Motor properties from persistence: a linear molecular walker lacking spatial and temporal asymmetry

Abstract

The stepping direction of linear molecular motors is usually defined by a spatial asymmetry of the motor, its track, or both. Here we present a model for a molecular walker that undergoes biased directional motion along a symmetric track in the presence of a temporally symmetric chemical cycle. Instead of using asymmetry, directionality is achieved by persistence. At small load force the walker can take on average thousands of steps in a given direction until it stochastically reverses direction. We discuss a specific experimental implementation of a synthetic motor based on this design and find, using Langevin and Monte Carlo simulations, that a realistic walker can work against load forces on the order of picoNewtons with an efficiency of ∼18%, comparable to that of kinesin. In principle, the walker can be turned into a permanent motor by externally monitoring the walker's momentary direction of motion, and using feedback to adjust the direction of a load force. We calculate the thermodynamic cost of using feedback to enhance motor performance in terms of the Shannon entropy, and find that it reduces the efficiency of a realistic motor only marginally. We discuss the implications for natural protein motor performance in the context of the strong performance of this design based only on a thermal ratchet.

The bar-hinge motor: a synthetic protein design exploiting conformational switching to achieve directional motility

“…We investigated the behaviour of the BHM by simulating its motion using a coarse-grained minimal model in conjunction with three-dimensional overdamped Langevin dynamics [5,6]. Figure 3(d) shows the coarsegrained model used in our simulations.…”

“…We have chosen a bipedal design for the BHM to emulate the dynamics of bipedal biological nanomotors such as kinesins and myosins. In contrast to our previous protein-based motor designs [4,5], the BHM concept addresses directly the use of conformational change as a means of achieving stepping directionality.…”

“…However, biological motors are predominantly protein-based. This has inspired efforts to design and synthesize directional molecular motors from protein-based components [4][5][6][7]. However, these protein-based concepts would achieve their motion only from diffusion, and lack a means to incorporate conformational change to stimulate directed motion.…”

“…We then describe a proposed experimental realization of the BHM using a combination of components from our previous nanomotor concepts. These include coiled-coil domains for structurally near-rigid components [4], ligand-gated DNAbinding protein domains [4][5][6]9], and a DNA track with corresponding binding sites [4,5,9]. To these we add a conformational switching moiety such as the photo-switchable molecule azobenzene [10].…”

“…Two orthogonally regulated track-binding domains (feet). As for other protein-based motor designs [4,5], we propose to use ligand-gated repressor proteins. As examples, TrpR and DtxR are repressor proteins which bind to specific DNA sequences in the presence of a specific ligand (tryptophan for TrpR [12], iron and some other divalent metals such as cobalt for DtxR [13,14]).…”