Polyelectrolyte and unfolded protein pore entrance depends on the pore geometry

We determined the ability of Maltose Binding Protein and the polyelectrolyte dextran sulfate to enter into and interact with channels formed by Staphylococcus aureus alpha-hemolysin. The entry of either macromolecule in the channel pore causes transient, but well-defined decreases in the single-channel ionic current. The protein and polyelectrolyte were more likely to enter the pore mouth at the channel's cap domain than at the stem side. When the cap domain was denatured in the presence of 4 M urea, the probability that either the denatured protein or polyelectrolyte entered the pore from the cap-domain side decreased. For channels in their native conformation, the polyelectrolyte-induced current blockades were characterized by two mean residence times that were independent of the side of entry. For channels with a denaturated cap domain, the mean polyelectrolyte residence times for relatively long-lived blockades decreased, while that for short-lived blockades were unchanged. For denatured protein, we also observed 2 characteristic residence times that were relatively fast. Only the relatively short-lived blockades were observed with native channels. When the alpha-hemolysin monomers in aqueous solution were incubated in 4 M urea before channel formation, the two characteristic residence times were greater than those for pre-formed pores that were subsequently perturbed by urea. These times might correspond to the interactions between the unfolded protein and the partially unfolded channel.