Understanding the Operational Principles of Molecular Motors: Building a Protease Lawnmower

Biological motors are involved in various cellular processes such as intracellular transport, DNA replication and cell motility. These examples involve multi-subunit proteins which transduce chemical energy into mechanical work. To better understand the underlying principles by which biological motors operate, it is instructive to study simpler motors which use Brownian diffusion coupled with asymmetry in the system to bias the direction of motion. Here, we describe a concept for a novel protein-based synthetic motor built on a fluorescent quantum dot hub to which are attached proteases via flexible linker molecules. The corresponding protease substrate is presented as a one-dimensional “lawn” of peptides tethered to a DNA track, suspended in a DNA “curtain”. The protease motor diffuses to the substrate track where productive binding between protease and substrate facilitates proteolytic cleavage of the substrate. Once cleaved, the decreased binding affinity between the protease and resulting product allows the motor to diffuse along the track and form new interactions with uncleaved substrate molecules. The protease motor thus acts as a “lawnmower” in that it “mows” the substrate lawn inducing an asymmetric track. The resulting asymmetry biases motor diffusion towards the uncleaved substrate portion of the track (Figure). By developing a motor which uses Brownian motion and track asymmetry to bias the direction of motion, we gain insight into the underlying principles by which such motors operate.