Effect of channel–protein interaction on translocation of a protein-like chain through a finite channel

We study the translocation of a protein-like chain through a finite cylindrical channel using the pruned-enriched Rosenbluth method (PERM) and the modified orientation-dependent monomer-monomer interaction (ODI) model. Attractive channels (ε_cp=-2.0, -1.0, -0.5), repulsive channels (ε_cp=0.5, 1.0, 2.0), and a neutral channel (ε_cp =0) are discussed. The results of the chain dimension and the energy show that Z₀=1.0 is an important case to distinguish the types of the channels. For the strong attractive channel, more contacts form during the process of translocation. It is also found that an external force is needed to drive the chain outside of the channel with the strong attraction. While for the neutral, the repulsive, and the weak attractive channels, the translocation is spontaneous.