Stress-Activated Sliding Motion: A Coupled-Potential Model

Abstract

In a notable study by Julicher & Bruinsma (BPJ 74, 1998), a model was presented describing the motion of an RNAP molecule during an elongation cycle. First, stepping motion of a catalytic (C)-site takes place. This generates stress in the molecule between this (C)-site and a front (F)-site. This stress activates forward sliding of the (F)-site by lowering the activation barrier hindering its motion.Here we look at this RNAP model in terms of a coupled-potential paradigm, taken from an inchworm-like model of a polymer chain. This model describes how stress produced by forward motion of a (C)-like site in the polymer leads to activated sliding of an (F)-like site (Joseph, J Polymer Sci 16, 1978). The (F)-like site has two positions - (1) and (2) - and so possesses a double-well potential. This site is coupled in series to a linear spring - with a single-well harmonic potential. A (C)-like site occupies the spring free end.We find that coupling (adding) these two potentials yields a net potential with the (F)-like site occupying position (1). Also, there is a large activation barrier hindering movement to position (2). However, when the (C)-like site at the spring free end is pulled forward, the stretching of the spring causes the equilibrium position of the harmonic potential minimum to be shifted forward. Coupling of this shifted potential reduces the net potential barrier, and this reduction activates forward sliding motion of the (F)-like site.We conclude that this type of coupled-potential inchworm model yields insight into how stress can activate sliding motion during the RNAP elongation cycle.