Knotted Proteins under Tension

Abstract

We study the behavior of two knotted proteins under stretching by a constant force within a coarse-grained structure-based model. One protein, with the structure code 1J85, has a knot that is deep and another, 2ETL, has a knot that is shallow. We demonstrate that tightening of the deep knot may take place before the ultimate end-to-end distance is achieved. However, as with proteins without knots, we observe the existence of a crossover between the low- and high-force regimes of the dependence of the mean unfolding time (as defined through properties of the end-to-end distance) on the applied force. We find little correlation between the unfolding time and the final placement of the tightened knot. We also consider the novel mechanical protection strategy in the single-molecule force spectroscopy of host-guest fusion proteins. We find that it should be useful in studies of guest proteins with knots in the constant-speed mode. However, at constant force, its usefulness is limited if the mechanostability of the host is larger than that of the guest molecule.