7 research outputs found
Chaperone driven polymer translocation through Nanopore: spatial distribution and binding energy
Chaperones are binding proteins which work as a driving force to bias the
biopolymer translocation by binding to it near the pore and preventing its
backsliding. Chaperones may have different spatial distribution. Recently we
show the importance of their spatial distribution in translocation and how it
effects on sequence dependency of the translocation time. Here we focus on
homopolymers and exponential distribution. As a result of the exponential
distribution of chaperones, energy dependency of the translocation time will
changed and one see a minimum in translocation time versus effective energy
curve. The same trend can be seen in scaling exponent of time versus polymer
length, (). Interestingly in some special cases e.g.
chaperones of size and with exponential distribution rate of
, the minimum reaches even to amount of less than (). We
explain the possibility of this rare result and base on a theoretical
discussion we show that by taking into account the velocity dependency of the
translocation on polymer length, one could truly predict the amount of this
minimum
Pore shapes effects on polymer translocation
We translocated polymers through pores of different shapes and interaction patterns in three dimensions by Langevin molecular dynamics. There were four simple cylindrical pores of the same length but with different diameters. The results showed that even though decreasing the pore diameter would always decrease the translocation velocity, it was strongly dependent on the shape of the increased pore diameter. Although increasing the pore diameter made the translocation faster in simple cylindrical pores, it was complicated in different pore shapes, e.g. increasing the diameter in the middle decreased the translocation velocity. Investigating polymer shapes through the translocation process and comparing the shapes by the cumulative waiting time for different pore structures reveals the non-equilibrium properties of translocation. Moreover, polymer shape parameters such as gyration radius, polymer center of mass, and average aspect ratio help us to distinguish different pore shapes and/or different polymers