Membrane Position Dependency of the pK a and Conductivity of the Protein Ion Channel

The dependency of current–voltage characteristics of the α-hemolysin channel on the channel position within the membrane was studied using Poisson–Nernst–Planck theory of ion conductivity with soft repulsion between mobile ions and protein atoms (SP-PNP). The presence of the membrane environment also influences the protonation state of the residues at the boundary of the water–lipid interface. In this work, we predict that Asp and Lys residues at the protein rim change their protonation state upon penetration to the lipid environment. Free energies of protein insertion in the membrane for different penetration depths were estimated using the Poisson–Boltzmann/solvent-accessible surface area (PB/SASA) model. The results show that rectification and reversal potentials are very sensitive to the relative position of channel in the membrane, which in turn contributes to alternative protonation states of lipid-penetrating ionizable groups. The prediction of channel position based on the matching of calculated rectification with experimentally determined rectification is in good agreement with recent neutron reflection experiments. Based on the results, we conclude that α-hemolysin membrane position is determined by a combination of factors and not only by the pattern of the surface hydrophobicity as is typically assumed.