scholarly journals Kinetic analysis methods applied to single motor protein trajectories

2018 ◽  
Author(s):  
A L Nord ◽  
A F Pols ◽  
M Depken ◽  
F Pedaci
Keyword(s):  
Single Molecule ◽  
Molecular Motors ◽  
Thermal Noise ◽  
Molecular Motor ◽  
Electrical Energy ◽  
Flagellar Motor ◽  
Step Size ◽  
Analysis Methods ◽  
Chemical States ◽  
Rate Limiting

Molecular motors convert chemical or electrical energy into mechanical displacement, either linear or rotary. Under ideal circumstances, single-molecule measurements can spatially and temporally resolve individual steps of the motor, revealing important properties of the underlying mechanochemical process. Unfortunately, steps are often hard to resolve, as they are masked by thermal noise. In such cases, details of the mechanochemistry can nonetheless be recovered by analyzing the fluctuations in the recorded traces. Here, we expand upon existing statistical analysis methods, providing two new avenues to extract the motor step size, the effective number of rate-limiting chemical states per translocation step, and the compliance of the link between the motor position and the probe particle. We first demonstrate the power and limitations of these methods using simulated molecular motor trajectories, and we then apply these methods to experimental data of kinesin, the bacterial flagellar motor, and F1-ATPase.

scholarly journals A model of processive walking and slipping of kinesin-8 molecular motors

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ping Xie
Keyword(s):  
Single Molecule ◽  
Molecular Motors ◽  
External Load ◽  
Molecular Motor ◽  
Velocity Versus ◽  
Stick Slip ◽  
Load Dependence ◽  
Chemomechanical Coupling ◽  
Similarities And Differences ◽  
Stick Slip Motion

AbstractKinesin-8 molecular motor can move with superprocessivity on microtubules towards the plus end by hydrolyzing ATP molecules, depolymerizing microtubules. The available single molecule data for yeast kinesin-8 (Kip3) motor showed that its superprocessive movement is frequently interrupted by brief stick–slip motion. Here, a model is presented for the chemomechanical coupling of the kinesin-8 motor. On the basis of the model, the dynamics of Kip3 motor is studied analytically. The analytical results reproduce quantitatively the available single molecule data on velocity without including the slip and that with including the slip versus external load at saturating ATP as well as slipping velocity versus external load at saturating ADP and no ATP. Predicted results on load dependence of stepping ratio at saturating ATP and load dependence of velocity at non-saturating ATP are provided. Similarities and differences between dynamics of kinesin-8 and that of kinesin-1 are discussed.

Molecular Motors: Force and Movement Generated by Single Myosin II Molecules

Physiology ◽  
2002 ◽  
Vol 17 (5) ◽  
pp. 213-218 ◽  
Author(s):  
Caspar Rüegg ◽  
Claudia Veigel ◽  
Justin E. Molloy ◽  
Stephan Schmitz ◽  
John C. Sparrow ◽  
...  
Keyword(s):  
Optical Tweezers ◽  
Single Molecule ◽  
Molecular Motors ◽  
Molecular Motor ◽  
Myosin Ii ◽  
Force Production ◽  
Myosin Isoforms ◽  
Single Molecule Level ◽  
Recent Developments ◽  
Muscle Myosin

Muscle myosin II is an ATP-driven, actin-based molecular motor. Recent developments in optical tweezers technology have made it possible to study movement and force production on the single-molecule level and to find out how different myosin isoforms may have adapted to their specific physiological roles.

scholarly journals Bacterial flagellar motor

2008 ◽  
Vol 41 (2) ◽  
pp. 103-132 ◽  
Author(s):  
Yoshiyuki Sowa ◽  
Richard M. Berry
Keyword(s):  
Single Molecule ◽  
Cell Envelope ◽  
Molecular Motor ◽  
Motive Force ◽  
Flagellar Motor ◽  
Large Size ◽  
Structural Details ◽  
Bacterial Flagellar Motor ◽  
And Function ◽  
Rotary Motor

AbstractThe bacterial flagellar motor is a reversible rotary nano-machine, about 45 nm in diameter, embedded in the bacterial cell envelope. It is powered by the flux of H+or Na+ions across the cytoplasmic membrane driven by an electrochemical gradient, the proton-motive force or the sodium-motive force. Each motor rotates a helical filament at several hundreds of revolutions per second (hertz). In many species, the motor switches direction stochastically, with the switching rates controlled by a network of sensory and signalling proteins. The bacterial flagellar motor was confirmed as a rotary motor in the early 1970s, the first direct observation of the function of a single molecular motor. However, because of the large size and complexity of the motor, much remains to be discovered, in particular, the structural details of the torque-generating mechanism. This review outlines what has been learned about the structure and function of the motor using a combination of genetics, single-molecule and biophysical techniques, with a focus on recent results and single-molecule techniques.

scholarly journals Quantifying the Heat Dissipation from Molecular Motor’s Transport Properties in Nonequilibrium Steady States

2016 ◽  
Author(s):  
Wonseok Hwang ◽  
Changbong Hyeon
Keyword(s):  
Single Molecule ◽  
Molecular Motors ◽  
Heat Dissipation ◽  
Molecular Motor ◽  
Diffusion Constant ◽  
Nonequilibrium Steady States ◽  
Directed Motion ◽  
Mean Velocity ◽  
Self Diffusion ◽  
Brownian Particles

Theoretical analysis, which maps single molecule time trajectories of a molecular motor onto unicyclic Markov processes, allows us to evaluate the heat dissipated from the motor and to elucidate its dependence on the mean velocity and diffusivity. Unlike passive Brownian particles in equilibrium, the velocity and diffusion constant of molecular motors are closely inter-related to each other. In particular, our study makes it clear that the increase of diffusivity with the heat production is a natural outcome of active particles, which is reminiscent of the recent experimental premise that the diffusion of an exothermic enzyme is enhanced by the heat released from its own catalytic turnover. Compared with freely diffusing exothermic enzymes, kinesin-1 whose dynamics is confined on one-dimensional tracks is highly efficient in transforming conformational fluctuations into a locally directed motion, thus displaying a significantly higher enhancement in diffusivity with its turnover rate. Putting molecular motors and freely diffusing enzymes on an equal footing, our study offers thermodynamic basis to understand the heat enhanced self-diffusion of exothermic enzymes.

scholarly journals Single-molecule FRET dynamics of molecular motors in an ABEL Trap

2020 ◽  
Author(s):  
Maria Dienerowitz ◽  
Jamieson A. L. Howard ◽  
Steven D. Quinn ◽  
Frank Dienerowitz ◽  
Mark C. Leake
Keyword(s):  
Dna Replication ◽  
Single Molecule ◽  
Conformational Changes ◽  
Molecular Motors ◽  
Rational Design ◽  
Molecular Motor ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Observation Time

AbstractSingle-molecule Förster resonance energy transfer (smFRET) of molecular motors provides transformative insights into their dynamics and conformational changes both at high temporal and spatial resolution simultaneously. However, a key challenge of such FRET investigations is to observe a molecule in action for long enough without restricting its natural function. The Anti-Brownian ELectrokinetic Trap (ABEL trap) sets out to combine smFRET with molecular confinement to enable observation times of up to several seconds while removing any requirement of tethered surface attachment of the molecule in question. In addition, the ABEL trap’s inherent ability to selectively capture FRET active molecules accelerates the data acquisition process. Here we exemplify the capabilities of the ABEL trap in performing extended timescale smFRET measurements on the molecular motor Rep, which is crucial for removing protein blocks ahead of the advancing DNA replication machinery and for restarting stalled DNA replication. We are able to monitor single Rep molecules up to 6 s with 1 ms time resolution capturing multiple conformational switching events during the observation time. Here we provide a step-by-step guide for the rational design, construction and implementation of the ABEL trap for smFRET detection of Rep in vitro. We include details of how to model the electric potential at the trap site and use Hidden Markov analysis of the smFRET trajectories.

Single-molecule mechanical study of an autonomous artificial translational molecular motor beyond bridge-burning design

Nanoscale ◽  
2021 ◽  
Author(s):  
Xinpeng Hu ◽  
Xiaodan Zhao ◽  
Iong Ying Loh ◽  
Jie Yan ◽  
Zhisong Wang
Keyword(s):  
Single Molecule ◽  
Molecular Motors ◽  
Molecular Motor ◽  
Force Generation ◽  
Single Motor ◽  
Mechanical Study

A key capability of molecular motors is sustainable force generation by a single motor copy. Direct force characterization at single-motor level is still missing for artificial molecular motors, though long...

Myosin learns to walk

2001 ◽  
Vol 114 (11) ◽  
pp. 1981-1998
Author(s):  
Amit Mehta
Keyword(s):  
Single Molecule ◽  
Atp Hydrolysis ◽  
Kinetic Scheme ◽  
Myosin V ◽  
Step Size ◽  
Class V ◽  
Adp Release ◽  
Solution Kinetic ◽  
Conventional Kinesin ◽  
Rate Limiting

Recent experiments, drawing upon single-molecule, solution kinetic and structural techniques, have clarified our mechanistic understanding of class V myosins. The findings of the past two years can be summarized as follows: (1) Myosin V is a highly efficient processive motor, surpassing even conventional kinesin in the distance that individual molecules can traverse. (2) The kinetic scheme underlying ATP turnover resembles those of myosins I and II but with rate constants tuned to favor strong binding to actin. ADP release precedes dissociation from actin and is rate-limiting in the cycle. (3) Myosin V walks in strides averaging ∼36 nm, the long pitch pseudo-repeat of the actin helix, each step coupled to a single ATP hydrolysis. Such a unitary displacement, the largest molecular step size measured to date, is required for a processive myosin motor to follow a linear trajectory along a helical actin track.

scholarly journals Molecular motors: forty years of interdisciplinary research

2011 ◽  
Vol 22 (21) ◽  
pp. 3936-3939 ◽  
Author(s):  
James A. Spudich
Keyword(s):  
Single Molecule ◽  
Molecular Motors ◽  
Atp Hydrolysis ◽  
Molecular Motor ◽  
Single Molecule Level ◽  
In Vitro Motility ◽  
Nonmuscle Cell ◽  
Nonmuscle Cells ◽  
City Plan

A mere forty years ago it was unclear what motor molecules exist in cells that could be responsible for the variety of nonmuscle cell movements, including the “saltatory cytoplasmic particle movements” apparent by light microscopy. One wondered whether nonmuscle cells might have a myosin-like molecule, well known to investigators of muscle. Now we know that there are more than a hundred different molecular motors in eukaryotic cells that drive numerous biological processes and organize the cell's dynamic city plan. Furthermore, in vitro motility assays, taken to the single-molecule level using techniques of physics, have allowed detailed characterization of the processes by which motor molecules transduce the chemical energy of ATP hydrolysis into mechanical movement. Molecular motor research is now at an exciting threshold of being able to enter into the realm of clinical applications.

scholarly journals Kinetic analysis methods applied to single motor protein trajectories

2018 ◽  
Vol 20 (27) ◽  
pp. 18775-18781
Author(s):  
A. L. Nord ◽  
A. F. Pols ◽  
M. Depken ◽  
F. Pedaci
Keyword(s):  
Kinetic Analysis ◽  
Molecular Motors ◽  
Motor Protein ◽  
Electrical Energy ◽  
Mechanical Displacement ◽  
Single Motor ◽  
Analysis Methods

Molecular motors convert chemical or electrical energy into mechanical displacement, either linear or rotary.

Theoretical Prediction of Run Speed Distribution for a Molecular Motor

2008 ◽  
Author(s):  
Sam Walcott ◽  
Neil M. Kad
Keyword(s):  
Molecular Motors ◽  
Molecular Motor ◽  
Realistic Model ◽  
Variable Step Size ◽  
Step Size ◽  
Run Length ◽  
Speed Distribution ◽  
Myosin Va ◽  
Cell Transforming ◽  
Run Speed

Processive molecular motors are large proteins that “walk” along filaments in a cell, transforming chemical energy into mechanical work. These microscopic motors behave, at least qualitatively, like macroscopic walking machines. The dynamics and stability of macroscopic walkers are understood by analysis of “stride functions” (Poincare´ maps from one step to the next). We show that molecular motors have linear, probabilistic stride functions. Using these functions, we derive expressions for three measurable distributions: step period, run length and average run speed. The former two distributions are well known, the latter is new. We validate our calculation with simulations of a realistic model for Myosin Va (a molecular motor). The parameters of the run speed distribution specify both the run-length and step period distributions. As step-period distributions are difficult to measure under physiologically relevant conditions, this technique provides new information. Finally, we discuss the effects of variable step size and experimental error.

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