Computer simulation of polypeptide translocation through a nanopore

Abstract

A simplified model of polypeptide chains was designed and studied by means of computer simulations. Chains were represented by a sequence of united atoms located at the positions of the alpha-carbons. A further assumption was the lattice approximation for the chains. We used a (310) lattice, which was found useful for studying properties of proteins. The force field used consisted of a long-range contact potential between amino-acid residues and a local preference for forming alpha-helical states. The chain consisted of two kinds of residues: hydrophilic (P) and hydrophobic (H) ones forming model helical septets--HHPPHPP--in a sequence. The chains were placed near an impenetrable surface with a square hole in it. The size of the hole was comparable or smaller than the size of a chain. The properties of these model chains were determined using the Monte-Carlo simulation method. During the simulations, translocation of the chain through the hole in the wall was observed. The influence of the chain length, the temperature differences on both sides of the wall and the force field on the chain properties were investigated. It was shown that the translocation time scales as N(2.2) and it was found that the presence of the local helical potential significantly slows down the process of translocation. [Figure: see text]. The snapshots of typical chain's conformation obtained during the simulation for chain consisted of N = 60. The values of the local potential epsilon(loc) = -8.