Interactions of peptides with a protein pore

The partitioning of polypeptides into nanoscale transmembrane pores is of fundamental importance in biology. Examples include protein translocation in the endoplasmic reticulum and the passage of proteins through the nuclear pore complex. Here we examine the exchange of cationic alpha-helical peptides between the bulk aqueous phase and the transmembrane beta-barrel of the alpha-hemolysin (alpha HL) protein pore at the single-molecule level. The experimental kinetic data suggest a two-barrier, single-well free energy pro. le for peptide transit through the alpha HL pore. This free energy pro. le is strongly voltage-and peptide-length-dependent. We used the Woodhull-Eyring formalism to rationalize the values measured for the association and dissociation rate constants k(on) and k(off), and to separate k(off) into individual rate constants for exit through each of the openings of the protein pore. The rate constants k(on), k(off)(cis), and k(off)(trans) decreased with the length of the peptide. At high transmembrane potentials, the alanine-based peptides, which include bulky lysine side chains, bind more strongly (formation constants K-f similar to tens of M-1) than highly flexible polyethylene glycols (K-f similar to M-1) to the lumen of the aHL protein pore. In contrast, at zero transmembrane potential, the peptides bind weakly to the lumen of the pore, and the affinity decreases with the peptide length, similar to the case of the polyethylene glycols. The binding is enhanced at increased transmembrane potentials, because the free energy contribution Delta G = -zeta delta FV/ RT predominates with the peptides. We suggest that the alpha HL protein may serve as a robust and versatile model for examining the interactions between positively charged signal peptides and a beta-barrel pore.