-known from X-ray crystallography. About halfway along each pore the channel has a narrow and highly charged constriction region. Mutation studies and DD simulations both indicate that the charge distribution in the constriction region plays an important role in the conductance properties of the channel. We use the BioMOCA simulator to further this line of enquiry using a detailed map for the permanent charge distribution to investigate the conduction properties of ompF.