A MOLECULAR-DYNAMICS STUDY OF THE PORES FORMED BY ESCHERICHIA-COLI OMPF PORIN IN A FULLY HYDRATED PALMITOYLOLEOYLPHOSPHATIDYLCHOLINE BILAYER

In this paper we study the properties of pores formed by OmpF porin fr om Escherichia coil, based on a molecular dynamics simulation of the O mpF trimer, 318 palmitoyl-oleoyl-phosphatidylethanolamine lipids, 27 N a+ ions, and 12,992 water molecules. After equilibration and a nanosec ond production run, the OmpF trimer exhibits a C-alpha root mean squar e deviation from the crystal structure of 0.23 nm and a stable seconda ry structure. No evidence is found for large-scale motions of the L3 l oop. We investigate the pore dimensions, conductance, and the properti es of water inside the pore. This water forms a complicated pattern, e ven when averaged over 1 ns of simulation time. Around the pore constr iction zone the water dipoles are highly structured in the plane of th e membrane, oriented by the strong transversal electric field. In addi tion, there is a net orientation along the pore axis pointing from the extracellular to the intracellular side of the bilayer. The diffusion coefficients of water inside the pore are greatly reduced compared to bulk. We compare our results to results from model pores (Breed et at ., 1996. Biophys. J. 70:1643-1661; Sansom et al. 1997. Biophys. J. 73: 2404-2415) and discuss implications for further theoretical work.