The role of long-range forces in porin channel conduction

The porin OmpF is a wide ion channel found in the outer membrane of Escherichia coli. It is a trimer with each subunit consisting of 16 /spl beta/-strands folded into a barrel structure. The barrel is constricted in the middle of the pore by a long polypeptide loop (L3). Charged residues surrounding the narrow constriction region generate a strong transverse electric field that plays a central role in ionic transport through the channel (Karshikoff et al., 1994). Brownian dynamics (BD) (Ermak, 1975; Turq et al., 1977) methods are attractive for modeling transport in porin because they represent an excellent compromise between computational accuracy and efficiency. Within the BD formalism, the channel is generally treated as a rigid structure and the water is treated implicitly, reducing the computational effort to ion trajectory tracking. Several BD simulations have been performed to investigate porin channels by modeling the macroscopic properties of ion conduction (Schirmer and Phale, 1999; Im and Roux, 2002; Im et al., 2000). However, the approaches used to model the electrostatic interactions in OmpF systems may be oversimplified. In particular, the use of periodic boundary conditions may not be adequate to realistically include effects due to the long-range forces within the system. In this work, a P/sup 3/M force field scheme (Hockney and Eastwood, 1988) is self-consistently coupled with a BD kernel to study the role of the long-range electrostatic forces in OmpF conduction. The P/sup 3/M method is well suited for investigating electrostatic effects in these systems because it can accurately account for the inhomogeneous, nonequilibrium behavior of the charge distribution.