Fig. 2.

Pathway to generating synthetic motor proteins. a Modular assembly of protein motors using a tool kit of discrete protein modules each with well-characterized molecular functions. Here, three track-binding domains (red, green and blue semicircles) are linked to spacer domains (purple rods) and then assembled into a three-legged structure, such as the tumbleweed (Bromley et al. 2009). b The principle of action for the tumbleweed clocked walker Brownian ratchet (Bromley et al. 2009). The track comprises double-stranded DNA with three cognate sites (A, B and C) for each of the DNA-binding domains in the tumbleweed. Top panel: the red domain binds to its cognate DNA site (labelled B) in the presence of the activating ligand (yellow star). Second panel: the addition of the activating ligand (magenta circle) for the blue domain traps it bound to its cognate ligand once it encounters this DNA site (labelled C) via Brownian motion. Third panel: the removal of the red domain ligand (yellow star) allows it to detach from the DNA track. Bottom panel: the introduction of the cognate ligand for the green domain (red cross) traps it once it collides with its cognate site on DNA (labelled A). c Design principles for an autonomous walker. Left side: the track-binding domain (green) is controlled by enzymatic activity. This is shown as a cycle, where the two-domain enzyme opens a cleft so that a substrate (pink dumbbell) enters the active site and is cleaved (two yellow circles); these products are released when the site reopens. Some form of asymmetry is needed in the design (shown as the polarity in the track (red arrows)) and polarity of the track binder (blue triangle on the bottom right). Finally, allosteric control is represented by communication between two track-binding domains (yellow arrow and lightning). The right-hand side of the panel puts these principles into action. Top panel: one binder attaches to the track with substrate (pink dumbbell) bound. Second panel: the second binder attaches to the same track upstream from the first. As it does so, it sends a signal to the original bound domain, activating the enzymatic activity of this latter domain. Third panel: the originally bound domain completes its enzymatic cycle, detaches from the track and releases the products of catalysis. Bottom panel: the system is now in the same state as the top panel with only one module bound to the track; however, the walker has progressed by one site along the track