Polymer translocation through a nanopore in the presence of chaperones: A three dimensional MD simulation study

Abstract

The chaperone assisted polymer translocation through a nanopore is studied using Langevin dynamics simulations in three dimensions. We investigate the effects of the polymer persistence length, the binding energy between the polymer and the chaperones and the chaperone concentration on the translocation. The results show that the probability of translocation increases and the mean translocation time decreases by increasing the chaperone concentration and the binding energy for all persistence lengths. The translocation probability also increases as the polymer persistence length increases, but the translocation process of stiffer polymers takes longer time compared with the flexible ones. Also, it is found that the strength of chaperone binding differently affects the translocation probabilities of flexible and stiff polymers. Dynamics of the translocation is described using the waiting time distribution of monomers for different persistence lengths. The obtained results can be exploited to understand some biological chaperone assisted translocations in which different conditions such as a variation in the value of temperature, pH or salt concentration change the chain flexibility.