Computer simulations of protein translocation

Abstract

Many biological processes, e.g. protein degradation by ATP dependent proteases and mitochondrial protein import, involve protein translocation through nanometer-sized pores. In this paper, we report on computer simulations of two models of protein translocation. In the first model, a protein domain is pulled mechanically through a narrow neutral pore. We compare the free energy cost of squeezing an initially folded protein into the pore with that for a random-coil-like homopolymer and show that the former case involves several partially folded intermediates. The second model involves electrophoretically driven translocation of a β-hairpin forming peptide across the α-hemolysin protein pore. The distribution of the time the peptide spends inside the pore is exponential at low forces, suggesting a single rate limiting barrier crossing step for the translocation process, while at higher forces this distribution tends to be a bell shaped curve. The dependence of the average translocation time 〈t〉 on the applied force f is well described by the exponential relationship: ln 〈t〉 = af + b at low forces, while at high forces the inverse translocation time is a linear function of the force, 〈t〉-1 = Af - B. © 2006 WILEY-VCH Verlag GmbH & Co. KGaA.