  Simulations can help unravel the complicated ways in which molecular
structure determines function. Here, we use molecular simulations to show how
slight alterations of a molecular motor's structure can cause the motor's
typical dynamical behavior to reverse directions. Inspired by autonomous
synthetic catenane motors, we study the molecular dynamics of a minimal motor
model, consisting of a shuttling ring that moves along a track containing
interspersed binding sites and catalytic sites. The binding sites attract the
shuttling ring while the catalytic sites speed up a reaction between molecular
species, which can be thought of as fuel and waste. When that fuel and waste
are held in a nonequilibrium steady-state concentration, the free energy from
the reaction drives directed motion of the shuttling ring along the track.
Using this model and nonequilibrium molecular dynamics, we show that the
shuttling ring's direction can be reversed by simply adjusting the spacing
between binding and catalytic sites on the track. We present a steric mechanism
behind the current reversal, supported by kinetic measurements from the
simulations. These results demonstrate how molecular simulation can guide
future development of artificial molecular motors.
