scholarly journals A Brownian ratchet model explains the biased sidestepping movement of single-headed kinesin-3 KIF1A

2019 ◽  
Author(s):  
A. Mitra ◽  
M. Suñé ◽  
S. Diez ◽  
J. M. Sancho ◽  
D. Oriola ◽  
...  
Keyword(s):  
Stochastic Simulations ◽  
Weakly Bound ◽  
Brownian Motors ◽  
Brownian Motor ◽  
Left Handed ◽  
Mechanochemical Cycle ◽  
Ratchet Model ◽  
Motor Density ◽  
Ratchet Potential

AbstractThe kinesin-3 motor KIF1A is involved in long-ranged axonal transport in neurons. In order to ensure vesicular delivery, motors need to navigate the microtubule lattice and overcome possible roadblocks along the way. The single-headed form of KIF1A is a highly diffusive motor that has been shown to be a prototype of Brownian motor by virtue of a weakly-bound diffusive state to the microtubule. Recently, groups of single-headed KIF1A motors were found to be able to sidestep along the microtubule lattice, creating left-handed helical membrane tubes when pulling on giant unilamellar vesicles in vitro. A possible hypothesis is that the diffusive state enables the motor to explore the microtubule lattice and switch protofilaments, leading to a left-handed helical motion. Here we study microtubule rotation driven by single-headed KIF1A motors using fluorescene-interference contrast (FLIC) microscopy. We find an average rotational pitch of ≃ 1.4 μm which is remarkably robust to changes in the gliding velocity, ATP concentration and motor density. Our experimental results are compared to stochastic simulations of Brownian motors moving on a two-dimensional continuum ratchet potential, which quantitatively agree with the FLIC experiments. We find that single-headed KIF1A sidestepping can be explained as a consequence of the intrinsic handedness and polarity of the microtubule lattice in combination with the diffusive mechanochemical cycle of the motor.

Supramolecular assemblies of the Ascaris suum major sperm protein (MSP) associated with amoeboid cell motility

1994 ◽  
Vol 107 (10) ◽  
pp. 2941-2949
Author(s):  
K.L. King ◽  
M. Stewart ◽  
T.M. Roberts
Keyword(s):  
Ascaris Suum ◽  
Leading Edge ◽  
Intrinsic Property ◽  
Basic Unit ◽  
Major Sperm Protein ◽  
Sperm Protein ◽  
Amoeboid Cell ◽  
Left Handed ◽  
Self Association

Sperm of the nematode, Ascaris suum, are amoeboid cells that do not require actin or myosin to crawl over solid substrata. In these cells, the role usually played by actin has been taken over by major sperm protein (MSP), which assembles into filaments that pack the sperm pseudopod. These MSP filaments are organized into multi-filament arrays called fiber complexes that flow centripetally from the leading edge of the pseudopod to the cell body in a pattern that is intimately associated with motility. We have characterized structurally a hierarchy of helical assemblies formed by MSP. The basic unit of the MSP cytoskeleton is a filament formed by two subfilaments coiled around one another along right-handed helical tracks. In vitro, higher-order assemblies (macrofibers) are formed by MSP filaments that coil around one another in a left-handed helical sense. The multi-filament assemblies formed by MSP in vitro are strikingly similar to the fiber complexes that characterize the sperm cytoskeleton. Thus, self-association is an intrinsic property of MSP filaments that distinguishes these fibers from actin filaments. The results obtained with MSP help clarify the roles of different aspects of the actin cytoskeleton in the generation of locomotion and, in particular, emphasize the contributions made by vectorial assembly and filament bundling.

scholarly journals Oligonucleotides DNA containing 8-trifluoromethyl-2′-deoxyguanosine for observing Z-DNA structure

2020 ◽  
Author(s):  
Hong-Liang Bao ◽  
Tatsuki Masuzawa ◽  
Takanori Oyoshi ◽  
Yan Xu
Keyword(s):  
Genetic Diseases ◽  
Dna Structure ◽  
2D Nmr ◽  
Living Cells ◽  
Molecular Probes ◽  
Alternative Form ◽  
Left Handed ◽  
Z Dna ◽  
And Function

Abstract Z-DNA is known to be a left-handed alternative form of DNA and has important biological roles as well as being related to cancer and other genetic diseases. It is therefore important to investigate Z-DNA structure and related biological events in living cells. However, the development of molecular probes for the observation of Z-DNA structures inside living cells has not yet been realized. Here, we have succeeded in developing site-specific trifluoromethyl oligonucleotide DNA by incorporation of 8-trifluoromethyl-2′-deoxyguanosine (FG). 2D NMR strongly suggested that FG adopted a syn conformation. Trifluoromethyl oligonucleotides dramatically stabilized Z-DNA, even under physiological salt concentrations. Furthermore, the trifluoromethyl DNA can be used to directly observe Z-form DNA structure and interaction of DNA with proteins in vitro, as well as in living human cells by19F NMR spectroscopy for the first time. These results provide valuable information to allow understanding of the structure and function of Z-DNA.

scholarly journals Stable tug-of-war between kinesin-1 and cytoplasmic dynein upon different ATP and roadblock concentrations

2020 ◽  
Author(s):  
Gina A. Monzon ◽  
Lara Scharrel ◽  
Ashwin DSouza ◽  
Ludger Santen ◽  
Stefan Diez
Keyword(s):  
Cytoplasmic Dynein ◽  
Gliding Motility ◽  
Force Balance ◽  
Stochastic Simulations ◽  
Transport Systems ◽  
Organelle Transport ◽  
Atp Concentration ◽  
Dynein Motor ◽  
Bidirectional Movement

ABSTRACTThe maintenance of intracellular processes like organelle transport and cell division depend on bidirectional movement along microtubules. These processes typically require kinesin and dynein motor proteins which move with opposite directionality. Because both types of motors are often simultaneously bound to the cargo, regulatory mechanisms are required to ensure controlled directional transport. Recently, it has been shown that parameters like mechanical motor activation, ATP concentration and roadblocks on the microtubule surface differentially influence the activity of kinesin and dynein motors in distinct manners. However, how these parameters affect bidirectional transport systems has not been studied. Here, we investigate the regulatory influence of these three parameter using in vitro gliding motility assays and stochastic simulations. We find that the number of active kinesin and dynein motors determines the transport direction and velocity, but that variations in ATP concentration and roadblock density have no significant effect. Thus, factors influencing the force balance between opposite motors appear to be important, whereas the detailed stepping kinetics and bypassing capabilities of the motors have only little effect.

scholarly journals Evidence that the metabolite repair enzyme NAD(P)HX epimerase has a moonlighting function

2018 ◽  
Vol 38 (3) ◽  
Author(s):  
Thomas D. Niehaus ◽  
Mona Elbadawi-Sidhu ◽  
Lili Huang ◽  
Laurence Prunetti ◽  
Jesse F. Gregory ◽  
...  
Keyword(s):  
Vitamin B6 ◽  
Weakly Bound ◽  
E Coli ◽  
Essentially Normal ◽  
Metabolite Repair ◽  
Mutant Cells ◽  
Dehydratase Activity ◽  
Related Compounds

NAD(P)H-hydrate epimerase (EC 5.1.99.6) is known to help repair NAD(P)H hydrates (NAD(P)HX), which are damage products existing as R and S epimers. The S epimer is reconverted to NAD(P)H by a dehydratase; the epimerase facilitates epimer interconversion. Epimerase deficiency in humans causes a lethal disorder attributed to NADHX accumulation. However, bioinformatic evidence suggest caution about this attribution by predicting that the epimerase has a second function connected to vitamin B6 (pyridoxal 5′-phosphate and related compounds). Specifically, (i) the epimerase is fused to a B6 salvage enzyme in plants, (ii) epimerase genes cluster on the chromosome with B6-related genes in bacteria, and (iii) epimerase and B6-related genes are coexpressed in yeast and Arabidopsis. The predicted second function was explored in Escherichia coli, whose epimerase and dehydratase are fused and encoded by yjeF. The putative NAD(P)HX epimerase active site has a conserved lysine residue (K192 in E. coli YjeF). Changing this residue to alanine cut in vitro epimerase activity by ≥95% but did not affect dehydratase activity. Mutant cells carrying the K192A mutation had essentially normal NAD(P)HX dehydratase activity and NAD(P)HX levels, showing that the mutation had little impact on NAD(P)HX repair in vivo. However, these cells showed metabolome changes, particularly in amino acids, which exceeded those in cells lacking the entire yjeF gene. The K192A mutant cells also had reduced levels of ‘free’ (i.e. weakly bound or unbound) pyridoxal 5'-phosphate. These results provide circumstantial evidence that the epimerase has a metabolic function beyond NAD(P)HX repair and that this function involves vitamin B6.

scholarly journals Self-Organization of Motor-Propelled Cytoskeletal Filaments at Topographically Defined Borders

2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Alf Månsson ◽  
Richard Bunk ◽  
Mark Sundberg ◽  
Lars Montelius
Keyword(s):  
Molecular Motor ◽  
Direct Consequence ◽  
Self Organization ◽  
Test Model ◽  
Structured Surfaces ◽  
Microstructured Surfaces ◽  
Living Organisms ◽  
Edge Tracing ◽  
Motor Density

Self-organization phenomena are of critical importance in living organisms and of great interest to exploit in nanotechnology. Here we describe in vitro self-organization of molecular motor-propelled actin filaments, manifested as a tendency of the filaments to accumulate in high density close to topographically defined edges on nano- and microstructured surfaces. We hypothesized that this “edge-tracing” effect either (1) results from increased motor density along the guiding edges or (2) is a direct consequence of the asymmetric constraints on stochastic changes in filament sliding direction imposed by the edges. The latter hypothesis is well captured by a model explicitly defining the constraints of motility on structured surfaces in combination with Monte-Carlo simulations [cf. Nitta et al. (2006)] of filament sliding. In support of hypothesis 2 we found that the model reproduced the edge tracing effect without the need to assume increased motor density at the edges. We then used model simulations to elucidate mechanistic details. The results are discussed in relation to nanotechnological applications and future experiments to test model predictions.

WALKING ON RATCHETS WITH TWO BROWNIAN MOTORS

2004 ◽  
Vol 04 (01) ◽  
pp. L161-L170 ◽  
Author(s):  
JOSE L. MATEOS
Keyword(s):  
Effective Diffusion ◽  
Diffusion Constant ◽  
Brownian Motors ◽  
Coherent Transport ◽  
Dimensionless Ratio ◽  
Bistable Potential ◽  
External Time ◽  
Stable Points ◽  
White Noises ◽  
Ratchet Potential

We analyze a model for a walker moving on an asymmetric periodic ratchet potential. This model is motivated by the properties of transport of the motor protein kinesin. The walker consists of two feet represented as two particles coupled nonlinearly through a double-well bistable potential. In contrast to linear coupling, the bistable potential admits a richer dynamics where the ordering of the particles can alternate during the walking. The transitions between the two stable points on the bistable potential, correspond to a walking with alternating particles. In our model, each particle is acted upon by independent white noises, modeling thermal noise, and additionally we have an external time-dependent force that drives the system out of equilibrium, allowing directed transport. In the equilibrium case, where only white noise is present, we perform a bifurcation analysis which reveals different walking patterns. In particular, we distinguish between two main walking styles: alternating and no alternating. These two ways of walking resemble the hand-over-hand and the inchworm walking in kinesin, respectively. Numerical simulations showed the existence of current reversals and significant changes in the effective diffusion constant. We obtained an optimal coherent transport, characterized by a maximum dimensionless ratio of the current and the effective diffusion (Péclet number), when the periodicity of the ratchet potential coincides with the equilibrium distance between the two particles.

scholarly journals Formation of helical membrane tubes around microtubules by single-headed kinesin KIF1A

2015 ◽  
Vol 6 (1) ◽  
Author(s):  
David Oriola ◽  
Sophie Roth ◽  
Marileen Dogterom ◽  
Jaume Casademunt
Keyword(s):  
Motor Performance ◽  
Vesicular Transport ◽  
Force Generation ◽  
Theoretical Studies ◽  
Giant Vesicles ◽  
Traffic Conditions ◽  
Self Organized ◽  
Mechanochemical Cycle ◽  
Axonal Trafficking

Abstract The kinesin-3 motor KIF1A is in charge of vesicular transport in neuronal axons. Its single-headed form is known to be very inefficient due to the presence of a diffusive state in the mechanochemical cycle. However, recent theoretical studies have suggested that these motors could largely enhance force generation by working in teams. Here we test this prediction by challenging single-headed KIF1A to extract membrane tubes from giant vesicles along microtubule filaments in a minimal in vitro system. Remarkably, not only KIF1A motors are able to extract tubes but they feature a novel phenomenon: tubes are wound around microtubules forming tubular helices. This finding reveals an unforeseen combination of cooperative force generation and self-organized manoeuvreing capability, suggesting that the diffusive state may be a key ingredient for collective motor performance under demanding traffic conditions. Hence, we conclude that KIF1A is a genuinely cooperative motor, possibly explaining its specificity to axonal trafficking.

scholarly journals Plus-end motors override minus-end motors during transport of squid axon vesicles on microtubules.

1996 ◽  
Vol 135 (2) ◽  
pp. 383-397 ◽  
Author(s):  
V Muresan ◽  
C P Godek ◽  
T S Reese ◽  
B J Schnapp
Keyword(s):  
Lipid Bilayers ◽  
Affinity Purification ◽  
Selective Extraction ◽  
Cytoplasmic Dynein ◽  
Isolated Populations ◽  
Kinesin Motor ◽  
Weakly Bound ◽  
Direction Of Movement ◽  
Vesicle Movement

Plus- and minus-end vesicle populations from squid axoplasm were isolated from each other by selective extraction of the minus-end vesicle motor followed by 5'-adenylyl imidodiphosphate (AMP-PNP)-induced microtubule affinity purification of the plus-end vesicles. In the presence of cytosol containing both plus- and minus-end motors, the isolated populations moved strictly in opposite directions along microtubules in vitro. Remarkably, when treated with trypsin before incubation with cytosol, purified plus-end vesicles moved exclusively to microtubule minus ends instead of moving in the normal plus-end direction. This reversal in the direction of movement of trypsinized plus-end vesicles, in light of further observation that cytosol promotes primarily minus-end movement of liposomes, suggests that the machinery for cytoplasmic dynein-driven, minus-end vesicle movement can establish a functional interaction with the lipid bilayers of both vesicle populations. The additional finding that kinesin overrides cytoplasmic dynein when both are bound to bead surfaces indicates that the direction of vesicle movement could be regulated simply by the presence or absence of a tightly bound, plus-end kinesin motor; being processive and tightly bound, the kinesin motor would override the activity of cytoplasmic dynein because the latter is weakly bound to vesicles and less processive. In support of this model, it was found that (a) only plus-end vesicles copurified with tightly bound kinesin motors; and (b) both plus- and minus-end vesicles bound cytoplasmic dynein from cytosol.

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