Through the Eyes of Creators: Observing Artificial Molecular Motors

Unksov, Ivan N.; Korosec, Chapin S.; Surendiran, Pradheebha; Verardo, Damiano; Lyttleton, Roman; Forde, Nancy R.; Linke, Heiner

doi:10.1021/acsnanoscienceau.1c00041

Cited by 12 publications

(10 citation statements)

References 223 publications

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“…We anticipate that the described current reversal mechanism will be relevant to many flavors of artificial molecular motors [41], particularly to those applications which require tracks to direct molecular motors [42]. The rotary motor of Ref.…”

Section: Discussionmentioning

confidence: 99%

Current Reversal in a Molecular Motor

Albaugh¹,

Gu²,

Gingrich³

2022

Preprint

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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 a nonequilibrium steady state, 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.

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Section: Discussionmentioning

confidence: 99%

Current Reversal in a Molecular Motor

Albaugh¹,

Gu²,

Gingrich³

2022

Preprint

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“…i k j j j y { z z z = (10) an equality resembling the current TUR inequality, eq 1. Now, the saturation of the TUR for J is determined by f(βΔμ/2) and g(η,ζ,λ) = η 2 λ/(ηλ + ζ) .…”

Section: Modelmentioning

confidence: 99%

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

Albaugh,

Fu,

et al. 2023

J. Chem. Theory Comput.

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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.

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“…Spatiotemporal resolutions and measurable force ranges of commonly used SMFS techniques are given in Table . ,,− …”

Section: Single-molecule Measurementsmentioning

confidence: 99%

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

et al. 2022

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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.

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Through the Eyes of Creators: Observing Artificial Molecular Motors

Cited by 12 publications

References 223 publications

Current Reversal in a Molecular Motor

Current Reversal in a Molecular Motor

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

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

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