The Effect of a Rearward Conservative Force and a Dragged Load on a Synthetic Nano-Motor Inspired by Kinesin

The object of our research is to design and measure the performance of synthetic protein constructs that mimic biological nano-motors. In a previous article we presented a persistent symmetric nano-walker design named Synthetic Kinesin Inspired Protein (SKIP). Here, we extend this design to an asymmetric, directional and processive nano-motor construct called SKIP-4R and describe and contrast the effect of a rearward conservative force and a dragged load on the motor properties of the system. Unlike kinesin, SKIP-4R's motor movement is controlled by clocked ligand pulses that activate the binding and unbinding of four different repressor proteins (RA, RB, RC, RD) to an asymmetric DNA track. To simplify future synthesis and assembly, we use a redesigned structure of SKIP (Roberta Davies, private communication) in terms of a composite of two short and two longer coiled coils (rods), each linking a different repressor RA, RB, RC or RD flexibly to a central hub. The motion of SKIP-4R was simulated using Langevin dynamics in the overdamped limit both for a rearward conservative force and a dragged load and we found that the motor both stalled and then reversed in the former case, whereas it simply stalled for large drag coefficients in the latter case. We also show that SKIP-4R can be reduced to a simpler motor (SKIP-3R) when one short rod is removed. The effects of both a rearward conservative force and a dragged load on the motion of SKIP-3R and SKIP-4R are described in detail.