1
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Kita T, Sasaki K, Niwa S. Modeling the motion of disease-associated KIF1A heterodimers. Biophys J 2023; 122:4348-4359. [PMID: 37853694 PMCID: PMC10698283 DOI: 10.1016/j.bpj.2023.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/12/2023] [Accepted: 10/13/2023] [Indexed: 10/20/2023] Open
Abstract
KIF1A is a member of the kinesin-3 motor protein family that transports synaptic vesicle precursors in axons. Mutations in the Kif1a gene cause neuronal diseases. Most patients are heterozygous and have both mutated and intact KIF1A alleles, suggesting that heterodimers composed of wild-type KIF1A and mutant KIF1A are likely involved in pathogenesis. In this study, we propose mathematical models to describe the motility of KIF1A heterodimers composed of wild-type KIF1A and mutant KIF1A. Our models precisely describe run length, run time, and velocity of KIF1A heterodimers using a few parameters obtained from two homodimers. The first model is a simple hand-over-hand model in which stepping and detachment rates from a microtubule of each head are identical to those in the respective homodimers. Although the velocities of heterodimers expected from this model were in good agreement with the experimental results, this model underestimated the run lengths and run times of some heterodimeric motors. To address this discrepancy, we propose the tethered-head affinity model, in which we hypothesize a tethered head, in addition to a microtubule-binding head, contributes to microtubule binding in a vulnerable one-head-bound state. The run lengths and run times of the KIF1A heterodimers predicted by the tethered-head affinity model matched well with experimental results, suggesting a possibility that the tethered head affects the microtubule binding of KIF1A. Our models provide insights into how each head contributes to the processive movement of KIF1A and can be used to estimate motile parameters of KIF1A heterodimers.
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Affiliation(s)
- Tomoki Kita
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan.
| | - Kazuo Sasaki
- Department of Applied Physics, Graduate School of Engineering, Tohoku University, Sendai, Miyagi, Japan
| | - Shinsuke Niwa
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan; Frontier Research Institute for Interdisciplinary Sciences (FRIS), Tohoku University, Sendai, Miyagi, Japan.
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2
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Wirth JO, Scheiderer L, Engelhardt T, Engelhardt J, Matthias J, Hell SW. MINFLUX dissects the unimpeded walking of kinesin-1. Science 2023; 379:1004-1010. [PMID: 36893244 DOI: 10.1126/science.ade2650] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 01/23/2023] [Indexed: 03/11/2023]
Abstract
We introduce an interferometric MINFLUX microscope that records protein movements with up to 1.7 nanometer per millisecond spatiotemporal precision. Such precision has previously required attaching disproportionately large beads to the protein, but MINFLUX requires the detection of only about 20 photons from an approximately 1-nanometer-sized fluorophore. Therefore, we were able to study the stepping of the motor protein kinesin-1 on microtubules at up to physiological adenosine-5'-triphosphate (ATP) concentrations. We uncovered rotations of the stalk and the heads of load-free kinesin during stepping and showed that ATP is taken up with a single head bound to the microtubule and that ATP hydrolysis occurs when both heads are bound. Our results show that MINFLUX quantifies (sub)millisecond conformational changes of proteins with minimal disturbance.
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Affiliation(s)
- Jan O Wirth
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Lukas Scheiderer
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Tobias Engelhardt
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Johann Engelhardt
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Jessica Matthias
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Stefan W Hell
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg, Germany
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
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3
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Zaniewski TM, Hancock WO. Positive charge in the K-loop of the kinesin-3 motor KIF1A regulates superprocessivity by enhancing microtubule affinity in the one-head-bound state. J Biol Chem 2023; 299:102818. [PMID: 36549649 PMCID: PMC9871336 DOI: 10.1016/j.jbc.2022.102818] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
KIF1A is an essential neuronal transport motor protein in the kinesin-3 family, known for its superprocessive motility. However, structural features underlying this function are unclear. Here, we determined that superprocessivity of KIF1A dimers originates from a unique structural domain, the lysine-rich insertion in loop-12 termed the 'K-loop', which enhances electrostatic interactions between the motor and the microtubule. In 80 mM PIPES buffer, replacing the native KIF1A loop-12 with that of kinesin-1 resulted in a 6-fold decrease in run length, whereas adding additional positive charge to loop-12 enhanced the run length. Interestingly, swapping the KIF1A loop-12 into kinesin-1 did not enhance its run length, consistent with the two motor families using different mechanochemical tuning to achieve persistent transport. To investigate the mechanism by which the KIF1A K-loop enhances processivity, we used microtubule pelleting and single-molecule dwell time assays in ATP and ADP. First, the microtubule affinity was similar in ATP and in ADP, consistent with the motor spending the majority of its cycle in a weakly bound state. Second, the microtubule affinity and single-molecule dwell time in ADP were 6-fold lower in the loop-swap mutant than WT. Thus, the positive charge in loop-12 of KIF1A enhances the run length by stabilizing binding of the motor in its vulnerable one-head-bound state. Finally, through a series of mutants with varying positive charge in the K-loop, we found that KIF1A processivity is linearly dependent on the charge of loop-12, further highlighting how loop-12 contributes to the function of this key motor protein.
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Affiliation(s)
- Taylor M Zaniewski
- Departments of Chemistry and Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania, USA
| | - William O Hancock
- Departments of Chemistry and Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania, USA.
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4
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Abstract
Coupling of motor proteins within arrays drives muscle contraction, flagellar beating, chromosome segregation, and other biological processes. Current models of motor coupling invoke either direct mechanical linkage or protein crowding, which rely on short-range motor-motor interactions. In contrast, coupling mechanisms that act at longer length scales remain largely unexplored. Here we report that microtubules can physically couple motor movement in the absence of detectable short-range interactions. The human kinesin-4 Kif4A changes the run length and velocity of other motors on the same microtubule in the dilute binding limit, when approximately 10-nm-sized motors are much farther apart than the motor size. This effect does not depend on specific motor-motor interactions because similar changes in Kif4A motility are induced by kinesin-1 motors. A micrometer-scale attractive interaction potential between motors is sufficient to recreate the experimental results in a biophysical model. Unexpectedly, our theory suggests that long-range microtubule-mediated coupling affects not only binding kinetics but also motor mechanochemistry. Therefore, the model predicts that motors can sense and respond to motors bound several micrometers away on a microtubule. Our results are consistent with a paradigm in which long-range motor interactions along the microtubule enable additional forms of collective motor behavior, possibly due to changes in the microtubule lattice.
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5
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Budaitis BG, Badieyan S, Yue Y, Blasius TL, Reinemann DN, Lang MJ, Cianfrocco MA, Verhey KJ. A kinesin-1 variant reveals motor-induced microtubule damage in cells. Curr Biol 2022; 32:2416-2429.e6. [PMID: 35504282 PMCID: PMC9993403 DOI: 10.1016/j.cub.2022.04.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 03/11/2022] [Accepted: 04/08/2022] [Indexed: 12/16/2022]
Abstract
Kinesins drive the transport of cellular cargoes as they walk along microtubule tracks; however, recent work has suggested that the physical act of kinesins walking along microtubules can stress the microtubule lattice. Here, we describe a kinesin-1 KIF5C mutant with an increased ability to generate damage sites in the microtubule lattice as compared with the wild-type motor. The expression of the mutant motor in cultured cells resulted in microtubule breakage and fragmentation, suggesting that kinesin-1 variants with increased damage activity would have been selected against during evolution. The increased ability to damage microtubules is not due to the enhanced motility properties of the mutant motor, as the expression of the kinesin-3 motor KIF1A, which has similar single-motor motility properties, also caused increased microtubule pausing, bending, and buckling but not breakage. In cells, motor-induced microtubule breakage could not be prevented by increased α-tubulin K40 acetylation, a post-translational modification known to increase microtubule flexibility. In vitro, lattice damage induced by wild-type KIF5C was repaired by soluble tubulin and resulted in increased rescues and overall microtubule growth, whereas lattice damage induced by the KIF5C mutant resulted in larger repair sites that made the microtubule vulnerable to breakage and fragmentation when under mechanical stress. These results demonstrate that kinesin-1 motility causes defects in and damage to the microtubule lattice in cells. While cells have the capacity to repair lattice damage, conditions that exceed this capacity result in microtubule breakage and fragmentation and may contribute to human disease.
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Affiliation(s)
- Breane G Budaitis
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA; Department of Cell & Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Somayesadat Badieyan
- Department of Biological Chemistry and Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yang Yue
- Department of Cell & Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - T Lynne Blasius
- Department of Cell & Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dana N Reinemann
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37240, USA
| | - Matthew J Lang
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37240, USA
| | - Michael A Cianfrocco
- Department of Biological Chemistry and Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kristen J Verhey
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA; Department of Cell & Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.
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6
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Hu X, Dinu CZ. Microtubules and Quantum Dots Integration Leads to Conjugates with Applications in Biosensors and Bionanodevices. Methods Mol Biol 2022; 2430:133-148. [PMID: 35476330 DOI: 10.1007/978-1-0716-1983-4_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This chapter describes compiled methods for the formation and manipulation of microtubule-kinesin-carbon nanodots conjugates in user-defined synthetic environments. Specifically, by using inherited self-assembly and self-recognition properties of tubulin cytoskeletal protein and by interfacing this protein with lab synthesized carbon nanodots, bio-nano hybrid interfaces were formed. Further manipulation of such biohybrids under the mechanical cycle of kinesin 1 ATP-ase molecular motor led to their integration on user-controlled engineered surfaces. Presented methods are foreseen to lead to microtubule-molecular motor-hybrid based assemblies formation with applications ranging from biosensing, to nanoelectronics and single molecule printing, just to name a few.
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Affiliation(s)
- Xiao Hu
- Department of Chemical and Biomedical Engineering, West Virginia University, Benjamin M. Statler College of Engineering and Mineral Resources, Morgantown, WV, USA
- Department of Anatomy and Structural Biology and Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Cerasela Zoica Dinu
- Department of Chemical and Biomedical Engineering, West Virginia University, Benjamin M. Statler College of Engineering and Mineral Resources, Morgantown, WV, USA.
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7
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Fiorenza SA, Steckhahn DG, Betterton MD. Modeling spatiotemporally varying protein-protein interactions in CyLaKS, the Cytoskeleton Lattice-based Kinetic Simulator. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2021; 44:105. [PMID: 34406510 PMCID: PMC10202044 DOI: 10.1140/epje/s10189-021-00097-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/21/2021] [Indexed: 05/24/2023]
Abstract
Interaction of cytoskeletal filaments, motor proteins, and crosslinking proteins drives important cellular processes such as cell division and cell movement. Cytoskeletal networks also exhibit nonequilibrium self-assembly in reconstituted systems. An emerging problem in cytoskeletal modeling and simulation is spatiotemporal alteration of the dynamics of filaments, motors, and associated proteins. This can occur due to motor crowding, obstacles along the filament, motor interactions and direction switching, and changes, defects, or heterogeneity in the filament binding lattice. How such spatiotemporally varying cytoskeletal filaments and motor interactions affect their collective properties is not fully understood. We developed the Cytoskeleton Lattice-based Kinetic Simulator (CyLaKS) to investigate such problems. The simulation model builds on previous work by incorporating motor mechanochemistry into a simulation with many interacting motors and/or associated proteins on a discretized lattice. CyLaKS also includes detailed balance in binding kinetics, movement, and lattice heterogeneity. The simulation framework is flexible and extensible for future modeling work and is available on GitHub for others to freely use or build upon. Here we illustrate the use of CyLaKS to study long-range motor interactions, microtubule lattice heterogeneity, motion of a heterodimeric motor, and how changing crosslinker number affects filament separation.
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Affiliation(s)
- Shane A Fiorenza
- Department of Physics, University of Colorado Boulder, Boulder, USA
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8
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Zaniewski TM, Gicking AM, Fricks J, Hancock WO. A kinetic dissection of the fast and superprocessive kinesin-3 KIF1A reveals a predominant one-head-bound state during its chemomechanical cycle. J Biol Chem 2020; 295:17889-17903. [PMID: 33082143 PMCID: PMC7939386 DOI: 10.1074/jbc.ra120.014961] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 10/14/2020] [Indexed: 12/15/2022] Open
Abstract
The kinesin-3 family contains the fastest and most processive motors of the three neuronal transport kinesin families, yet the sequence of states and rates of kinetic transitions that comprise the chemomechanical cycle and give rise to their unique properties are poorly understood. We used stopped-flow fluorescence spectroscopy and single-molecule motility assays to delineate the chemomechanical cycle of the kinesin-3, KIF1A. Our bacterially expressed KIF1A construct, dimerized via a kinesin-1 coiled-coil, exhibits fast velocity and superprocessivity behavior similar to WT KIF1A. We established that the KIF1A forward step is triggered by hydrolysis of ATP and not by ATP binding, meaning that KIF1A follows the same chemomechanical cycle as established for kinesin-1 and -2. The ATP-triggered half-site release rate of KIF1A was similar to the stepping rate, indicating that during stepping, rear-head detachment is an order of magnitude faster than in kinesin-1 and kinesin-2. Thus, KIF1A spends the majority of its hydrolysis cycle in a one-head-bound state. Both the ADP off-rate and the ATP on-rate at physiological ATP concentration were fast, eliminating these steps as possible rate-limiting transitions. Based on the measured run length and the relatively slow off-rate in ADP, we conclude that attachment of the tethered head is the rate-limiting transition in the KIF1A stepping cycle. Thus, KIF1A's activity can be explained by a fast rear-head detachment rate, a rate-limiting step of tethered-head attachment that follows ATP hydrolysis, and a relatively strong electrostatic interaction with the microtubule in the weakly bound post-hydrolysis state.
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Affiliation(s)
- Taylor M Zaniewski
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Allison M Gicking
- Department of Biomedical Engineering and Bioengineering Graduate Program, Pennsylvania State University, University Park, Pennsylvania, USA
| | - John Fricks
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, Arizona, USA
| | - William O Hancock
- Department of Biomedical Engineering and Bioengineering Graduate Program, Pennsylvania State University, University Park, Pennsylvania, USA.
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9
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Klobusicky JJ, Fricks J, Kramer PR. Effective behavior of cooperative and nonidentical molecular motors. RESEARCH IN THE MATHEMATICAL SCIENCES 2020; 7:29. [PMID: 33870090 PMCID: PMC8049358 DOI: 10.1007/s40687-020-00230-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 09/04/2020] [Indexed: 06/12/2023]
Abstract
Analytical formulas for effective drift, diffusivity, run times, and run lengths are derived for an intracellular transport system consisting of a cargo attached to two cooperative but not identical molecular motors (for example, kinesin-1 and kinesin-2) which can each attach and detach from a microtubule. The dynamics of the motor and cargo in each phase are governed by stochastic differential equations, and the switching rates depend on the spatial configuration of the motor and cargo. This system is analyzed in a limit where the detached motors have faster dynamics than the cargo, which in turn has faster dynamics than the attached motors. The attachment and detachment rates are also taken to be slow relative to the spatial dynamics. Through an application of iterated stochastic averaging to this system, and the use of renewal-reward theory to stitch together the progress within each switching phase, we obtain explicit analytical expressions for the effective drift, diffusivity, and processivity of the motor-cargo system. Our approach accounts in particular for jumps in motor-cargo position that occur during attachment and detachment events, as the cargo tracking variable makes a rapid adjustment due to the averaged fast scales. The asymptotic formulas are in generally good agreement with direct stochastic simulations of the detailed model based on experimental parameters for various pairings of kinesin-1 and kinesin-2 under assisting, hindering, or no load.
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Affiliation(s)
| | - John Fricks
- Arizona State University, School of Mathematical and Statistical Sciences, Tempe, AZ, USA
| | - Peter R Kramer
- Rensselaer Polytechnic Institute, Mathematical Science Department, Troy, NY, USA
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10
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Toleikis A, Carter NJ, Cross RA. Backstepping Mechanism of Kinesin-1. Biophys J 2020; 119:1984-1994. [PMID: 33091340 PMCID: PMC7732724 DOI: 10.1016/j.bpj.2020.09.034] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 01/19/2023] Open
Abstract
Kinesin-1 is an ATP-driven molecular motor that transports cellular cargo along microtubules. At low loads, kinesin-1 almost always steps forward, toward microtubule plus ends, but at higher loads, it can also step backward. Backsteps are usually 8 nm but can be larger. These larger backward events of 16 nm, 24 nm, or more are thought to be slips rather than steps because they are too fast to consist of multiple, tightly coupled 8-nm steps. Here, we propose that not only these larger backsteps, but all kinesin-1 backsteps, are slips. We show first that kinesin waits before forward steps for less time than before backsteps and detachments; second, we show that kinesin waits for the same amount of time before backsteps and detachments; and third, we show that by varying the microtubule type, we can change the ratio of backsteps to detachments without affecting forward stepping. Our findings indicate that backsteps and detachments originate from the same state and that this state arises later in the mechanochemical cycle than the state that gives rise to forward steps. To explain our data, we propose that, in each cycle of ATP turnover, forward kinesin steps can only occur before Pi release, whereas backslips and detachments can only occur after Pi release. In the scheme we propose, Pi release gates access to a weak binding K⋅ADP-K⋅ADP state that can slip back along the microtubule, re-engage, release ADP, and try again to take an ATP-driven forward step. We predict that this rescued detachment pathway is key to maintaining kinesin processivity under load.
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Affiliation(s)
- Algirdas Toleikis
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Coventry, United Kingdom
| | - Nicholas J Carter
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Coventry, United Kingdom
| | - Robert A Cross
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Coventry, United Kingdom.
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11
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Tseng KF, Mickolajczyk KJ, Feng G, Feng Q, Kwok ES, Howe J, Barbar EJ, Dawson SC, Hancock WO, Qiu W. The Tail of Kinesin-14a in Giardia Is a Dual Regulator of Motility. Curr Biol 2020; 30:3664-3671.e4. [PMID: 32735815 DOI: 10.1016/j.cub.2020.06.090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 05/25/2020] [Accepted: 06/25/2020] [Indexed: 12/14/2022]
Abstract
Kinesin-14s are microtubule-based motor proteins that play important roles in mitotic spindle assembly [1]. Ncd-type kinesin-14s are a subset of kinesin-14 motors that exist as homodimers with an N-terminal microtubule-binding tail, a coiled-coil central stalk (central stalk), a neck, and two identical C-terminal motor domains. To date, no Ncd-type kinesin-14 has been found to naturally exhibit long-distance minus-end-directed processive motility on single microtubules as individual homodimers. Here, we show that GiKIN14a from Giardia intestinalis [2] is an unconventional Ncd-type kinesin-14 that uses its N-terminal microtubule-binding tail to achieve minus-end-directed processivity on single microtubules over micrometer distances as a homodimer. We further find that although truncation of the N-terminal tail greatly reduces GiKIN14a processivity, the resulting tailless construct GiKIN14a-Δtail is still a minimally processive motor and moves its center of mass via discrete 8-nm steps on the microtubule. In addition, full-length GiKIN14a has significantly higher stepping and ATP hydrolysis rates than does GiKIN14a-Δtail. Inserting a flexible polypeptide linker into the central stalk of full-length GiKIN14a nearly reduces its ATP hydrolysis rate to that of GiKIN14a-Δtail. Collectively, our results reveal that the N-terminal tail of GiKIN14a is a de facto dual regulator of motility and reinforce the notion of the central stalk as a key mechanical determinant of kinesin-14 motility [3].
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Affiliation(s)
- Kuo-Fu Tseng
- Department of Physics, Oregon State University, Corvallis, OR 97331, USA
| | - Keith J Mickolajczyk
- Department of Biomedical Engineering, Penn State University, University Park, PA 16802, USA; Intercollege Graduate Degree Program in Bioengineering, Penn State University, University Park, PA 16802, USA
| | - Guangxi Feng
- Department of Physics, Oregon State University, Corvallis, OR 97331, USA
| | - Qingzhou Feng
- Department of Biomedical Engineering, Penn State University, University Park, PA 16802, USA
| | - Ethiene S Kwok
- Department of Physics, Oregon State University, Corvallis, OR 97331, USA
| | - Jesse Howe
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Elisar J Barbar
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Scott C Dawson
- Department of Microbiology, University of California, Davis, Davis, CA 95616, USA
| | - William O Hancock
- Department of Biomedical Engineering, Penn State University, University Park, PA 16802, USA; Intercollege Graduate Degree Program in Bioengineering, Penn State University, University Park, PA 16802, USA
| | - Weihong Qiu
- Department of Physics, Oregon State University, Corvallis, OR 97331, USA; Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA.
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12
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The mechanochemistry of the kinesin-2 KIF3AC heterodimer is related to strain-dependent kinetic properties of KIF3A and KIF3C. Proc Natl Acad Sci U S A 2020; 117:15632-15641. [PMID: 32571914 DOI: 10.1073/pnas.1916343117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
KIF3AC is a mammalian neuron-specific kinesin-2 implicated in intracellular cargo transport. It is a heterodimer of KIF3A and KIF3C motor polypeptides which have distinct biochemical and motile properties as engineered homodimers. Single-molecule motility assays show that KIF3AC moves processively along microtubules at a rate faster than expected given the motility rates of the KIF3AA and much slower KIF3CC homodimers. To resolve the stepping kinetics of KIF3A and KIF3C motors in homo- and heterodimeric constructs and determine their transport potential under load, we assayed motor activity using interferometric scattering microscopy and optical trapping. The distribution of stepping durations of KIF3AC molecules is described by a rate (k 1 = 11 s-1) without apparent kinetic asymmetry. Asymmetry was also not apparent under hindering or assisting mechanical loads in the optical trap. KIF3AC shows increased force sensitivity relative to KIF3AA yet is more capable of stepping against mechanical load than KIF3CC. Interestingly, the behavior of KIF3C mirrors prior studies of kinesins with increased interhead compliance. Microtubule gliding assays containing 1:1 mixtures of KIF3AA and KIF3CC result in speeds similar to KIF3AC, suggesting the homodimers mechanically impact each other's motility to reproduce the behavior of the heterodimer. Our observations are consistent with a mechanism in which the stepping of KIF3C can be activated by KIF3A in a strain-dependent manner, similar to application of an assisting load. These results suggest that the mechanochemical properties of KIF3AC can be explained by the strain-dependent kinetics of KIF3A and KIF3C.
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13
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Mitochondria-adaptor TRAK1 promotes kinesin-1 driven transport in crowded environments. Nat Commun 2020; 11:3123. [PMID: 32561740 PMCID: PMC7305210 DOI: 10.1038/s41467-020-16972-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 06/02/2020] [Indexed: 01/20/2023] Open
Abstract
Intracellular trafficking of organelles, driven by kinesin-1 stepping along microtubules, underpins essential cellular processes. In absence of other proteins on the microtubule surface, kinesin-1 performs micron-long runs. Under crowding conditions, however, kinesin-1 motility is drastically impeded. It is thus unclear how kinesin-1 acts as an efficient transporter in intracellular environments. Here, we demonstrate that TRAK1 (Milton), an adaptor protein essential for mitochondrial trafficking, activates kinesin-1 and increases robustness of kinesin-1 stepping on crowded microtubule surfaces. Interaction with TRAK1 i) facilitates kinesin-1 navigation around obstacles, ii) increases the probability of kinesin-1 passing through cohesive islands of tau and iii) increases the run length of kinesin-1 in cell lysate. We explain the enhanced motility by the observed direct interaction of TRAK1 with microtubules, providing an additional anchor for the kinesin-1-TRAK1 complex. Furthermore, TRAK1 enables mitochondrial transport in vitro. We propose adaptor-mediated tethering as a mechanism regulating kinesin-1 motility in various cellular environments. Intracellular trafficking of organelles is driven by kinesin-1 stepping along microtubules, but crowding conditions impede kinesin-1 motility. Here authors demonstrate that TRAK1, an adaptor protein essential for mitochondrial trafficking, activates kinesin-1 and increases robustness of kinesin-1 stepping on crowded microtubule surfaces.
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14
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Braun M, Diez S, Lansky Z. Cytoskeletal organization through multivalent interactions. J Cell Sci 2020; 133:133/12/jcs234393. [PMID: 32540925 DOI: 10.1242/jcs.234393] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The cytoskeleton consists of polymeric protein filaments with periodic lattices displaying identical binding sites, which establish a multivalent platform for the binding of a plethora of filament-associated ligand proteins. Multivalent ligand proteins can tether themselves to the filaments through one of their binding sites, resulting in an enhanced reaction kinetics for the remaining binding sites. In this Opinion, we discuss a number of cytoskeletal phenomena underpinned by such multivalent interactions, namely (1) generation of entropic forces by filament crosslinkers, (2) processivity of molecular motors, (3) spatial sorting of proteins, and (4) concentration-dependent unbinding of filament-associated proteins. These examples highlight that cytoskeletal filaments constitute the basis for the formation of microenvironments, which cytoskeletal ligand proteins can associate with and, once engaged, can act within at altered reaction kinetics. We thus argue that multivalency is one of the properties crucial for the functionality of the cytoskeleton.
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Affiliation(s)
- Marcus Braun
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, 25250 Vestec, Prague West, Czech Republic
| | - Stefan Diez
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden 01307, Germany .,Cluster of Excellence Physics of Life, Technische Universität Dresden, Dresden 01307, Germany.,Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
| | - Zdenek Lansky
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, 25250 Vestec, Prague West, Czech Republic
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15
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Feng Q, Gicking AM, Hancock WO. Dynactin p150 promotes processive motility of DDB complexes by minimizing diffusional behavior of dynein. Mol Biol Cell 2020; 31:782-792. [PMID: 32023147 PMCID: PMC7185967 DOI: 10.1091/mbc.e19-09-0495] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 01/08/2020] [Accepted: 01/28/2020] [Indexed: 11/11/2022] Open
Abstract
Cytoplasmic dynein is activated by forming a complex with dynactin and the adaptor protein BicD2. We used interferometric scattering (iSCAT) microscopy to track dynein-dynactin-BicD2 (DDB) complexes in vitro and developed a regression-based algorithm to classify switching between processive, diffusive, and stuck motility states. We find that DDB spends 65% of its time undergoing processive stepping, 4% undergoing 1D diffusion, and the remaining time transiently stuck to the microtubule. Although the p150 subunit was previously shown to enable dynactin diffusion along microtubules, blocking p150 enhanced the proportion of time DDB diffused and reduced the time DDB processively walked. Thus, DDB diffusive behavior most likely results from dynein switching into an inactive (diffusive) state, rather than p150 tethering the complex to the microtubule. DDB-kinesin-1 complexes, formed using a DNA adapter, moved slowly and persistently, and blocking p150 led to a 70 nm/s plus-end shift in the average velocity of the complexes, in quantitative agreement with the shift of isolated DDB into the diffusive state. The data suggest a DDB activation model in which dynactin p150 enhances dynein processivity not solely by acting as a diffusive tether that maintains microtubule association, but rather by acting as an allosteric activator that promotes a conformation of dynein optimal for processive stepping. In bidirectional cargo transport driven by the opposing activities of kinesin and dynein-dynactin-BicD2, the dynactin p150 subunit promotes retrograde transport and could serve as a target for regulators of transport.
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Affiliation(s)
- Qingzhou Feng
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802
- Molecular Cellular and Integrative Biological Sciences Program, Huck Institute of Life Sciences, Pennsylvania State University, University Park, PA 16802
| | - Allison M. Gicking
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802
| | - William O. Hancock
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802
- Molecular Cellular and Integrative Biological Sciences Program, Huck Institute of Life Sciences, Pennsylvania State University, University Park, PA 16802
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16
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Microtubule binding kinetics of membrane-bound kinesin-1 predicts high motor copy numbers on intracellular cargo. Proc Natl Acad Sci U S A 2019; 116:26564-26570. [PMID: 31822619 DOI: 10.1073/pnas.1916204116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bidirectional vesicle transport along microtubules is necessary for cell viability and function, particularly in neurons. When multiple motors are attached to a vesicle, the distance a vesicle travels before dissociating is determined by the race between detachment of the bound motors and attachment of the unbound motors. Motor detachment rate constants (k off) can be measured via single-molecule experiments, but motor reattachment rate constants (k on) are generally unknown, as they involve diffusion through the bilayer, geometrical considerations of the motor tether length, and the intrinsic microtubule binding rate of the motor. To understand the attachment dynamics of motors bound to fluid lipid bilayers, we quantified the microtubule accumulation rate of fluorescently labeled kinesin-1 motors in a 2-dimensional (2D) system where motors were linked to a supported lipid bilayer. From the first-order accumulation rate at varying motor densities, we extrapolated a k off that matched single-molecule measurements and measured a 2D k on for membrane-bound kinesin-1 motors binding to the microtubule. This k on is consistent with kinesin-1 being able to reach roughly 20 tubulin subunits when attaching to a microtubule. By incorporating cholesterol to reduce membrane diffusivity, we demonstrate that this k on is not limited by the motor diffusion rate, but instead is determined by the intrinsic motor binding rate. For intracellular vesicle trafficking, this 2D k on predicts that long-range transport of 100-nm-diameter vesicles requires 35 kinesin-1 motors, suggesting that teamwork between different motor classes and motor clustering may play significant roles in long-range vesicle transport.
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17
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Shi XX, Guo SK, Wang PY, Chen H, Xie P. All-atom molecular dynamics simulations reveal how kinesin transits from one-head-bound to two-heads-bound state. Proteins 2019; 88:545-557. [PMID: 31589786 DOI: 10.1002/prot.25833] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 08/19/2019] [Accepted: 09/17/2019] [Indexed: 12/15/2022]
Abstract
Kinesin dimer walks processively along a microtubule (MT) protofilament in a hand-over-hand manner, transiting alternately between one-head-bound (1HB) and two-heads-bound (2HB) states. In 1HB state, one head bound by adenosine diphosphate (ADP) is detached from MT and the other head is bound to MT. Here, using all-atom molecular dynamics simulations we determined the position and orientation of the detached ADP-head relative to the MT-bound head in 1HB state. We showed that in 1HB state when the MT-bound head is in ADP or nucleotide-free state, with its neck linker being undocked, the detached ADP-head and the MT-bound head have the high binding energy, and after adenosine triphosphate (ATP) binds to the MT-bound head, with its neck linker being docked, the binding energy between the two heads is reduced greatly. These results reveal how the kinesin dimer retains 1HB state before ATP binding and how the dimer transits from 1HB to 2HB state after ATP binding. Key residues involved in the head-head interaction in 1HB state were identified.
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Affiliation(s)
- Xiao-Xuan Shi
- School of Material Science and Engineering, Central South University of Forestry and Technology, Changsha, China.,Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Si-Kao Guo
- Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Peng-Ye Wang
- Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Hong Chen
- School of Materials Science and Energy Engineering, FoShan University, Guangdong, China
| | - Ping Xie
- Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
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18
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Stepp WL, Ökten Z. Resolving kinesin stepping: one head at a time. Life Sci Alliance 2019; 2:2/5/e201900456. [PMID: 31601622 PMCID: PMC6788457 DOI: 10.26508/lsa.201900456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 09/27/2019] [Accepted: 09/27/2019] [Indexed: 11/24/2022] Open
Abstract
Kinesins are well known to power diverse long-range transport processes in virtually all eukaryotic cells. The ATP-dependent processive stepping as well as the regulation of kinesin' activity have, thus, been the focus of extensive studies over the past decades. It is widely accepted that kinesin motors can self-regulate their activity by suppressing the catalytic activity of the "heads." The distal random coil at the C terminus, termed "tail domain," is proposed to mediate this autoinhibition; however, a direct regulatory influence of the tail on the processive stepping of kinesin proved difficult to capture. Here, we simultaneously tracked the two distinct head domains in the kinesin-2 motor using dual-color super resolution microscopy (dcFIONA) and reveal for the first time their individual properties during processive stepping. We show that the autoinhibitory wild-type conformation selectively impacts one head in the heterodimer but not the other. Our results provide insights into the regulated kinesin stepping that had escaped experimental scrutiny so far.
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Affiliation(s)
- Willi L Stepp
- Physik Department E22, Technische Universität München, Garching, Germany
| | - Zeynep Ökten
- Physik Department E22, Technische Universität München, Garching, Germany .,Munich Center for Integrated Protein Science, Munich, Germany
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19
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Mickolajczyk KJ, Cook ASI, Jevtha JP, Fricks J, Hancock WO. Insights into Kinesin-1 Stepping from Simulations and Tracking of Gold Nanoparticle-Labeled Motors. Biophys J 2019; 117:331-345. [PMID: 31301807 DOI: 10.1016/j.bpj.2019.06.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 06/04/2019] [Accepted: 06/10/2019] [Indexed: 02/02/2023] Open
Abstract
High-resolution tracking of gold nanoparticle-labeled proteins has emerged as a powerful technique for measuring the structural kinetics of processive enzymes and other biomacromolecules. These techniques use point spread function (PSF) fitting methods borrowed from single-molecule fluorescence imaging to determine molecular positions below the diffraction limit. However, compared to fluorescence, gold nanoparticle tracking experiments are performed at significantly higher frame rates and utilize much larger probes. In the current work, we use Brownian dynamics simulations of nanoparticle-labeled proteins to investigate the regimes in which the fundamental assumptions of PSF fitting hold and where they begin to break down. We find that because gold nanoparticles undergo tethered diffusion around their anchor point, PSF fitting cannot be extended to arbitrarily fast frame rates. Instead, camera exposure times that allow the nanoparticle to fully populate its stationary positional distribution achieve a spatial averaging that increases fitting precision. We furthermore find that changes in the rotational freedom of the tagged protein can lead to artifactual translations in the fitted particle position. Finally, we apply these lessons to dissect a standing controversy in the kinesin field over the structure of a dimer in the ATP waiting state. Combining new experiments with simulations, we determine that the rear kinesin head in the ATP waiting state is unbound but not displaced from its previous microtubule binding site and that apparent differences in separately published reports were simply due to differences in the gold nanoparticle attachment position. Our results highlight the importance of gold conjugation decisions and imaging parameters to high-resolution tracking results and will serve as a useful guide for the design of future gold nanoparticle tracking experiments.
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Affiliation(s)
- Keith J Mickolajczyk
- Department of Biomedical Engineering; Intercollege Graduate Degree Program in Bioengineering
| | - Annan S I Cook
- Department of Biomedical Engineering; Department of Physics, Pennsylvania State University, University Park, Pennsylvania
| | | | - John Fricks
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, Arizona
| | - William O Hancock
- Department of Biomedical Engineering; Intercollege Graduate Degree Program in Bioengineering.
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20
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Affiliation(s)
- Charles V Sindelar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut.
| | - Daifei Liu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
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21
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Abstract
Kinesin motor proteins that drive intracellular transport share an overall architecture of two motor domain-containing subunits that dimerize through a coiled-coil stalk. Dimerization allows kinesins to be processive motors, taking many steps along the microtubule track before detaching. However, whether dimerization is required for intracellular transport remains unknown. Here, we address this issue using a combination of in vitro and cellular assays to directly compare dimeric motors across the kinesin-1, -2, and -3 families to their minimal monomeric forms. Surprisingly, we find that monomeric motors are able to work in teams to drive peroxisome dispersion in cells. However, peroxisome transport requires minimal force output, and we find that most monomeric motors are unable to disperse the Golgi complex, a high-load cargo. Strikingly, monomeric versions of the kinesin-2 family motors KIF3A and KIF3B are able to drive Golgi dispersion in cells, and teams of monomeric KIF3B motors can generate over 8 pN of force in an optical trap. We find that intracellular transport and force output by monomeric motors, but not dimeric motors, are significantly decreased by the addition of longer and more flexible motor-to-cargo linkers. Together, these results suggest that dimerization of kinesin motors is not required for intracellular transport; however, it enables motor-to-motor coordination and high force generation regardless of motor-to-cargo distance. Dimerization of kinesin motors is thus critical for cellular events that require an ability to generate or withstand high forces.
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22
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Abstract
This chapter describes methods for high-speed, unloaded, in vitro single-molecule kinesin tracking experiments. Instructions are presented for constructing a total internal reflection dark-field microscope (TIRDFM) and labeling motors with gold nanoparticles. An AMP-PNP unlocking assay is introduced as a specialized means of capturing processive events in a reduced field of view. Finally, step-finding tools for analyzing high frame-rate tracking data are described.
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23
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Gicking AM, Wang P, Liu C, Mickolajczyk KJ, Guo L, Hancock WO, Qiu W. The Orphan Kinesin PAKRP2 Achieves Processive Motility via a Noncanonical Stepping Mechanism. Biophys J 2019; 116:1270-1281. [PMID: 30902363 DOI: 10.1016/j.bpj.2019.02.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 02/07/2019] [Accepted: 02/19/2019] [Indexed: 12/27/2022] Open
Abstract
Phragmoplast-associated kinesin-related protein 2 (PAKRP2) is an orphan kinesin in Arabidopsis thaliana that is thought to transport vesicles along phragmoplast microtubules for cell plate formation. Here, using single-molecule fluorescence microscopy, we show that PAKRP2 is the first orphan kinesin to exhibit processive plus-end-directed motility on single microtubules as individual homodimers. Our results show that PAKRP2 processivity is achieved despite having an exceptionally long (32 residues) neck linker. Furthermore, using high-resolution nanoparticle tracking, we find that PAKRP2 steps via a hand-over-hand mechanism that includes frequent side steps, a prolonged diffusional search of the tethered head, and tight coupling of the ATP hydrolysis cycle to the forward-stepping cycle. Interestingly, truncating the PAKRP2 neck linker to 14 residues decreases the run length of PAKRP2; thus, the long neck linker enhances the processive behavior. Based on the canonical model of kinesin stepping, such a long neck linker is expected to decrease the processivity and disrupt the coupling of ATP hydrolysis to forward stepping. Therefore, we conclude that PAKRP2 employs a noncanonical strategy for processive motility, wherein a long neck linker is coupled with a slow ATP hydrolysis rate to allow for an extended diffusional search during each step without sacrificing processivity or efficiency.
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Affiliation(s)
| | - Pan Wang
- Department of Physics, Oregon State University, Corvallis, Oregon; School of Physics and Electronics, Henan University, Kaifeng, Henan, China
| | - Chun Liu
- Pearl River Fisheries Research Institute, Guangzhou, China
| | - Keith J Mickolajczyk
- Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania; Intercollege Graduate Degree Program in Bioengineering, Penn State University, University Park, Pennsylvania
| | - Lijun Guo
- School of Physics and Electronics, Henan University, Kaifeng, Henan, China
| | - William O Hancock
- Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania; Intercollege Graduate Degree Program in Bioengineering, Penn State University, University Park, Pennsylvania
| | - Weihong Qiu
- Department of Physics, Oregon State University, Corvallis, Oregon; Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon.
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24
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Direct observation of individual tubulin dimers binding to growing microtubules. Proc Natl Acad Sci U S A 2019; 116:7314-7322. [PMID: 30804205 DOI: 10.1073/pnas.1815823116] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The biochemical basis of microtubule growth has remained elusive for over 30 years despite being fundamental for both cell division and associated chemotherapy strategies. Here, we combine interferometric scattering microscopy with recombinant tubulin to monitor individual tubulins binding to and dissociating from growing microtubule tips. We make direct, single-molecule measurements of tubulin association and dissociation rates. We detect two populations of transient dwell times and determine via binding-interface mutants that they are distinguished by the formation of one interprotofilament bond. Applying a computational model, we find that slow association kinetics with strong interactions along protofilaments best recapitulate our data and, furthermore, predicts plus-end tapering. Overall, we provide the most direct and complete experimental quantification of how microtubules grow to date.
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25
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Force Dependence of Velocity and Run Length of Kinesin-1, Kinesin-2 and Kinesin-5 Family Molecular Motors. Molecules 2019; 24:molecules24020287. [PMID: 30646587 PMCID: PMC6358798 DOI: 10.3390/molecules24020287] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/10/2019] [Accepted: 01/11/2019] [Indexed: 11/17/2022] Open
Abstract
Kinesin-1, kinesin-2 and kinesin-5 are three families of a superfamily of motor proteins; which can walk processively on microtubule filaments by hydrolyzing ATP. It was experimentally shown that while the three kinesin dimers show similar feature on the force dependence of velocity, they show rather different features on the force dependence of run length. However, why the three families of kinesins show these rather different features is unclear. Here, we computationally studied the movement dynamics of the three dimers based on our proposed model. The simulated results reproduce well the available experimental data on the force dependence of velocity and run length. Moreover, the simulated results on the velocity and run length for the three dimers with altered neck linker lengths are also in quantitative agreement with the available experimental data. The studies indicate that the three families of kinesins show much similar movement mechanism and the rather different features on the force dependence of run length arise mainly from the difference in rate constants of the ATPase activity and neck linker docking. Additionally, the asymmetric (limping) movement dynamics of the three families of homodimers with and without altered neck linker lengths are studied, providing predicted results.
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26
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Popchock AR, Jana S, Mehl RA, Qiu W. Engineering Heterodimeric Kinesins through Genetic Incorporation of Noncanonical Amino Acids. ACS Chem Biol 2018; 13:2229-2236. [PMID: 29894152 DOI: 10.1021/acschembio.8b00399] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Kinesins are commonly homodimers with two identical heavy chains (protomers) and play indispensable roles in many intracellular processes. Engineered heterodimeric kinesins with two distinct protomers are important tools for dissecting coordination and regulation of naturally occurring kinesin homodimers. Here, we report a chemical-biology-based approach that generates kinesin heterodimers by combining genetic incorporation of reactive noncanonical amino acids and small-molecule-based cross-linking. We verified using yeast kinesin-8/Kip3 as a model system that our method yields kinesin heterodimers of desired properties without introducing unintended motility disruption. To demonstrate the utility of our method, we engineered a crippled Kip3 heterodimer that contains both a wild-type-like protomer and a catalytically inactive one, and our results revealed that the resulting heterodimer moves on the microtubule with a significant reduction in velocity but not processivity. Due to its versatility, we expect that our method can be broadly adopted to create novel heterodimers for other kinesins and will thus greatly expand the studies on kinesin mechanisms.
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Affiliation(s)
- Andrew R. Popchock
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Subhashis Jana
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Ryan A. Mehl
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Weihong Qiu
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
- Department of Physics, Oregon State University, Corvallis, Oregon 97331, United States
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27
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Directionally biased sidestepping of Kip3/kinesin-8 is regulated by ATP waiting time and motor-microtubule interaction strength. Proc Natl Acad Sci U S A 2018; 115:E7950-E7959. [PMID: 30093386 DOI: 10.1073/pnas.1801820115] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Kinesin-8 motors, which move in a highly processive manner toward microtubule plus ends where they act as depolymerases, are essential regulators of microtubule dynamics in cells. To understand their navigation strategy on the microtubule lattice, we studied the 3D motion of single yeast kinesin-8 motors, Kip3, on freely suspended microtubules in vitro. We observed short-pitch, left-handed helical trajectories indicating that kinesin-8 motors frequently switch protofilaments in a directionally biased manner. Intriguingly, sidestepping was not directly coupled to forward stepping but rather depended on the average dwell time per forward step under limiting ATP concentrations. Based on our experimental findings and numerical simulations we propose that effective sidestepping toward the left is regulated by a bifurcation in the Kip3 step cycle, involving a transition from a two-head-bound to a one-head-bound conformation in the ATP-waiting state. Results from a kinesin-1 mutant with extended neck linker hint toward a generic sidestepping mechanism for processive kinesins, facilitating the circumvention of intracellular obstacles on the microtubule surface.
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28
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Guo SK, Shi XX, Wang PY, Xie P. Processivity of dimeric kinesin-1 molecular motors. FEBS Open Bio 2018; 8:1332-1351. [PMID: 30087836 PMCID: PMC6070657 DOI: 10.1002/2211-5463.12486] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 06/19/2018] [Accepted: 06/25/2018] [Indexed: 11/25/2022] Open
Abstract
Kinesin‐1 is a homodimeric motor protein that can move along microtubule filaments by hydrolyzing ATP with a high processivity. How the two motor domains are coordinated to achieve such high processivity is not clear. To address this issue, we computationally studied the run length of the dimer with our proposed model. The computational data quantitatively reproduced the puzzling experimental data, including the dramatically asymmetric character of the run length with respect to the direction of external load acting on the coiled‐coil stalk, the enhancement of the run length by addition of phosphate, and the contrary features of the run length for different types of kinesin‐1 with extensions of their neck linkers compared with those without extension of the neck linker. The computational data on other aspects of the movement dynamics such as velocity and durations of one‐head‐bound and two‐head‐bound states in a mechanochemical coupling cycle were also in quantitative agreement with the available experimental data. Moreover, predicted results are provided on dependence of the run length upon external load acting on one head of the dimer, which can be easily tested in the future using single‐molecule optical trapping assays.
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Affiliation(s)
- Si-Kao Guo
- Key Laboratory of Soft Matter Physics Beijing National Laboratory for Condensed Matter Physics Institute of Physics Chinese Academy of Science Beijing China.,School of Physical Sciences University of Chinese Academy of Sciences Beijing China
| | - Xiao-Xuan Shi
- Key Laboratory of Soft Matter Physics Beijing National Laboratory for Condensed Matter Physics Institute of Physics Chinese Academy of Science Beijing China.,School of Physical Sciences University of Chinese Academy of Sciences Beijing China
| | - Peng-Ye Wang
- Key Laboratory of Soft Matter Physics Beijing National Laboratory for Condensed Matter Physics Institute of Physics Chinese Academy of Science Beijing China.,School of Physical Sciences University of Chinese Academy of Sciences Beijing China
| | - Ping Xie
- Key Laboratory of Soft Matter Physics Beijing National Laboratory for Condensed Matter Physics Institute of Physics Chinese Academy of Science Beijing China.,School of Physical Sciences University of Chinese Academy of Sciences Beijing China
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29
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Nord AL, Pols AF, Depken M, Pedaci F. Kinetic analysis methods applied to single motor protein trajectories. Phys Chem Chem Phys 2018; 20:18775-18781. [PMID: 29961801 DOI: 10.1039/c8cp03056a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
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 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.
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Affiliation(s)
- A L Nord
- CBS, Univ. Montpellier, CNRS, INSERM, Montpellier, France.
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30
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Gilbert SP, Guzik-Lendrum S, Rayment I. Kinesin-2 motors: Kinetics and biophysics. J Biol Chem 2018; 293:4510-4518. [PMID: 29444824 DOI: 10.1074/jbc.r117.001324] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Kinesin-2s are major transporters of cellular cargoes. This subfamily contains both homodimeric kinesins whose catalytic domains result from the same gene product and heterodimeric kinesins with motor domains derived from two different gene products. In this Minireview, we focus on the progress to define the biochemical and biophysical properties of the kinesin-2 family members. Our understanding of their mechanochemical capabilities has been advanced by the ability to identify the kinesin-2 genes in multiple species, expression and purification of these motors for single-molecule and ensemble assays, and development of new technologies enabling quantitative measurements of kinesin activity with greater sensitivity.
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Affiliation(s)
- Susan P Gilbert
- From the Department of Biological Sciences and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180 and
| | - Stephanie Guzik-Lendrum
- From the Department of Biological Sciences and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180 and
| | - Ivan Rayment
- the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
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31
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Feng Q, Mickolajczyk KJ, Chen GY, Hancock WO. Motor Reattachment Kinetics Play a Dominant Role in Multimotor-Driven Cargo Transport. Biophys J 2018; 114:400-409. [PMID: 29401437 PMCID: PMC5985011 DOI: 10.1016/j.bpj.2017.11.016] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/10/2017] [Accepted: 11/13/2017] [Indexed: 01/10/2023] Open
Abstract
Kinesin-based cargo transport in cells frequently involves the coordinated activity of multiple motors, including kinesins from different families that move at different speeds. However, compared to the progress at the single-molecule level, mechanisms by which multiple kinesins coordinate their activity during cargo transport are poorly understood. To understand these multimotor coordination mechanisms, defined pairs of kinesin-1 and kinesin-2 motors were assembled on DNA scaffolds and their motility examined in vitro. Although less processive than kinesin-1 at the single-molecule level, addition of kinesin-2 motors more effectively amplified cargo run lengths. By applying the law of total expectation to cargo binding durations in ADP, the kinesin-2 microtubule reattachment rate was shown to be fourfold faster than that of kinesin-1. This difference in microtubule binding rates was also observed in solution by stopped-flow. High-resolution tracking of a gold-nanoparticle-labeled motor with 1 ms and 2 nm precision revealed that kinesin-2 motors detach and rebind to the microtubule much more frequently than does kinesin-1. Finally, compared to cargo transported by two kinesin-1, cargo transported by two kinesin-2 motors more effectively navigated roadblocks on the microtubule track. These results highlight the importance of motor reattachment kinetics during multimotor transport and suggest a coordinated transport model in which kinesin-1 motors step effectively against loads whereas kinesin-2 motors rapidly unbind and rebind to the microtubule. This dynamic tethering by kinesin-2 maintains the cargo near the microtubule and enables effective navigation along crowded microtubules.
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Affiliation(s)
- Qingzhou Feng
- Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania; Molecular Cellular and Integrative Biological Sciences Program in Huck Institute of Life Sciences, Penn State University, University Park, Pennsylvania
| | - Keith J Mickolajczyk
- Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania; Intercollege Graduate Degree Program in Bioengineering, Penn State University, University Park, Pennsylvania
| | - Geng-Yuan Chen
- Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania; Intercollege Graduate Degree Program in Bioengineering, Penn State University, University Park, Pennsylvania
| | - William O Hancock
- Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania; Intercollege Graduate Degree Program in Bioengineering, Penn State University, University Park, Pennsylvania; Molecular Cellular and Integrative Biological Sciences Program in Huck Institute of Life Sciences, Penn State University, University Park, Pennsylvania.
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