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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Genova M, Grycova L, Puttrich V, Magiera MM, Lansky Z, Janke C, Braun M. Tubulin polyglutamylation differentially regulates microtubule-interacting proteins. EMBO J 2023; 42:e112101. [PMID: 36636822 PMCID: PMC9975938 DOI: 10.15252/embj.2022112101] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 12/16/2022] [Accepted: 12/22/2022] [Indexed: 01/14/2023] Open
Abstract
Tubulin posttranslational modifications have been predicted to control cytoskeletal functions by coordinating the molecular interactions between microtubules and their associating proteins. A prominent tubulin modification in neurons is polyglutamylation, the deregulation of which causes neurodegeneration. Yet, the underlying molecular mechanisms have remained elusive. Here, using in-vitro reconstitution, we determine how polyglutamylation generated by the two predominant neuronal polyglutamylases, TTLL1 and TTLL7, specifically modulates the activities of three major microtubule interactors: the microtubule-associated protein Tau, the microtubule-severing enzyme katanin and the molecular motor kinesin-1. We demonstrate that the unique modification patterns generated by TTLL1 and TTLL7 differentially impact those three effector proteins, thus allowing for their selective regulation. Given that our experiments were performed with brain tubulin from mouse models in which physiological levels and patterns of polyglutamylation were altered by the genetic knockout of the main modifying enzymes, our quantitative measurements provide direct mechanistic insight into how polyglutamylation could selectively control microtubule interactions in neurons.
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Affiliation(s)
- Mariya Genova
- Institut Curie, Université PSL, CNRS UMR3348OrsayFrance
- Université Paris‐Saclay, CNRS UMR3348OrsayFrance
| | - Lenka Grycova
- Institute of BiotechnologyCzech Academy of Sciences, BIOCEVPrague WestCzech Republic
| | - Verena Puttrich
- Institute of BiotechnologyCzech Academy of Sciences, BIOCEVPrague WestCzech Republic
| | - Maria M Magiera
- Institut Curie, Université PSL, CNRS UMR3348OrsayFrance
- Université Paris‐Saclay, CNRS UMR3348OrsayFrance
| | - Zdenek Lansky
- Institute of BiotechnologyCzech Academy of Sciences, BIOCEVPrague WestCzech Republic
| | - Carsten Janke
- Institut Curie, Université PSL, CNRS UMR3348OrsayFrance
- Université Paris‐Saclay, CNRS UMR3348OrsayFrance
| | - Marcus Braun
- Institute of BiotechnologyCzech Academy of Sciences, BIOCEVPrague WestCzech Republic
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3
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Feng Q, Gicking AM, Hancock WO. High-Resolution Tracking of Dynein-Dynactin-BicD2 Complexes. Methods Mol Biol 2023; 2623:177-186. [PMID: 36602686 DOI: 10.1007/978-1-0716-2958-1_11] [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: 06/17/2023]
Abstract
The adapter dynactin and the activator BicD2 associate with dynein to form the highly motile dynein-dynactin-BicD2 (DDB) complex. In single-molecule assays, DDB displays processive runs, diffusive episodes, and transient pauses. The switching rates and durations of the different phases can be determined by tracking gold nanoparticle-labeled DDB complexes with interferometric scattering (iSCAT) microscopy and using an algorithm to separate out different motility phases. Here we describe methods for purifying DDB complexes from brain lysate, labeling with gold nanoparticles, imaging by iSCAT, and analyzing the resulting trajectories.
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Affiliation(s)
- Qingzhou Feng
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
| | - Allison M Gicking
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
| | - William O Hancock
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA.
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4
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Puttrich V, Rohlena J, Braun M, Lansky Z. In Vitro Reconstitution of Molecular Motor-Driven Mitochondrial Transport. Methods Mol Biol 2022; 2431:533-546. [PMID: 35412296 DOI: 10.1007/978-1-0716-1990-2_28] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Intracellular trafficking of organelles driven by molecular motors underlies essential cellular processes. Mitochondria, the powerhouses of the cell, are one of the major cargoes of molecular motors. Efficient distribution of mitochondria ensures cellular fitness while defects in this process contribute to severe pathologies, such as neurodegenerative diseases. Reconstitution of the mitochondrial microtubule-based transport in vitro in a bottom-up approach provides a powerful tool to investigate the mitochondrial trafficking machinery in a controlled environment in the absence of complex intracellular interactions. In this chapter, we describe the procedures for achieving such reconstitution of mitochondrial transport.
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Affiliation(s)
- Verena Puttrich
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Prague West, Czech Republic
| | - Jakub Rohlena
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Prague West, Czech Republic
| | - Marcus Braun
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Prague West, Czech Republic
| | - Zdenek Lansky
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Prague West, Czech Republic.
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5
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Urbanska M, Lüdecke A, Walter WJ, van Oijen AM, Duderstadt KE, Diez S. Highly-Parallel Microfluidics-Based Force Spectroscopy on Single Cytoskeletal Motors. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2007388. [PMID: 33759372 DOI: 10.1002/smll.202007388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/22/2021] [Indexed: 06/12/2023]
Abstract
Cytoskeletal motors transform chemical energy into mechanical work to drive essential cellular functions. Optical trapping experiments have provided crucial insights into the operation of these molecular machines under load. However, the throughput of such force spectroscopy experiments is typically limited to one measurement at a time. Here, a highly-parallel, microfluidics-based method that allows for rapid collection of force-dependent motility parameters of cytoskeletal motors with two orders of magnitude improvement in throughput compared to currently available methods is introduced. Tunable hydrodynamic forces to stepping kinesin-1 motors via DNA-tethered beads and utilize a large field of view to simultaneously track the velocities, run lengths, and interaction times of hundreds of individual kinesin-1 molecules under varying resisting and assisting loads are applied. Importantly, the 16 µm long DNA tethers between the motors and the beads significantly reduces the vertical component of the applied force pulling the motors away from the microtubule. The approach is readily applicable to other molecular systems and constitutes a new methodology for parallelized single-molecule force studies on cytoskeletal motors.
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Affiliation(s)
- Marta Urbanska
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, 01069, Dresden, Germany
| | - Annemarie Lüdecke
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, 01069, Dresden, Germany
| | - Wilhelm J Walter
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, 01069, Dresden, Germany
| | - Antoine M van Oijen
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, AE, 9700, Netherlands
- Molecular Horizons, University of Wollongong, Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia
| | - Karl E Duderstadt
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, AE, 9700, Netherlands
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
- Physics Department, Technische Universität München, 85748, Garching, Germany
| | - Stefan Diez
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, 01069, Dresden, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, 01062, Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
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6
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Budaitis BG, Jariwala S, Rao L, Yue Y, Sept D, Verhey KJ, Gennerich A. Pathogenic mutations in the kinesin-3 motor KIF1A diminish force generation and movement through allosteric mechanisms. J Cell Biol 2021; 220:211720. [PMID: 33496723 PMCID: PMC7844421 DOI: 10.1083/jcb.202004227] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 10/27/2020] [Accepted: 12/30/2020] [Indexed: 02/07/2023] Open
Abstract
The kinesin-3 motor KIF1A functions in neurons, where its fast and superprocessive motility facilitates long-distance transport, but little is known about its force-generating properties. Using optical tweezers, we demonstrate that KIF1A stalls at an opposing load of ~3 pN but more frequently detaches at lower forces. KIF1A rapidly reattaches to the microtubule to resume motion due to its class-specific K-loop, resulting in a unique clustering of force generation events. To test the importance of neck linker docking in KIF1A force generation, we introduced mutations linked to human neurodevelopmental disorders. Molecular dynamics simulations predict that V8M and Y89D mutations impair neck linker docking. Indeed, both mutations dramatically reduce the force generation of KIF1A but not the motor’s ability to rapidly reattach to the microtubule. Although both mutations relieve autoinhibition of the full-length motor, the mutant motors display decreased velocities, run lengths, and landing rates and delayed cargo transport in cells. These results advance our understanding of how mutations in KIF1A can manifest in disease.
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Affiliation(s)
- Breane G Budaitis
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI
| | - Shashank Jariwala
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI.,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI
| | - Lu Rao
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, New York, NY
| | - Yang Yue
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - David Sept
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI
| | - Kristen J Verhey
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI.,Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Arne Gennerich
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, New York, NY
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7
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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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8
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Zhernov I, Diez S, Braun M, Lansky Z. Intrinsically Disordered Domain of Kinesin-3 Kif14 Enables Unique Functional Diversity. Curr Biol 2020; 30:3342-3351.e5. [PMID: 32649913 DOI: 10.1016/j.cub.2020.06.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 05/06/2020] [Accepted: 06/11/2020] [Indexed: 12/12/2022]
Abstract
In addition to their force-generating motor domains, kinesin motor proteins feature various accessory domains enabling them to fulfill a variety of functions in the cell. Human kinesin-3, Kif14, localizes to the midbody of the mitotic spindle and is involved in the progression of cytokinesis. The specific motor properties enabling Kif14's cellular functions, however, remain unknown. Here, we show in vitro that the intrinsically disordered N-terminal domain of Kif14 enables unique functional diversity of the kinesin. Using single molecule TIRF microscopy, we found that Kif14 exists either as a diffusible monomer or as processive dimer and that the disordered domain (1) enables diffusibility of the monomeric Kif14, (2) renders the dimeric Kif14 super-processive and enables the kinesin to pass through highly crowded areas, (3) enables robust, autonomous Kif14 tracking of growing microtubule tips, independent of microtubule end-binding (EB) proteins, and (4) is sufficient to enable crosslinking of parallel microtubules and necessary to enable Kif14-driven sliding of antiparallel ones. We explain these features of Kif14 by the observed diffusible interaction of the disordered domain with the microtubule lattice and the observed increased affinity of the disordered domain for GTP-bound tubulin. We suggest that the disordered domain tethers the motor domain to the microtubule providing a diffusible foothold and a regulatory hub, tuning the kinesin's interaction with microtubules. Our findings thus exemplify pliable protein tethering as a fundamental mechanism of molecular motor regulation.
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Affiliation(s)
- Ilia Zhernov
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Prague West, Czech Republic; Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16 Prague, Czech Republic
| | - Stefan Diez
- B CUBE - Center for Molecular Bioengineering, TU Dresden, Tatzberg 41, 01307 Dresden, Germany; Cluster of Excellence Physics of Life, TU Dresden, Tatzberg 47/49, 01307 Dresden, Germany; Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, Dresden 01307, Germany
| | - Marcus Braun
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Prague West, Czech Republic.
| | - Zdenek Lansky
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Prague West, Czech Republic.
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9
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Kinesin-14 motors drive a right-handed helical motion of antiparallel microtubules around each other. Nat Commun 2020; 11:2565. [PMID: 32444784 PMCID: PMC7244531 DOI: 10.1038/s41467-020-16328-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 04/08/2020] [Indexed: 12/30/2022] Open
Abstract
Within the mitotic spindle, kinesin motors cross-link and slide overlapping microtubules. Some of these motors exhibit off-axis power strokes, but their impact on motility and force generation in microtubule overlaps has not been investigated. Here, we develop and utilize a three-dimensional in vitro motility assay to explore kinesin-14, Ncd, driven sliding of cross-linked microtubules. We observe that free microtubules, sliding on suspended microtubules, not only rotate around their own axis but also move around the suspended microtubules with right-handed helical trajectories. Importantly, the associated torque is large enough to cause microtubule twisting and coiling. Further, our technique allows us to measure the in situ spatial extension of the motors between cross-linked microtubules to be about 20 nm. We argue that the capability of microtubule-crosslinking kinesins to cause helical motion of overlapping microtubules around each other allows for flexible filament organization, roadblock circumvention and torque generation in the mitotic spindle. Some kinesins exhibit off-axis power strokes but their impact on motility and force generation in microtubule overlaps has not been investigated so far. Here authors use a 3D in vitro motility assay and find that Ndc’s off-axis motor forces generate torque in antiparallel microtubules which causes microtubule twisting and coiling.
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10
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Sudhakar S, Jachowski TJ, Kittelberger M, Maqbool A, Hermsdorf GL, Abdosamadi MK, Schäffer E. Supported Solid Lipid Bilayers as a Platform for Single-Molecule Force Measurements. NANO LETTERS 2019; 19:8877-8886. [PMID: 31746618 DOI: 10.1021/acs.nanolett.9b03761] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Biocompatible surfaces are important for basic and applied research in life science with experiments ranging from the organismal to the single-molecule level. For the latter, examples include the translocation of kinesin motor proteins along microtubule cytoskeletal filaments or the study of DNA-protein interactions. Such experiments often employ single-molecule fluorescence or force microscopy. In particular for force measurements, a key requirement is to prevent nonspecific interactions of biomolecules and force probes with the surface, while providing specific attachments that can sustain loads. Common approaches to reduce nonspecific interactions include supported lipid bilayers or PEGylated surfaces. However, fluid lipid bilayers do not support loads and PEGylation may require harsh chemical surface treatments and have limited reproducibility. Here, we developed and applied a supported solid lipid bilayer (SSLB) as a platform for specific, load bearing attachments with minimal nonspecific interactions. Apart from single-molecule fluorescence measurements, anchoring molecules to lipids in the solid phase enabled us to perform force measurements of molecular motors and overstretch DNA. Furthermore, using a heating laser, we could switch the SSLB to its fluid state allowing for manipulation of anchoring points. The assay had little nonspecific interactions, was robust, reproducible, and time-efficient, and required less hazardous and toxic chemicals for preparation. In the long term, we expect that SSLBs can be widely employed for single-molecule fluorescence microscopy, force spectroscopy, and cellular assays in mechanobiology.
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Affiliation(s)
- Swathi Sudhakar
- Eberheard Karls Universität Tübingen , ZMBP , Auf der Morgenstelle 32 , 72076 Tübingen , Germany
| | - Tobias Jörg Jachowski
- Eberheard Karls Universität Tübingen , ZMBP , Auf der Morgenstelle 32 , 72076 Tübingen , Germany
| | - Michael Kittelberger
- Eberheard Karls Universität Tübingen , ZMBP , Auf der Morgenstelle 32 , 72076 Tübingen , Germany
| | - Ammara Maqbool
- Eberheard Karls Universität Tübingen , ZMBP , Auf der Morgenstelle 32 , 72076 Tübingen , Germany
| | - Gero Lutz Hermsdorf
- Eberheard Karls Universität Tübingen , ZMBP , Auf der Morgenstelle 32 , 72076 Tübingen , Germany
| | | | - Erik Schäffer
- Eberheard Karls Universität Tübingen , ZMBP , Auf der Morgenstelle 32 , 72076 Tübingen , Germany
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11
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Rahman MA, Reuther C, Lindberg FW, Mengoni M, Salhotra A, Heldt G, Linke H, Diez S, Månsson A. Regeneration of Assembled, Molecular-Motor-Based Bionanodevices. NANO LETTERS 2019; 19:7155-7163. [PMID: 31512480 DOI: 10.1021/acs.nanolett.9b02738] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The guided gliding of cytoskeletal filaments, driven by biomolecular motors on nano/microstructured chips, enables novel applications in biosensing and biocomputation. However, expensive and time-consuming chip production hampers the developments. It is therefore important to establish protocols to regenerate the chips, preferably without the need to dismantle the assembled microfluidic devices which contain the structured chips. We here describe a novel method toward this end. Specifically, we use the small, nonselective proteolytic enzyme, proteinase K to cleave all surface-adsorbed proteins, including myosin and kinesin motors. Subsequently, we apply a detergent (5% SDS or 0.05% Triton X100) to remove the protein remnants. After this procedure, fresh motor proteins and filaments can be added for new experiments. Both, silanized glass surfaces for actin-myosin motility and pure glass surfaces for microtubule-kinesin motility were repeatedly regenerated using this approach. Moreover, we demonstrate the applicability of the method for the regeneration of nano/microstructured silicon-based chips with selectively functionalized areas for supporting or suppressing gliding motility for both motor systems. The results substantiate the versatility and a promising broad use of the method for regenerating a wide range of protein-based nano/microdevices.
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Affiliation(s)
- Mohammad A Rahman
- Department of Chemistry and Biomedical Sciences , Linnaeus University , Kalmar , Sweden , 39182
| | - Cordula Reuther
- B CUBE - Center for Molecular Bioengineering , Technische Universität Dresden , Sachsen , Germany , 01062
- Max Planck Institute of Molecular Cell Biology and Genetics , 01307 Dresden , Germany
| | | | - Martina Mengoni
- B CUBE - Center for Molecular Bioengineering , Technische Universität Dresden , Sachsen , Germany , 01062
- Max Planck Institute of Molecular Cell Biology and Genetics , 01307 Dresden , Germany
| | - Aseem Salhotra
- Department of Chemistry and Biomedical Sciences , Linnaeus University , Kalmar , Sweden , 39182
| | - Georg Heldt
- Fraunhofer Institute for Electronic Nano Systems , Chemnitz , Germany 09126
| | | | - Stefan Diez
- B CUBE - Center for Molecular Bioengineering , Technische Universität Dresden , Sachsen , Germany , 01062
- Max Planck Institute of Molecular Cell Biology and Genetics , 01307 Dresden , Germany
| | - Alf Månsson
- Department of Chemistry and Biomedical Sciences , Linnaeus University , Kalmar , Sweden , 39182
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12
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Berger F, Klumpp S, Lipowsky R. Force-Dependent Unbinding Rate of Molecular Motors from Stationary Optical Trap Data. NANO LETTERS 2019; 19:2598-2602. [PMID: 30835477 DOI: 10.1021/acs.nanolett.9b00417] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Molecular motors walk along filaments until they detach stochastically with a force-dependent unbinding rate. Here, we show how this unbinding rate can be obtained from the analysis of experimental data of molecular motors moving in stationary optical traps. Two complementary methods are presented, based on the analysis of the distribution for the unbinding forces and of the motor's force traces. In the first method, analytically derived force distributions for slip bonds, slip-ideal bonds, and catch bonds are used to fit the cumulative distributions of the unbinding forces. The second method is based on the statistical analysis of the observed force traces. We validate both methods with stochastic simulations and apply them to experimental data for kinesin-1.
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Affiliation(s)
- Florian Berger
- Laboratory of Sensory Neuroscience , The Rockefeller University , New York , New York 10065 , United States
| | - Stefan Klumpp
- Institute for the Dynamics of Complex Systems , Georg-August University Göttingen , 37077 Göttingen , Germany
| | - Reinhard Lipowsky
- Theory and Bio-Systems , Max Planck Institute of Colloids and Interfaces , 14424 Potsdam , Germany
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13
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MTrack: Automated Detection, Tracking, and Analysis of Dynamic Microtubules. Sci Rep 2019; 9:3794. [PMID: 30846705 PMCID: PMC6405942 DOI: 10.1038/s41598-018-37767-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 12/05/2018] [Indexed: 11/11/2022] Open
Abstract
Microtubules are polar, dynamic filaments fundamental to many cellular processes. In vitro reconstitution approaches with purified tubulin are essential to elucidate different aspects of microtubule behavior. To date, deriving data from fluorescence microscopy images by manually creating and analyzing kymographs is still commonplace. Here, we present MTrack, implemented as a plug-in for the open-source platform Fiji, which automatically identifies and tracks dynamic microtubules with sub-pixel resolution using advanced objection recognition. MTrack provides automatic data interpretation yielding relevant parameters of microtubule dynamic instability together with population statistics. The application of our software produces unbiased and comparable quantitative datasets in a fully automated fashion. This helps the experimentalist to achieve higher reproducibility at higher throughput on a user-friendly platform. We use simulated data and real data to benchmark our algorithm and show that it reliably detects, tracks, and analyzes dynamic microtubules and achieves sub-pixel precision even at low signal-to-noise ratios.
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14
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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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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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