Through the Eyes of Creators: Observing Artificial Molecular Motors

Kinetics and Optimality of Influenza A Virus Locomotion

Influenza A viruses (IAVs) must navigate through a dense extracellular mucus to infect airway epithelial cells. The mucous layer, composed of glycosylated biopolymers (mucins), presents sialic acid that binds to ligands on the viral envelope and can be irreversibly cleaved by viral enzymes. It was recently discovered that filamentous IAVs exhibit directed persistent motion along their long axis on sialic acid-coated surfaces. This Letter demonstrates through stochastic simulations and mean-field theory, how IAVs harness a "burnt-bridge" Brownian ratchet mechanism for directed persistent translational motion. Importantly, our analysis reveals that equilibrium features of the system primarily control the dynamics, even out of equilibrium, and that asymmetric distribution of ligands on the virus allows for more robust directed transport. We show viruses occupy the optimal parameter range ("Goldilocks zone") for efficient mucous transport, possibly due to the evolutionary adaptation of enzyme kinetics. Our findings suggest novel therapeutic targets and provide insight into possible mechanisms of zoonotic transmission.

Motility of an autonomous protein-based artificial motor that operates via a burnt-bridge principle

Inspired by biology, great progress has been made in creating artificial molecular motors. However, the dream of harnessing proteins - the building blocks selected by nature - to design autonomous motors has so far remained elusive. Here we report the synthesis and characterization of the Lawnmower, an autonomous, protein-based artificial molecular motor comprised of a spherical hub decorated with proteases. Its "burnt-bridge" motion is directed by cleavage of a peptide lawn, promoting motion towards unvisited substrate. We find that Lawnmowers exhibit directional motion with average speeds of up to 80 nm/s, comparable to biological motors. By selectively patterning the peptide lawn on microfabricated tracks, we furthermore show that the Lawnmower is capable of track-guided motion. Our work opens an avenue towards nanotechnology applications of artificial protein motors.

Theoretical trends in the dynamics simulations of molecular machines across multiple scales

Over the past few decades, molecular machines have been extensively studied, since they are composed of single molecules for functional materials capable of responding to external stimuli, enabling motion at scales ranging from the microscopic to the macroscopic level within molecular aggregates. This advancement holds the potential to efficiently transform external resources into mechanical movement, achieved through precise control of conformational changes in stimuli-responsive materials. However, the underlying mechanism that links microscopic and macroscopic motions remains unclear, demanding computational development associated with simulating the construction of molecular machines from single molecules. This bottleneck has impeded the design of more efficient functional materials. Advancements in theoretical simulations have successfully been developed in various computational models to unveil the operational mechanisms of stimulus-responsive molecular machines, which could help us reduce the costs in experimental trial-and-error procedures. It opens doors to the computer-aided design of innovative functional materials. In this perspective, we have reviewed theoretical approaches employed in simulating dynamic processes involving conformational changes in molecular machines, spanning different scales and environmental conditions. In addition, we have highlighted current challenges and anticipated future trends in the collective control of aggregates within molecular machines. Our goal is to provide a comprehensive overview of recent theoretical advancements in the field of molecular machines, offering valuable insights for the design of novel smart materials.

Limits on the Precision of Catenane Molecular Motors: Insights from Thermodynamics and Molecular Dynamics Simulations

Thermodynamic uncertainty relations (TURs) relate precision to the dissipation rate, yet the inequalities can be far from saturation. Indeed, in catenane molecular motor simulations, we record precision far below the TUR limit. We further show that this inefficiency can be anticipated by four physical parameters: the thermodynamic driving force, fuel decomposition rate, coupling between fuel decomposition and motor motion, and rate of undriven motor motion. The physical insights might assist in designing molecular motors in the future.

Sterically driven current reversal in a molecular motor model

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 nonequilibrium steady-state concentrations, 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.

A photochemical method to evidence directional molecular motions

Light driven synthetic molecular motors represent crucial building blocks for advanced molecular machines and their applications. A standing challenge is the development of very fast molecular motors able to perform rotations with kHz, MHz or even faster frequencies. Central to this challenge is the direct experimental evidence of directionality because analytical methods able to follow very fast motions rarely deliver precise geometrical insights. Here, a general photochemical method for elucidation of directional motions is presented. In a macrocyclization approach the molecular motor rotations are restricted and forced to proceed in two separate ~180° rotation-photoequilibria. Therefore, all four possible photoinduced rotation steps (clockwise and counterclockwise directions) can be quantified. Comparison of the corresponding quantum yields to the unrestricted motor delivers direct evidence for unidirectionality. This method can be used for any ultrafast molecular motor even in cases where no high energy intermediates are present during the rotation cycle.

Single-Molecule Optical Tweezers As a Tool for Delineating the Mechanisms of Protein-Processing Mechanoenzymes

Mechanoenzymes convert chemical energy from the hydrolysis of nucleotide triphosphates to mechanical energy for carrying out cellular functions ranging from DNA unwinding to protein degradation. Protein-processing mechanoenzymes either remodel the protein structures or translocate them across cellular compartments in an energy-dependent manner. Optical-tweezer-based single-molecule force spectroscopy assays have divulged information on details of chemo-mechanical coupling, directed motion, as well as mechanical forces these enzymes are capable of generating. In this review, we introduce the working principles of optical tweezers as a single-molecule force spectroscopy tool and assays developed to decipher the properties such as unfolding kinetics, translocation velocities, and step sizes by protein remodeling mechanoenzymes. We focus on molecular motors involved in protein degradation and disaggregation, i.e., ClpXP, ClpAP, and ClpB, and insights provided by single-molecule assays on kinetics and stepping dynamics during protein unfolding and translocation. Cellular activities such as protein synthesis, folding, and translocation across membranes are also energy dependent, and the recent single-molecule studies decoding the role of mechanical forces on these processes have been discussed.