1
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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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2
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Zhang C, Guo C, Russell RW, Quinn CM, Li M, Williams JC, Gronenborn AM, Polenova T. Magic-angle-spinning NMR structure of the kinesin-1 motor domain assembled with microtubules reveals the elusive neck linker orientation. Nat Commun 2022; 13:6795. [PMID: 36357375 PMCID: PMC9649657 DOI: 10.1038/s41467-022-34026-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 10/10/2022] [Indexed: 11/12/2022] Open
Abstract
Microtubules (MTs) and their associated proteins play essential roles in maintaining cell structure, organelle transport, cell motility, and cell division. Two motors, kinesin and cytoplasmic dynein link the MT network to transported cargos using ATP for force generation. Here, we report an all-atom NMR structure of nucleotide-free kinesin-1 motor domain (apo-KIF5B) in complex with paclitaxel-stabilized microtubules using magic-angle-spinning (MAS) NMR spectroscopy. The structure reveals the position and orientation of the functionally important neck linker and how ADP induces structural and dynamic changes that ensue in the neck linker. These results demonstrate that the neck linker is in the undocked conformation and oriented in the direction opposite to the KIF5B movement. Chemical shift perturbations and intensity changes indicate that a significant portion of ADP-KIF5B is in the neck linker docked state. This study also highlights the unique capability of MAS NMR to provide atomic-level information on dynamic regions of biological assemblies.
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Affiliation(s)
- Chunting Zhang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Changmiao Guo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Ryan W Russell
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Caitlin M Quinn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Mingyue Li
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - John C Williams
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA, USA.
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA, 15261, USA.
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA.
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA, 15261, USA.
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3
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Cytoskeletal regulation of a transcription factor by DNA mimicry via coiled-coil interactions. Nat Cell Biol 2022; 24:1088-1098. [PMID: 35725768 PMCID: PMC10016618 DOI: 10.1038/s41556-022-00935-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 05/06/2022] [Indexed: 02/07/2023]
Abstract
A long-established strategy for transcription regulation is the tethering of transcription factors to cellular membranes. By contrast, the principal effectors of Hedgehog signalling, the GLI transcription factors, are regulated by microtubules in the primary cilium and the cytoplasm. How GLI is tethered to microtubules remains unclear. Here, we uncover DNA mimicry by the ciliary kinesin KIF7 as a mechanism for the recruitment of GLI to microtubules, wherein the coiled-coil dimerization domain of KIF7, characterized by its striking shape, size and charge similarity to DNA, forms a complex with the DNA-binding zinc fingers in GLI, thus revealing a mode of tethering a DNA-binding protein to the cytoskeleton. GLI increases KIF7 microtubule affinity and consequently modulates the localization of both proteins to microtubules and the cilium tip. Thus, the kinesin-microtubule system is not a passive GLI tether but a regulatable platform tuned by the kinesin-transcription factor interaction. We retooled this coiled-coil-based GLI-KIF7 interaction to inhibit the nuclear and cilium localization of GLI. This strategy can potentially be exploited to downregulate erroneously activated GLI in human cancers.
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4
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Revealing the assembly of filamentous proteins with scanning transmission electron microscopy. PLoS One 2019; 14:e0226277. [PMID: 31860683 PMCID: PMC6924676 DOI: 10.1371/journal.pone.0226277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 11/22/2019] [Indexed: 11/19/2022] Open
Abstract
Filamentous proteins are responsible for the superior mechanical strength of our cells and tissues. The remarkable mechanical properties of protein filaments are tied to their complex molecular packing structure. However, since these filaments have widths of several to tens of nanometers, it has remained challenging to quantitatively probe their molecular mass density and three-dimensional packing order. Scanning transmission electron microscopy (STEM) is a powerful tool to perform simultaneous mass and morphology measurements on filamentous proteins at high resolution, but its applicability has been greatly limited by the lack of automated image processing methods. Here, we demonstrate a semi-automated tracking algorithm that is capable of analyzing the molecular packing density of intra- and extracellular protein filaments over a broad mass range from STEM images. We prove the wide applicability of the technique by analyzing the mass densities of two cytoskeletal proteins (actin and microtubules) and of the main protein in the extracellular matrix, collagen. The high-throughput and spatial resolution of our approach allow us to quantify the internal packing of these filaments and their polymorphism by correlating mass and morphology information. Moreover, we are able to identify periodic mass variations in collagen fibrils that reveal details of their axially ordered longitudinal self-assembly. STEM-based mass mapping coupled with our tracking algorithm is therefore a powerful technique in the characterization of a wide range of biological and synthetic filaments.
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5
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Wijeratne S, Subramanian R. Geometry of antiparallel microtubule bundles regulates relative sliding and stalling by PRC1 and Kif4A. eLife 2018; 7:32595. [PMID: 30353849 PMCID: PMC6200392 DOI: 10.7554/elife.32595] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 09/28/2018] [Indexed: 12/12/2022] Open
Abstract
Motor and non-motor crosslinking proteins play critical roles in determining the size and stability of microtubule-based architectures. Currently, we have a limited understanding of how geometrical properties of microtubule arrays, in turn, regulate the output of crosslinking proteins. Here we investigate this problem in the context of microtubule sliding by two interacting proteins: the non-motor crosslinker PRC1 and the kinesin Kif4A. The collective activity of PRC1 and Kif4A also results in their accumulation at microtubule plus-ends (‘end-tag’). Sliding stalls when the end-tags on antiparallel microtubules collide, forming a stable overlap. Interestingly, we find that structural properties of the initial array regulate microtubule organization by PRC1-Kif4A. First, sliding velocity scales with initial microtubule-overlap length. Second, the width of the final overlap scales with microtubule lengths. Our analyses reveal how micron-scale geometrical features of antiparallel microtubules can regulate the activity of nanometer-sized proteins to define the structure and mechanics of microtubule-based architectures.
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Affiliation(s)
- Sithara Wijeratne
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States.,Department of Genetics, Harvard Medical School, Boston, United States
| | - Radhika Subramanian
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States.,Department of Genetics, Harvard Medical School, Boston, United States
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6
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Vulinovic F, Krajka V, Hausrat TJ, Seibler P, Alvarez-Fischer D, Madoev H, Park JS, Kumar KR, Sue CM, Lohmann K, Kneussel M, Klein C, Rakovic A. Motor protein binding and mitochondrial transport are altered by pathogenic TUBB4A variants. Hum Mutat 2018; 39:1901-1915. [PMID: 30079973 DOI: 10.1002/humu.23602] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/05/2018] [Accepted: 07/29/2018] [Indexed: 12/21/2022]
Abstract
Mutations in TUBB4A have been identified to cause a wide phenotypic spectrum of diseases ranging from hereditary generalized dystonia with whispering dysphonia (DYT-TUBB4A) and hereditary spastic paraplegia (HSP) to leukodystrophy hypomyelination with atrophy of the basal ganglia and cerebellum (H-ABC). TUBB4A encodes the brain-specific β-tubulin isotype, β-tubulin 4A. To elucidate the pathogenic mechanisms conferred by TUBB4A mutations leading to the different phenotypes, we functionally characterized three pathogenic TUBB4A variants (c.4C>G,p.R2G; c.745G>A,p.D249N; c.811G>A, p.A271T) as representatives of the mutational and disease spectrum) in human neuroblastoma cells and human induced pluripotent stem cell (iPSC)-derived neurons. We showed that mRNA stability was not affected by any of the TUBB4A variants. Although two mutations (p.R2G and p.D249N) are located at the α/β-tubulin interdimer interface, we confirmed incorporation of all TUBB4A mutants into the microtubule network. However, we showed that the mutations p.D249N and p.A271T interfered with motor protein binding to microtubules and impaired neurite outgrowth and microtubule dynamics. Finally, TUBB4A mutations, as well as heterozygous knockout of TUBB4A, disrupted mitochondrial transport in iPSC-derived neurons. Taken together, our findings suggest that functional impairment of microtubule-associated transport is a shared pathogenic mechanism by which the TUBB4A mutations studied here cause a spectrum of diseases.
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Affiliation(s)
- Franca Vulinovic
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Victor Krajka
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Torben J Hausrat
- Institute of Molecular Neurogenetics, Center for Molecular Neurobiology, ZMNH, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Philip Seibler
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | | | - Harutyun Madoev
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Jin-Sung Park
- Department of Neurogenetics, Kolling Institute, Royal North Shore Hospital and the University of Sydney, St. Leonards, New South Wales, Australia
| | - Kishore R Kumar
- Department of Neurogenetics, Kolling Institute, Royal North Shore Hospital and the University of Sydney, St. Leonards, New South Wales, Australia
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Australia
| | - Carolyn M Sue
- Department of Neurogenetics, Kolling Institute, Royal North Shore Hospital and the University of Sydney, St. Leonards, New South Wales, Australia
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Matthias Kneussel
- Institute of Molecular Neurogenetics, Center for Molecular Neurobiology, ZMNH, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
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7
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Liu D, Liu X, Shang Z, Sindelar CV. Structural basis of cooperativity in kinesin revealed by 3D reconstruction of a two-head-bound state on microtubules. eLife 2017; 6. [PMID: 28504639 PMCID: PMC5459574 DOI: 10.7554/elife.24490] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 05/09/2017] [Indexed: 12/26/2022] Open
Abstract
The detailed basis of walking by dimeric molecules of kinesin along microtubules has remained unclear, partly because available structural methods have been unable to capture microtubule-bound intermediates of this process. Utilizing novel electron cryomicroscopy methods, we solved structures of microtubule-attached, dimeric kinesin bound to an ATP analog. We find that under these conditions, the kinesin dimer can attach to the microtubule with either one or two motor domains, and we present sub-nanometer resolution reconstructions of both states. The former structure reveals a novel kinesin conformation that revises the current understanding of how ATP binding is coupled to forward stepping of the motor. The latter structure indicates how tension between the two motor domains keeps their cycles out of phase in order to stimulate directional motility. The methods presented here pave the way for future structural studies of a variety of challenging macromolecules that bind to microtubules and other filaments.
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Affiliation(s)
- Daifei Liu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, United States
| | - Xueqi Liu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, United States
| | - Zhiguo Shang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, United States
| | - Charles V Sindelar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, United States
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8
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Lopez BJ, Valentine MT. The +TIP coordinating protein EB1 is highly dynamic and diffusive on microtubules, sensitive to GTP analog, ionic strength, and EB1 concentration. Cytoskeleton (Hoboken) 2016; 73:23-34. [PMID: 26663881 DOI: 10.1002/cm.21267] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 12/04/2015] [Accepted: 12/04/2015] [Indexed: 01/06/2023]
Abstract
Using single-molecule fluorescence microscopy, we investigated the dynamics of dye-labeled EB1, a +TIP microtubule binding protein. To promote EB1 binding along the entire microtubule length, we formed microtubules using the nonhydrolyzable GTP analogs GMPCPP and GTPγS. Through precise tracking of the motions of individual dye-labeled proteins, we found EB1 to be highly dynamic and continuously diffusive while bound to a microtubule, with a diffusion coefficient and characteristic binding lifetime that were sensitive to both the choice of GTP analog and the buffer ionic strength. Using fluorescence-based equilibrium binding measurements, we found EB1 binding to be cooperative and also sensitive to GTP analog and ionic strength. By tracking the motion of a small number of individually-labeled EB1 proteins within a bath of unlabeled EB1 proteins, we determined the effects of increasing the total EB1 concentration on binding and dynamics. We found that the diffusion coefficient decreased with increasing EB1 concentration, which may be due at least in part, to the cooperativity of EB1 binding. Our results may have important consequences for the assembly and organization of the growing microtubule plus-end.
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Affiliation(s)
- Benjamin J Lopez
- Department of Mechanical Engineering and the Neuroscience Research Institute, University of California, Santa Barbara, California
| | - Megan T Valentine
- Department of Mechanical Engineering and the Neuroscience Research Institute, University of California, Santa Barbara, California
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9
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Böhm KJ, Shabanpour M, Kalchishkova N. Aluminum-Induced Kinesin Inactivation as Potential Molecular Cause of Impairment of Neuronal Transport Processes. Chem Res Toxicol 2015; 28:1275-81. [DOI: 10.1021/acs.chemrestox.5b00077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Konrad J. Böhm
- Leibniz Institute for Age Research -
Fritz Lipmann Institute (FLI), Beutenbergstraße
11, D-07745 Jena, Germany
| | - Mitra Shabanpour
- Leibniz Institute for Age Research -
Fritz Lipmann Institute (FLI), Beutenbergstraße
11, D-07745 Jena, Germany
| | - Nikolina Kalchishkova
- Leibniz Institute for Age Research -
Fritz Lipmann Institute (FLI), Beutenbergstraße
11, D-07745 Jena, Germany
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10
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Vilfan A. Ensemble velocity of non-processive molecular motors with multiple chemical states. Interface Focus 2014; 4:20140032. [PMID: 25485083 DOI: 10.1098/rsfs.2014.0032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We study the ensemble velocity of non-processive motor proteins, described with multiple chemical states. In particular, we discuss the velocity as a function of ATP concentration. Even a simple model which neglects the strain dependence of transition rates, reverse transition rates and nonlinearities in the elasticity can show interesting functional dependencies, which deviate significantly from the frequently assumed Michaelis-Menten form. We discuss how the order of events in the duty cycle can be inferred from the measured dependence. The model also predicts the possibility of velocity reversal at a certain ATP concentration if the duty cycle contains several conformational changes of opposite directionalities.
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Affiliation(s)
- Andrej Vilfan
- J. Stefan Institute , Jamova 39, 1000 Ljubljana , Slovenia ; Faculty of Mathematics and Physics , University of Ljubljana , Jadranska 19, 1000 Ljubljana , Slovenia
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11
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Niwa S, Takahashi H, Hirokawa N. β-Tubulin mutations that cause severe neuropathies disrupt axonal transport. EMBO J 2013; 32:1352-64. [PMID: 23503589 DOI: 10.1038/emboj.2013.59] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 02/22/2013] [Indexed: 12/30/2022] Open
Abstract
Microtubules are fundamental to neuronal morphogenesis and function. Mutations in tubulin, the major constituent of microtubules, result in neuronal diseases. Here, we have analysed β-tubulin mutations that cause neuronal diseases and we have identified mutations that strongly inhibit axonal transport of vesicles and mitochondria. These mutations are in the H12 helix of β-tubulin and change the negative charge on the surface of the microtubule. This surface is the interface between microtubules and kinesin superfamily motor proteins (KIF). The binding of axonal transport KIFs to microtubules is dominant negatively disrupted by these mutations, which alters the localization of KIFs in neurons and inhibits axon elongation in vivo. In humans, these mutations induce broad neurological symptoms, such as loss of axons in the central nervous system and peripheral neuropathy. Thus, our data identified the critical region of β-tubulin required for axonal transport and suggest a molecular mechanism for human neuronal diseases caused by tubulin mutations.
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Affiliation(s)
- Shinsuke Niwa
- Department of Cell Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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12
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Cope J, Rank KC, Gilbert SP, Rayment I, Hoenger A. Kar3Vik1 uses a minus-end directed powerstroke for movement along microtubules. PLoS One 2013; 8:e53792. [PMID: 23342004 PMCID: PMC3544905 DOI: 10.1371/journal.pone.0053792] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 12/05/2012] [Indexed: 11/19/2022] Open
Abstract
We have used cryo-electron microscopy (cryo-EM) and helical averaging to examine the 3-D structure of the heterodimeric kinesin-14 Kar3Vik1 complexed to microtubules at a resolution of 2.5 nm. 3-D maps were obtained at key points in Kar3Vik1's nucleotide hydrolysis cycle to gain insight into the mechanism that this motor uses for retrograde motility. In all states where Kar3Vik1 maintained a strong interaction with the microtubule, we found, as observed by cryo-EM, that the motor bound with one head domain while the second head extended outwards. 3-D reconstructions of Kar3Vik1-microtubule complexes revealed that in the nucleotide-free state, the motor's coiled-coil stalk points toward the plus-end of the microtubule. In the ATP-state, the outer head is shown to undergo a large rotation that reorients the stalk ∼75° to point toward the microtubule minus-end. To determine which of the two heads binds to tubulin in each nucleotide state, we employed specific Nanogold®-labeling of Vik1. The resulting maps confirmed that in the nucleotide-free, ATP and ADP+Pi states, Kar3 maintains contact with the microtubule surface, while Vik1 extends away from the microtubule and tracks with the coiled-coil as it rotates towards the microtubule minus-end. While many previous investigations have focused on the mechanisms of homodimeric kinesins, this work presents the first comprehensive study of the powerstroke of a heterodimeric kinesin. The stalk rotation shown here for Kar3Vik1 is highly reminiscent of that reported for the homodimeric kinesin-14 Ncd, emphasizing the conservation of a mechanism for minus-end directed motility.
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Affiliation(s)
- Julia Cope
- The Boulder Laboratory for 3-D Microscopy of Cells, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Katherine C. Rank
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Susan P. Gilbert
- Department of Biology and the Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, United States of America
| | - Ivan Rayment
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Andreas Hoenger
- The Boulder Laboratory for 3-D Microscopy of Cells, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America
- * E-mail:
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13
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Schwartz CL, Heumann JM, Dawson SC, Hoenger A. A detailed, hierarchical study of Giardia lamblia's ventral disc reveals novel microtubule-associated protein complexes. PLoS One 2012; 7:e43783. [PMID: 22984443 PMCID: PMC3439489 DOI: 10.1371/journal.pone.0043783] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 07/24/2012] [Indexed: 01/01/2023] Open
Abstract
Giardia lamblia is a flagellated, unicellular parasite of mammals infecting over one billion people worldwide. Giardia's two-stage life cycle includes a motile trophozoite stage that colonizes the host small intestine and an infectious cyst form that can persist in the environment. Similar to many eukaryotic cells, Giardia contains several complex microtubule arrays that are involved in motility, chromosome segregation, organelle transport, maintenance of cell shape and transformation between the two life cycle stages. Giardia trophozoites also possess a unique spiral microtubule array, the ventral disc, made of approximately 50 parallel microtubules and associated microribbons, as well as a variety of associated proteins. The ventral disc maintains trophozoite attachment to the host intestinal epithelium. With the help of a combined SEM/microtome based slice and view method called 3View® (Gatan Inc., Pleasanton, CA), we present an entire trophozoite cell reconstruction and describe the arrangement of the major cytoskeletal elements. To aid in future analyses of disc-mediated attachment, we used electron-tomography of freeze-substituted, plastic-embedded trophozoites to explore the detailed architecture of ventral disc microtubules and their associated components. Lastly, we examined the disc microtubule array in three dimensions in unprecedented detail using cryo-electron tomography combined with internal sub-tomogram volume averaging of repetitive domains. We discovered details of protein complexes stabilizing microtubules by attachment to their inner and outer wall. A unique tri-laminar microribbon structure is attached vertically to the disc microtubules and is connected to neighboring microribbons via crossbridges. This work provides novel insight into the structure of the ventral disc microtubules, microribbons and associated proteins. Knowledge of the components comprising these structures and their three-dimensional organization is crucial toward understanding how attachment via the ventral disc occurs in vivo.
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Affiliation(s)
- Cindi L. Schwartz
- Boulder Lab for 3-D Electron Microscopy of Cells, Department of MCD Biology, University of Colorado, Boulder, Colorado, United States of America
| | - John M. Heumann
- Boulder Lab for 3-D Electron Microscopy of Cells, Department of MCD Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Scott C. Dawson
- Department Microbiology, University of California Davis, Davis, California, United States of America
| | - Andreas Hoenger
- Boulder Lab for 3-D Electron Microscopy of Cells, Department of MCD Biology, University of Colorado, Boulder, Colorado, United States of America
- * E-mail:
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14
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DREBLOW KERSTIN, KALCHISHKOVA NIKOLINA, BÖHM KONRADJ. KINESIN BYPASSING BLOCKAGES ON MICROTUBULE RAILS. ACTA ACUST UNITED AC 2011. [DOI: 10.1142/s1793048009000958] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Kinesins are motor proteins which convert the chemical energy of ATP into mechanical energy to move along proteinaceous microtubule rails and to transport different cargoes to defined intracellular destinations. It is well documented that following the track of a single protofilament is the thermodynamically most effective mechanism of kinesin movement along microtubules. However, the question arises what happens when a kinesin molecule encounters a hindrance along the protofilament. The present study describes a simple, cell-free approach which enables to study the effects of structural blockages on kinesin-based transport. This experimental approach uses dimeric conventional kinesin moving nanometre-sized gold beads along immobilized microtubules whose surface has been irreversibly decorated by blocking proteins. We demonstrated that the continuous bead transport temporarily stopped at sites of blockages, but usually continued after a certain resting time. Our results suggest that single dimeric kinesin molecules are able to change to another protofilament if the next tubulin dimer where the second head should bind is blocked. A bypassing mechanism is discussed which is considered to be one fundamental prerequisite to realize a kinesin-mediated cargo-transport along microtubules over long distances, required for e.g., the fast axonal transport in motor neurons.
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Affiliation(s)
- KERSTIN DREBLOW
- Leibniz Institute for Age Research – Fritz Lipmann Institute, Beutenbergstraße 11, 07745 Jena, Germany
| | - NIKOLINA KALCHISHKOVA
- Leibniz Institute for Age Research – Fritz Lipmann Institute, Beutenbergstraße 11, 07745 Jena, Germany
| | - KONRAD J. BÖHM
- Leibniz Institute for Age Research – Fritz Lipmann Institute, Beutenbergstraße 11, 07745 Jena, Germany
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15
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Abstract
Myosin VIIA, thought to be involved in human auditory function, is a gene responsible for human Usher syndrome type 1B, which causes hearing and visual loss. Recent studies have suggested that it can move processively if it forms a dimer. Nevertheless, it exists as a monomer in vitro, unlike the well-known two-headed processive myosin Va. Here we studied the molecular mechanism, which is currently unknown, of activating myosin VIIA as a cargo-transporting motor. Human myosin VIIA was present throughout cytosol, but it moved to the tip of filopodia upon the formation of dimer induced by dimer-inducing reagent. The forced dimer of myosin VIIA translocated its cargo molecule, MyRip, to the tip of filopodia, whereas myosin VIIA without the forced dimer-forming module does not translocate to the filopodial tips. These results suggest that dimer formation of myosin VIIA is important for its cargo-transporting activity. On the other hand, myosin VIIA without the forced dimerization module became translocated to the filopodial tips in the presence of cargo complex, i.e., MyRip/Rab27a, and transported its cargo complex to the tip. Coexpression of MyRip promoted the association of myosin VIIA to vesicles and the dimer formation. These results suggest that association of myosin VIIA monomers with membrane via the MyRip/Rab27a complex facilitates the cargo-transporting activity of myosin VIIA, which is achieved by cluster formation on the membrane, where it possibly forms a dimer. Present findings support that MyRip, a cargo molecule, functions as an activator of myosin VIIA transporter function.
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16
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Abstract
Kar3 is a kinesin motor that facilitates chromosome segregation during cell division. Unlike many members of the kinesin superfamily, Kar3 forms a heterodimer with non-motor protein Vik1 or Cik1 in vivo. The heterodimers show ATP-driven minus-end directed motility along a microtubule (MT) lattice, and also serve as depolymerase at the MT ends. The molecular mechanisms behind this dual functionality remain mysterious. Here, a molecular mechanical model for the Kar3/Vik1 heterodimer based on structural, kinetic and motility data reveals a long-range chemomechanical transmission mechanism that resembles a familiar fishing tactic. By this molecular 'fishing', ATP-binding to Kar3 dissociates catalytically inactive Vik1 off MT to facilitate minus-end sliding of the dimer on the MT lattice. When the dimer binds the frayed ends of MT, the fishing channels ATP hydrolysis energy into MT depolymerization by a mechanochemical effect. The molecular fishing thus provides a unified mechanistic ground for Kar3's dual functionality. The fishing-promoted depolymerization differs from the depolymerase mechanisms found in homodimeric kinesins. The fishing also enables intermolecular coordination with a chemomechanical coupling feature different from the paradigmatic pattern of homodimeric motors. This study rationalizes some puzzling experimental observation, and suggests new experiments for further elucidation of the fishing mechanism.
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Affiliation(s)
- Ruizheng Hou
- Department of Physics, NUS Graduate School for Integrative Sciences and Engineering, and Center for Computational Science & Engineering, National University of Singapore, Singapore
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17
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Structure and dynamics of the kinesin-microtubule interaction revealed by fluorescence polarization microscopy. Methods Cell Biol 2010. [PMID: 20466150 DOI: 10.1016/s0091-679x(10)95025-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2024]
Abstract
Fluorescence polarization microscopy (FPM) is the analysis of the polarization of light in a fluorescent microscope in order to determine the angular orientation and rotational mobility of fluorescent molecules. Key advantages of FPM, relative to other structural analysis techniques, are that it allows the detection of conformational changes of fluorescently labeled macromolecules in real time in physiological conditions and at the single-molecule level. In this chapter we describe in detail the FPM experimental set-up and analysis methods we have used to investigate structural intermediates of the motor protein kinesin-1 associated with its walking mechanism along microtubules. We also briefly describe additional FPM methods that have been used to investigate other macromolecular complexes.
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18
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Abstract
Almost 25 years of kinesin research have led to the accumulation of a large body of knowledge about this widespread superfamily of motor and nonmotor proteins present in all eukaryotic cells. This review covers developments in kinesin research with an emphasis on structural aspects obtained by X-ray crystallography and cryoelectron microscopy 3-D analysis on kinesin motor domains complexed to microtubules.
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Affiliation(s)
- Alexander Marx
- Max-Planck-Unit for Structural Molecular Biology, c/o DESY, Hamburg, Germany.
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19
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FRET measurements of kinesin neck orientation reveal a structural basis for processivity and asymmetry. Proc Natl Acad Sci U S A 2010; 107:5453-8. [PMID: 20212149 DOI: 10.1073/pnas.0914924107] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
As the smallest and simplest motor enzymes, kinesins have served as the prototype for understanding the relationship between protein structure and mechanochemical function of enzymes in this class. Conventional kinesin (kinesin-1) is a motor enzyme that transports cargo toward the plus end of microtubules by a processive, asymmetric hand-over-hand mechanism. The coiled-coil neck domain, which connects the two kinesin motor domains, contributes to kinesin processivity (the ability to take many steps in a row) and is proposed to be a key determinant of the asymmetry in the kinesin mechanism. While previous studies have defined the orientation and position of microtubule-bound kinesin motor domains, the disposition of the neck coiled-coil remains uncertain. We determined the neck coiled-coil orientation using a multidonor fluorescence resonance energy transfer (FRET) technique to measure distances between microtubules and bound kinesin molecules. Microtubules were labeled with a new fluorescent taxol donor, TAMRA-X-taxol, and kinesin derivatives with an acceptor fluorophore attached at positions on the motor and neck coiled-coil domains were used to reconstruct the positions and orientations of the domains. FRET measurements to positions on the motor domain were largely consistent with the domain orientation determined in previous studies, validating the technique. Measurements to positions on the neck coiled-coil were inconsistent with a radial orientation and instead demonstrated that the neck coiled-coil is parallel to the microtubule surface. The measured orientation provides a structural explanation for how neck surface residues enhance processivity and suggests a simple hypothesis for the origin of kinesin step asymmetry and "limping."
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20
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Kocik E, Skowronek KJ, Kasprzak AA. Interactions between subunits in heterodimeric Ncd molecules. J Biol Chem 2010; 284:35735-45. [PMID: 19858211 DOI: 10.1074/jbc.m109.024240] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The nonprocessive minus-end-directed kinesin-14 Ncd is involved in the organization of the microtubule (MT) network during mitosis. Only one of the two motor domains is involved in the interaction with the MT. The other head is tethered to the bound one. Here we prepared, purified, and characterized mutated Ncd molecules carrying point mutations in one of the heads, thus producing heterodimeric motors. The mutations tested included substitutions in Switch I and II: R552A, E585A, and E585D; the decoupling mutant N600K; and a deletion in the motor domain in one of the subunits resulting in a single-headed molecule (NcN). These proteins were isolated by two sequential affinity chromatography steps, followed by measurements of their affinities to MT, enzymatic properties, and the velocity of the microtubule gliding test in vitro. A striking observation is a low affinity of the single-headed NcN for MT both without nucleotides and in the presence of 5'-adenylyl-beta,gamma-imidodiphosphate, implying that the tethered head has a profound effect on the structure of the Ncd-MT complex. Mutated homodimers had no MT-activated ATPase and no motility, whereas NcN had motility comparable with that of the wild type Ncd. Although the heterodimers had one fully active and one inactive head, the ATPase and motility of Ncd heterodimers varied dramatically, clearly demonstrating that interactions between motor domains exist in Ncd. We also show that the bulk property of dimeric proteins that interact with the filament with only one of its heads depends also on the distribution of the filament-interacting subunits.
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Affiliation(s)
- Elzbieta Kocik
- Motor Proteins Laboratory, Department of Biochemistry, Nencki Institute of Experimental Biology, 3 Pasteur Street, 02-093 Warsaw
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21
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Cope J, Gilbert S, Rayment I, Mastronarde D, Hoenger A. Cryo-electron tomography of microtubule-kinesin motor complexes. J Struct Biol 2009; 170:257-65. [PMID: 20025975 DOI: 10.1016/j.jsb.2009.12.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Accepted: 12/03/2009] [Indexed: 01/14/2023]
Abstract
Microtubules complexed with molecular motors of the kinesin family or non-motor microtubule associated proteins (MAPs) such as tau or EB1 have been the subject of cryo-electron microcopy based 3-D studies for several years. Most of these studies that targeted complexes with intact microtubules have been carried out by helical 3-D reconstruction, while few were analyzed by single particle approaches or from 2-D crystalline arrays. Helical reconstruction of microtubule-MAP or motor complexes has been extremely successful but by definition, all helical 3-D reconstruction attempts require perfectly helical assemblies, which presents a serious limitation and confines the attempts to 15- or 16-protofilament microtubules, microtubule configurations that are very rare in nature. The rise of cryo-electron tomography within the last few years has now opened a new avenue towards solving 3-D structures of microtubule-MAP complexes that do not form helical assemblies, most importantly for the subject here, all microtubules that exhibit a lattice seam. In addition, not all motor domains or MAPs decorate the microtubule surface regularly enough to match the underlying microtubule lattice, or they adopt conformations that deviate from helical symmetry. Here we demonstrate the power and limitation of cryo-electron tomography using two kinesin motor domains, the monomeric Eg5 motor domain, and the heterodimeric Kar3Vik1 motor. We show here that tomography does not exclude the possibility of post-tomographic averaging when identical sub-volumes can be extracted from tomograms and in both cases we were able to reconstruct 3-D maps of conformations that are not possible to obtain using helical or other averaging-based methods.
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Affiliation(s)
- Julia Cope
- The Boulder Laboratory for 3-D Microscopy of Cells, University of Colorado at Boulder, Department of Molecular, Cellular, and Developmental Biology, Boulder, CO 80309-0347, USA
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22
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Fehr AN, Gutiérrez-Medina B, Asbury CL, Block SM. On the origin of kinesin limping. Biophys J 2009; 97:1663-70. [PMID: 19751671 DOI: 10.1016/j.bpj.2009.07.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Revised: 07/06/2009] [Accepted: 07/09/2009] [Indexed: 10/20/2022] Open
Abstract
Kinesin is a dimeric motor with twin catalytic heads joined to a common stalk. Kinesin molecules move processively along microtubules in a hand-over-hand walk, with the two heads advancing alternately. Recombinant kinesin constructs with short stalks have been found to "limp", i.e., exhibit alternation in the dwell times of successive steps. Limping behavior implies that the molecular rearrangements underlying even- and odd-numbered steps must differ, but the mechanism by which such rearrangements lead to limping remains unsolved. Here, we used an optical force clamp to measure individual, recombinant dimers and test candidate explanations for limping. Introducing a covalent cross-link into the stalk region near the heads had no effect on limping, ruling out possible stalk misregistration during coiled-coil formation as a cause. Limping was equally unaffected by mutations that produced 50-fold changes in stalk stiffness, ruling out models where limping arises from an asymmetry in torsional strain. However, limping was enhanced by perturbations that increased the vertical component of load on the motor, including increases in bead size or net load, and decreases in the stalk length. These results suggest that kinesin heads take different vertical trajectories during alternate steps, and that the rates for these motions are differentially sensitive to load.
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Affiliation(s)
- Adrian N Fehr
- Department of Applied Physics, Stanford University, Stanford, California, USA
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23
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Direct measurements of kinesin torsional properties reveal flexible domains and occasional stalk reversals during stepping. Proc Natl Acad Sci U S A 2009; 106:17007-12. [PMID: 19805111 DOI: 10.1073/pnas.0907133106] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Kinesin is a homodimeric motor with two catalytic heads joined to a stalk via short neck linkers (NLs). We measured the torsional properties of single recombinant molecules by tracking the thermal angular motions of fluorescently labeled beads bound to the C terminus of the stalk. When kinesin heads were immobilized on microtubules (MTs) under varied nucleotide conditions, we observed bounded or unbounded angular diffusion, depending on whether one or both heads were attached to the MT. Free rotation implies that NLs act as swivels. From data on constrained diffusion, we conclude that the coiled-coil stalk domains are approximately 30-fold stiffer than its flexible "hinge" regions. Surprisingly, while tracking processive kinesin motion at low ATP concentrations, we observed occasional abrupt reversals in the directional orientations of the stalk. Our results impose constraints on kinesin walking models and suggest a role for rotational freedom in cargo transport.
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24
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Energetics of kinesin-1 stepping mechanism. FEBS Lett 2008; 582:3719-22. [PMID: 18948105 DOI: 10.1016/j.febslet.2008.10.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2008] [Revised: 10/12/2008] [Accepted: 10/14/2008] [Indexed: 11/22/2022]
Abstract
Kinesin-1 is a dimeric motor protein that transports cellular cargo along microtubules by using the energy released from ATP hydrolysis and moving processively in 8-nm steps. Recent novel studies at the single molecular level have provided extensive knowledge on how kinesin-1 converts the free energy of ATP hydrolysis and uses it for "walking" along microtubules. In this review, I have discussed the important topics pertaining to the energetics of kinesin-1 stepping mechanism and the consensus walking model.
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25
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Thoresen T, Gelles J. Processive movement by a kinesin heterodimer with an inactivating mutation in one head. Biochemistry 2008; 47:9514-21. [PMID: 18702529 PMCID: PMC2586147 DOI: 10.1021/bi800747e] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A single molecule of the motor enzyme kinesin-1 keeps a tight grip on its microtubule track, making tens or hundreds of discrete, unidirectional 8 nm steps before dissociating. This high duty ratio processive movement is thought to require a mechanism in which alternating stepping of the two head domains of the kinesin dimer is driven by alternating, overlapped cycles of ATP hydrolysis by the two heads. The R210K point mutation in Drosophila kinesin heavy chain was reported to disrupt the ability of the enzyme active site to catalyze ATP P-O bond cleavage. We expressed R210K homodimers as well as isolated R210K heads and confirmed that both are essentially inactive. We then coexpressed tagged R210K subunits with untagged wild-type subunits and affinity purified R210K/wild-type heterodimers together with the inactive R210K homodimers. In contrast to the R210K head or homodimer, the heterodimer was a highly active (>50% of wild-type) microtubule-stimulated ATPase, and the heterodimer displayed high duty ratio processive movement in single-molecule motility experiments. Thus, dimerization of a subunit containing the inactivating mutation with a functional subunit can complement the mutation; this must occur either by lowering or by bypassing kinetic barriers in the ATPase or mechanical cycles of the mutant head. The observations provide support for kinesin-1 gating mechanisms in which one head stimulates the rate of essential processes in the other.
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Affiliation(s)
- Todd Thoresen
- Biochemistry Department and Biophysics & Structural Biology Graduate Program, Brandeis University, Waltham, Massachusetts 02454-9110, USA
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26
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Amos LA, Hirose K. A cool look at the structural changes in kinesin motor domains. J Cell Sci 2008; 120:3919-27. [PMID: 17989090 DOI: 10.1242/jcs.016931] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Recently, several 3D images of kinesin-family motor domains interacting with microtubules have been obtained by analysis of electron microscope images of frozen hydrated complexes at much higher resolutions (9-12 A) than in previous reports (15-30 A). The high-resolution maps show a complex interaction interface between kinesin and tubulin, in which kinesin's switch II helix alpha4 is a central feature. Differences due to the presence of ADP, as compared with ATP analogues, support previously determined crystal structures of kinesins alone in suggesting that alpha4 is part of a pathway linking the nucleotide-binding site and the neck that connects to cargo. A 3D structure of the microtubule-bound Kar3 motor domain in a nucleotide-free state has revealed dramatic changes not yet reported for any crystal structure, including melting of the switch II helix, that may be part of the mechanism by which information is transmitted. A nucleotide-dependent movement of helix alpha6, first seen in crystal structures of Kif1a, appears to bring it into contact with tubulin and may provide another communication link. A microtubule-induced movement of loop L7 and a related distortion of the central beta-sheet, detected only in the empty state, may also send a signal to the region of the motor core that interacts with the neck. Earlier images of a kinesin-1 dimer in the empty state, showing a close interaction between the two motor heads, can now be interpreted in terms of a communication route from the active site of the directly bound head via its central beta-sheet to the tethered head.
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Affiliation(s)
- Linda A Amos
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK.
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27
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Subramanian R, Gelles J. Two distinct modes of processive kinesin movement in mixtures of ATP and AMP-PNP. ACTA ACUST UNITED AC 2008; 130:445-55. [PMID: 17968024 PMCID: PMC2151671 DOI: 10.1085/jgp.200709866] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
An enzyme is frequently conceived of as having a single functional mechanism. This is particularly true for motor enzymes, where the necessity for tight coupling of mechanical and chemical cycles imposes rigid constraints on the reaction pathway. In mixtures of substrate (ATP) and an inhibitor (adenosine 5′-(β,γ-imido)triphosphate or AMP-PNP), single kinesin molecules move on microtubules in two distinct types of multiple-turnover “runs” that differ in their susceptibility to inhibition. Longer (less susceptible) runs are consistent with movement driven by the alternating-sites mechanism previously proposed for uninhibited kinesin. In contrast, kinesin molecules in shorter runs step with AMP-PNP continuously bound to one of the two active sites of the enzyme. Thus, in this mixture of substrate and inhibitor, kinesin can function as a motor enzyme using either of two distinct mechanisms. In one of these, the enzyme can accomplish high-duty-ratio processive movement without alternating-sites ATP hydrolysis.
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28
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Marx A, Müller J, Mandelkow EM, Woehlke G, Bouchet-Marquis C, Hoenger A, Mandelkow E. X-ray Structure and Microtubule Interaction of the Motor Domain of Neurospora crassa NcKin3, a Kinesin with Unusual Processivity,. Biochemistry 2008; 47:1848-61. [DOI: 10.1021/bi701483h] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Alexander Marx
- Max-Planck-Unit for Structural Molecular Biology, Notkestrasse 85, 22607 Hamburg, Germany, Institute for Cell Biology, Ludwig-Maximilians-University Munich, Schillerstrasse 42, 80336, Germany, and Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309-0347
| | - Jens Müller
- Max-Planck-Unit for Structural Molecular Biology, Notkestrasse 85, 22607 Hamburg, Germany, Institute for Cell Biology, Ludwig-Maximilians-University Munich, Schillerstrasse 42, 80336, Germany, and Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309-0347
| | - Eva-Maria Mandelkow
- Max-Planck-Unit for Structural Molecular Biology, Notkestrasse 85, 22607 Hamburg, Germany, Institute for Cell Biology, Ludwig-Maximilians-University Munich, Schillerstrasse 42, 80336, Germany, and Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309-0347
| | - Günther Woehlke
- Max-Planck-Unit for Structural Molecular Biology, Notkestrasse 85, 22607 Hamburg, Germany, Institute for Cell Biology, Ludwig-Maximilians-University Munich, Schillerstrasse 42, 80336, Germany, and Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309-0347
| | - Cedric Bouchet-Marquis
- Max-Planck-Unit for Structural Molecular Biology, Notkestrasse 85, 22607 Hamburg, Germany, Institute for Cell Biology, Ludwig-Maximilians-University Munich, Schillerstrasse 42, 80336, Germany, and Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309-0347
| | - Andreas Hoenger
- Max-Planck-Unit for Structural Molecular Biology, Notkestrasse 85, 22607 Hamburg, Germany, Institute for Cell Biology, Ludwig-Maximilians-University Munich, Schillerstrasse 42, 80336, Germany, and Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309-0347
| | - Eckhard Mandelkow
- Max-Planck-Unit for Structural Molecular Biology, Notkestrasse 85, 22607 Hamburg, Germany, Institute for Cell Biology, Ludwig-Maximilians-University Munich, Schillerstrasse 42, 80336, Germany, and Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309-0347
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29
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Kenzaki H, Kikuchi M. Free-energy landscape of kinesin by a realistic lattice model. Proteins 2008; 71:389-95. [DOI: 10.1002/prot.21707] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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30
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31
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Davis TN, Wordeman L. Rings, bracelets, sleeves, and chevrons: new structures of kinetochore proteins. Trends Cell Biol 2007; 17:377-82. [PMID: 17766118 PMCID: PMC2908952 DOI: 10.1016/j.tcb.2007.08.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2007] [Revised: 07/18/2007] [Accepted: 08/16/2007] [Indexed: 11/22/2022]
Abstract
Electron microscopy has recently revealed striking structural orderliness in kinetochore proteins and protein complexes that associate with microtubules. In addition to their astonishing appearance and intrinsic beauty, the structures are functionally informative. The Dam1 and Ndc80 complexes bind to the microtubule lattice as rings and chevrons, respectively. These structures give insight into how the kinetochore couples to dynamic microtubules, a process crucial to the accurate segregation of chromosomes. HURP and kinesin-13 arrange tubulin into sleeves and bracelets surrounding the microtubule lattice. These structures might reflect the ability of these proteins to modulate microtubule dynamics by interacting with specialized tubulin configurations. In this review, we compare and contrast the structure of these proteins and their interactions with microtubules to illustrate how they attach to and modulate the dynamics of microtubules.
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Affiliation(s)
- Trisha N Davis
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
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32
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Wang Z, Feng M, Zheng W, Fan D. Kinesin is an evolutionarily fine-tuned molecular ratchet-and-pawl device of decisively locked direction. Biophys J 2007; 93:3363-72. [PMID: 17675343 PMCID: PMC2072077 DOI: 10.1529/biophysj.107.108233] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Conventional kinesin is a dimeric motor protein that transports membranous organelles toward the plus-end of microtubules (MTs). Individual kinesin dimers show steadfast directionality and hundreds of consecutive steps, yet the detailed physical mechanism remains unclear. Here we compute free energies for the entire dimer-MT system for all possible interacting configurations by taking full account of molecular details. Employing merely first principles and several measured binding and barrier energies, the system-level analysis reveals insurmountable energy gaps between configurations, asymmetric ground state caused by mechanically lifted configurational degeneracy, and forbidden transitions ensuring coordination between both motor domains for alternating catalysis. This wealth of physical effects converts a kinesin dimer into a molecular ratchet-and-pawl device, which determinedly locks the dimer's movement into the MT plus-end and ensures consecutive steps in hand-over-hand gait. Under a certain range of extreme loads, however, the ratchet-and-pawl device becomes defective but not entirely abolished to allow consecutive back-steps. This study yielded quantitative evidence that kinesin's multiple molecular properties have been evolutionarily adapted to fine-tune the ratchet-and-pawl device so as to ensure the motor's distinguished performance.
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Affiliation(s)
- Zhisong Wang
- Institute of Modern Physics and Applied Ion Beam Physics Laboratory, Fudan University, Shanghai, China.
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33
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Skowronek KJ, Kocik E, Kasprzak AA. Subunits interactions in kinesin motors. Eur J Cell Biol 2007; 86:559-68. [PMID: 17628208 DOI: 10.1016/j.ejcb.2007.05.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2007] [Revised: 05/21/2007] [Accepted: 05/29/2007] [Indexed: 12/30/2022] Open
Abstract
Kinesins form a large and diverse superfamily of proteins involved in numerous important cellular processes. The majority of them are molecular motors moving along microtubules. Conversion of chemical energy into mechanical work is accomplished in a sequence of events involving both biochemical and conformational alternation of the motor structure called the mechanochemical cycle. Different members of the kinesin superfamily can either perform their function in large groups or act as single molecules. Conventional kinesin, a member of the kinesin-1 subfamily, exemplifies the second type of motor which requires tight coordination of the mechanochemical cycle in two identical subunits to accomplish processive movement toward the microtubule plus end. Recent results strongly support an asymmetric hand-over-hand model of "walking" for this protein. Conformational strain between two subunits at the stage of the cycle where both heads are attached to the microtubule seems to be a major factor in intersubunit coordination, although molecular and kinetic details of this phenomenon are not yet deciphered. We discuss also current knowledge concerning intersubunit coordination in other kinesin subfamilies. Members of the kinesin-3 class use at least three different mechanisms of movement and can translocate in monomeric or dimeric forms. It is not known to what extent intersubunit coordination takes place in Ncd, a dimeric member of the kinesin-14 subfamily which, unlike conventional kinesin, exercises a power-stroke toward the microtubule minus end. Eg5, a member of the kinesin-5 subfamily is a homotetrameric protein with two kinesin-1-like dimeric halves controlled by their relative orientation on two microtubules. It seems that diversity of subunit organization, quaternary structures and cellular functions in the kinesin superfamily are reflected also by the divergent extent and mechanism of intersubunit coordination during kinesin movement along microtubules.
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Affiliation(s)
- Krzysztof J Skowronek
- Motor Proteins Laboratory, Department of Biochemistry, Nencki Institute of Experimental Biology, 3 Pasteur Street, 02-093 Warsaw, Poland
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34
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Grant BJ, McCammon JA, Caves LSD, Cross RA. Multivariate Analysis of Conserved Sequence–Structure Relationships in Kinesins: Coupling of the Active Site and a Tubulin-binding Sub-domain. J Mol Biol 2007; 368:1231-48. [PMID: 17399740 DOI: 10.1016/j.jmb.2007.02.049] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2006] [Revised: 01/30/2007] [Accepted: 02/06/2007] [Indexed: 11/17/2022]
Abstract
An extensive computational analysis of available sequence and crystal structure data was used to identify functionally important residue interactions within the motor domain of the kinesin molecular motor. Principal component analysis revealed that all current kinesin crystal structures reside in one of two main conformations, which differ at the active site, and in the position of a microtubule-binding sub-domain relative to a rigid central core. This sub-domain consists of secondary structure elements alpha4-loop12-alpha5-loop13 and contains a conserved hydrophilic surface patch that may be involved in strong binding to microtubules. A hinge point for the sub-domain motion lies near a conserved glycine at position 292. Statistical coupling analysis revealed a network of co-evolving positions that link this region to the nucleotide-binding site, via a highly conserved histidine in the switch I loop. The data are consistent with a model in which the nucleotide status of the active site shifts kinesin between weak and strong binding conformations via reconfiguration of the identified sub-domain. Our data provide a statistically supported framework for further examination of this and other structure-function relationships in the kinesin family.
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Affiliation(s)
- Barry J Grant
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.
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35
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Miranda JJL, King DS, Harrison SC. Protein arms in the kinetochore-microtubule interface of the yeast DASH complex. Mol Biol Cell 2007; 18:2503-10. [PMID: 17460120 PMCID: PMC1924804 DOI: 10.1091/mbc.e07-02-0135] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The yeast DASH complex is a heterodecameric component of the kinetochore necessary for accurate chromosome segregation. DASH forms closed rings around microtubules with a large gap between the DASH ring and the microtubule cylinder. We characterized the microtubule-binding properties of limited proteolysis products and subcomplexes of DASH, thus identifying candidate polypeptide extensions involved in establishing the DASH-microtubule interface. The acidic C-terminal extensions of tubulin subunits are not essential for DASH binding. We also measured the molecular mass of DASH rings on microtubules with scanning transmission electron microscopy and found that approximately 25 DASH heterodecamers assemble to form each ring. Dynamic association and relocation of multiple flexible appendages of DASH may allow the kinetochore to translate along the microtubule surface.
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Affiliation(s)
- JJ L. Miranda
- *Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - David S. King
- Department of Molecular and Cell Biology, and Howard Hughes Medical Institute, University of California, Berkeley, CA 94720; and
| | - Stephen C. Harrison
- Department of Biological Chemistry and Molecular Pharmacology, and Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115
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36
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Affiliation(s)
- David D Hackney
- Department of Biological Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
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37
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Ikegami K, Heier RL, Taruishi M, Takagi H, Mukai M, Shimma S, Taira S, Hatanaka K, Morone N, Yao I, Campbell PK, Yuasa S, Janke C, MacGregor GR, Setou M. Loss of alpha-tubulin polyglutamylation in ROSA22 mice is associated with abnormal targeting of KIF1A and modulated synaptic function. Proc Natl Acad Sci U S A 2007; 104:3213-8. [PMID: 17360631 PMCID: PMC1802010 DOI: 10.1073/pnas.0611547104] [Citation(s) in RCA: 176] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Microtubules function as molecular tracks along which motor proteins transport a variety of cargo to discrete destinations within the cell. The carboxyl termini of alpha- and beta-tubulin can undergo different posttranslational modifications, including polyglutamylation, which is particularly abundant within the mammalian nervous system. Thus, this modification could serve as a molecular "traffic sign" for motor proteins in neuronal cells. To investigate whether polyglutamylated alpha-tubulin could perform this function, we analyzed ROSA22 mice that lack functional PGs1, a subunit of alpha-tubulin-selective polyglutamylase. In wild-type mice, polyglutamylated alpha-tubulin is abundant in both axonal and dendritic neurites. ROSA22 mutants display a striking loss of polyglutamylated alpha-tubulin within neurons, including their neurites, which is associated with decreased binding affinity of certain structural microtubule-associated proteins and motor proteins, including kinesins, to microtubules purified from ROSA22-mutant brain. Of the kinesins examined, KIF1A, a subfamily of kinesin-3, was less abundant in neurites from ROSA22 mutants in vitro and in vivo, whereas the distribution of KIF3A (kinesin-2) and KIF5 (kinesin-1) appeared unaltered. The density of synaptic vesicles, a cargo of KIF1A, was decreased in synaptic terminals in the CA1 region of hippocampus in ROSA22 mutants. Consistent with this finding, ROSA22 mutants displayed more rapid depletion of synaptic vesicles than wild-type littermates after high-frequency stimulation. These data provide evidence for a role of polyglutamylation of alpha-tubulin in vivo, as a molecular traffic sign for targeting of KIF1 kinesin required for continuous synaptic transmission.
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Affiliation(s)
- Koji Ikegami
- *Mitsubishi Kagaku Institute of Life Sciences, Machida, Tokyo 194-8511, Japan
| | - Robb L. Heier
- Department of Developmental and Cell Biology, Developmental Biology Center, and Center for Molecular and Mitochondrial Medicine and Genetics, University of California, Irvine, CA 92697-3940
| | - Midori Taruishi
- *Mitsubishi Kagaku Institute of Life Sciences, Machida, Tokyo 194-8511, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi City, Saitama 332-0012, Japan
| | - Hiroshi Takagi
- *Mitsubishi Kagaku Institute of Life Sciences, Machida, Tokyo 194-8511, Japan
| | - Masahiro Mukai
- *Mitsubishi Kagaku Institute of Life Sciences, Machida, Tokyo 194-8511, Japan
| | - Shuichi Shimma
- National Institute for Physiological Sciences, Okazaki, Aichi 444-8787, Japan
| | - Shu Taira
- *Mitsubishi Kagaku Institute of Life Sciences, Machida, Tokyo 194-8511, Japan
| | - Ken Hatanaka
- *Mitsubishi Kagaku Institute of Life Sciences, Machida, Tokyo 194-8511, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi City, Saitama 332-0012, Japan
- Laboratory of Neurobiophysics, School of Pharmaceutical Sciences, University of Tokyo, Tokyo 113-0033, Japan
| | - Nobuhiro Morone
- Department of Ultrastructural Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8502, Japan; and
| | - Ikuko Yao
- *Mitsubishi Kagaku Institute of Life Sciences, Machida, Tokyo 194-8511, Japan
| | - Patrick K. Campbell
- Department of Developmental and Cell Biology, Developmental Biology Center, and Center for Molecular and Mitochondrial Medicine and Genetics, University of California, Irvine, CA 92697-3940
| | - Shigeki Yuasa
- Department of Ultrastructural Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8502, Japan; and
| | - Carsten Janke
- **Centre de Rechérches en Biochimie Macromoléculaire, Centre National de la Recherche Scientifique, 34293 Montpellier, France
| | - Grant R. MacGregor
- Department of Developmental and Cell Biology, Developmental Biology Center, and Center for Molecular and Mitochondrial Medicine and Genetics, University of California, Irvine, CA 92697-3940
- To whom correspondence may be addressed. E-mail:
| | - Mitsutoshi Setou
- *Mitsubishi Kagaku Institute of Life Sciences, Machida, Tokyo 194-8511, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi City, Saitama 332-0012, Japan
- National Institute for Physiological Sciences, Okazaki, Aichi 444-8787, Japan
- To whom correspondence may be addressed. E-mail:
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38
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Sandblad L, Busch KE, Tittmann P, Gross H, Brunner D, Hoenger A. The Schizosaccharomyces pombe EB1 homolog Mal3p binds and stabilizes the microtubule lattice seam. Cell 2007; 127:1415-24. [PMID: 17190604 DOI: 10.1016/j.cell.2006.11.025] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2006] [Revised: 10/06/2006] [Accepted: 11/03/2006] [Indexed: 11/19/2022]
Abstract
End binding 1 (EB1) proteins are highly conserved regulators of microtubule dynamics. Using electron microscopy (EM) and high-resolution surface shadowing we have studied the microtubule-binding properties of the fission yeast EB1 homolog Mal3p. This allowed for a direct visualization of Mal3p bound on the surface of microtubules. Mal3p particles usually formed a single line on each microtubule along just one of the multiple grooves that are formed by adjacent protofilaments. We provide structural data showing that the alignment of Mal3p molecules coincides with the microtubule lattice seam as well as data suggesting that Mal3p not only binds but also stabilizes this seam. Accordingly, Mal3p stabilizes microtubules through a specific interaction with what is potentially the weakest part of the microtubule in a way not previously demonstrated. Our findings further suggest that microtubules exhibit two distinct reaction platforms on their surface that can independently interact with target structures such as microtubule-associated proteins, motors, kinetochores, or membranes.
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Affiliation(s)
- Linda Sandblad
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
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39
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Affiliation(s)
- Andreas Hoenger
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
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40
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Cai D, Hoppe AD, Swanson JA, Verhey KJ. Kinesin-1 structural organization and conformational changes revealed by FRET stoichiometry in live cells. J Cell Biol 2007; 176:51-63. [PMID: 17200416 PMCID: PMC2063625 DOI: 10.1083/jcb.200605097] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2006] [Accepted: 12/01/2006] [Indexed: 11/22/2022] Open
Abstract
Kinesin motor proteins drive the transport of cellular cargoes along microtubule tracks. How motor protein activity is controlled in cells is unresolved, but it is likely coupled to changes in protein conformation and cargo association. By applying the quantitative method fluorescence resonance energy transfer (FRET) stoichiometry to fluorescent protein (FP)-labeled kinesin heavy chain (KHC) and kinesin light chain (KLC) subunits in live cells, we studied the overall structural organization and conformation of Kinesin-1 in the active and inactive states. Inactive Kinesin-1 molecules are folded and autoinhibited such that the KHC tail blocks the initial interaction of the KHC motor with the microtubule. In addition, in the inactive state, the KHC motor domains are pushed apart by the KLC subunit. Thus, FRET stoichiometry reveals conformational changes of a protein complex in live cells. For Kinesin-1, activation requires a global conformational change that separates the KHC motor and tail domains and a local conformational change that moves the KHC motor domains closer together.
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Affiliation(s)
- Dawen Cai
- Biophysics Research Division, University of Michigan, Ann Arbor, MI 48109, USA
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41
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Uchimura S, Oguchi Y, Katsuki M, Usui T, Osada H, Nikawa JI, Ishiwata S, Muto E. Identification of a strong binding site for kinesin on the microtubule using mutant analysis of tubulin. EMBO J 2006; 25:5932-41. [PMID: 17124495 PMCID: PMC1698889 DOI: 10.1038/sj.emboj.7601442] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2006] [Accepted: 10/23/2006] [Indexed: 11/09/2022] Open
Abstract
The kinesin-binding site on the microtubule has not been identified because of the technical difficulties involved in the mutant analyses of tubulin. Exploiting the budding yeast expression system, we succeeded in replacing the negatively charged residues in the alpha-helix 12 of beta-tubulin with alanine and analyzed their effect on kinesin-microtubule interaction in vitro. The microtubule gliding assay showed that the affinity of the microtubules for kinesin was significantly reduced in E410A, D417A, and E421A, but not in E412A mutant. The unbinding force measurement revealed that in the former three mutants, the kinesin-microtubule interaction in the adenosine 5'-[beta,gamma-imido]triphosphate state (AMP-PNP state) became less stable when a load was imposed towards the microtubule minus end. In parallel with this decreased stability, the stall force of kinesin was reduced. Our results implicate residues E410, D417, and E421 as crucial for the kinesin-microtubule interaction in the strong binding state, thereby governing the size of kinesin stall force.
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Affiliation(s)
- Seiichi Uchimura
- Brain Development Research Group, Brain Science Institute, RIKEN, Wako, Saitama, Japan
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Fukuoka, Japan
| | - Yusuke Oguchi
- Department of Physics, School of Science and Engineering, Waseda University, Tokyo, Japan
| | - Miho Katsuki
- Brain Development Research Group, Brain Science Institute, RIKEN, Wako, Saitama, Japan
| | - Takeo Usui
- Antibiotics Laboratory, Discovery Research Institute, RIKEN, Wako, Saitama, Japan
| | - Hiroyuki Osada
- Antibiotics Laboratory, Discovery Research Institute, RIKEN, Wako, Saitama, Japan
| | - Jun-ichi Nikawa
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Fukuoka, Japan
| | - Shin'ichi Ishiwata
- Department of Physics, School of Science and Engineering, Waseda University, Tokyo, Japan
- Advanced Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
| | - Etsuko Muto
- Brain Development Research Group, Brain Science Institute, RIKEN, Wako, Saitama, Japan
- Brain Development Research Group, Brain Science Institute, RIKEN, Hirosawa 2-1, Wako, Saitama 351-0198, Japan. Tel.: +81 48 467 6959; Fax: +81 48 467 7145; E-mail:
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42
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Hirose K, Akimaru E, Akiba T, Endow SA, Amos LA. Large conformational changes in a kinesin motor catalyzed by interaction with microtubules. Mol Cell 2006; 23:913-23. [PMID: 16973442 PMCID: PMC1635653 DOI: 10.1016/j.molcel.2006.07.020] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2006] [Revised: 05/15/2006] [Accepted: 07/17/2006] [Indexed: 11/17/2022]
Abstract
Kinesin motor proteins release nucleotide upon interaction with microtubules (MTs), then bind and hydrolyze ATP to move along the MT. Although crystal structures of kinesin motors bound to nucleotides have been solved, nucleotide-free structures have not. Here, using cryomicroscopy and three-dimensional (3D) reconstruction, we report the structure of MTs decorated with a Kinesin-14 motor, Kar3, in the nucleotide-free state, as well as with ADP and AMPPNP, with resolution sufficient to show alpha helices. We find large structural changes in the empty motor, including melting of the switch II helix alpha4, closure of the nucleotide binding pocket, and changes in the central beta sheet reminiscent of those reported for nucleotide-free myosin crystal structures. We propose that the switch II region of the motor controls docking of the Kar3 neck by conformational changes in the central beta sheet, similar to myosin, rather than by rotation of the motor domain, as proposed for the Kif1A kinesin motor.
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Affiliation(s)
- Keiko Hirose
- Gene Function Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8562, Japan.
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43
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Xie P, Dou SX, Wang PY. Model for kinetics of wild-type and mutant kinesins. Biosystems 2006; 84:24-38. [PMID: 16378677 DOI: 10.1016/j.biosystems.2005.09.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2005] [Revised: 09/30/2005] [Accepted: 09/30/2005] [Indexed: 11/21/2022]
Abstract
A hand-over-hand model is presented for the processive movement of two-headed kinesin based on previous structural and biochemical studies. In the model, the ATPase activities of the two heads are regulated by forces, both from internal elasticity and external load, exerted on their neck linkers. The results from the model show that the two heads may be partially coordinated in their ATPase cycles: in the case of backward load or low forward load, the ATPase cycles of its two heads are well coordinated, whereas in the case of high forward load, they are no longer well coordinated. The model gives results that show good quantitative agreement with both previous biochemical and mechanical experimental results such as the limping of homodimers and the dependences of mean velocity on [ATP] and on loads (both positive and negative). Furthermore, using the model we study the kinetics of a number of mutant kinesin homodimers and heterodimers, showing that the two heads' ATPase activities of some of these molecules are not well coordinated and they move processively with low mechanochemical coupling efficiencies even under no load. The theoretical results of ATPase rate per head, moving velocity, and stall force of the motors show good quantitative agreement with the experimental ones. The puzzling dynamic behaviours of mutant homodimeric and heterodimeric kinesins become understandable.
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Affiliation(s)
- Ping Xie
- Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100080, China.
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44
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Hizlan D, Mishima M, Tittmann P, Gross H, Glotzer M, Hoenger A. Structural analysis of the ZEN-4/CeMKLP1 motor domain and its interaction with microtubules. J Struct Biol 2006; 153:73-84. [PMID: 16361109 DOI: 10.1016/j.jsb.2005.10.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2005] [Revised: 10/17/2005] [Accepted: 10/27/2005] [Indexed: 11/25/2022]
Abstract
The centralspindlin complex is required for the assembly and maintenance of the central spindle during late anaphase and the completion of cytokinesis. It is composed of two copies each of the kinesin-like protein ZEN-4, a Caenorhabditis elegans MKLP-1 (Kinesin-6 family), and the RhoGAP CYK-4. By using cryo-electron microscopy and helical 3D reconstruction, we are investigating the structural features of the interactions between monomeric and dimeric motor domain constructs of ZEN-4 and microtubules. We have calculated helically averaged 3D maps of microtubules decorated with ZEN-4 motor domain in the presence of AMP-PNP, ADP, ADP-AlF(4)(-), and nucleotide-free conditions. We used statistical difference mapping to compare these maps among each other and to related maps obtained from microtubules decorated with a well-characterized Kinesin-1 motor domain from Neurospora crassa. Thereby, we found distinct structural features in microtubule-ZEN-4 complexes that may directly relate to the functional properties of ZEN-4 and centralspindlin. Furthermore, we investigated the location, structure, and function of a highly conserved extension of approximately 50 residues unique to the Kinesin-6 subfamily, located in the motor core loop6/beta4 region.
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Affiliation(s)
- Dilem Hizlan
- European Molecular Biology Laboratory, Structural Biology and Biocomputing Programme, Heidelberg, Germany
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45
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Atzberger PJ, Peskin CS. A Brownian Dynamics model of kinesin in three dimensions incorporating the force-extension profile of the coiled-coil cargo tether. Bull Math Biol 2006; 68:131-60. [PMID: 16794924 DOI: 10.1007/s11538-005-9003-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2004] [Accepted: 03/15/2005] [Indexed: 10/25/2022]
Abstract
The kinesin family of motor proteins are involved in a variety of cellular processes that transport materials and generate force. With recent advances in experimental techniques, such as optical tweezers can probe individual molecules, there has been an increasing interest in understanding the mechanisms by which motor proteins convert chemical energy into mechanical work. Here we present a mathematical model for the chemistry and three dimensional mechanics of the kinesin motor protein which captures many of the force dependent features of the motor. For the elasticity of the tether that attaches cargo to the motor we develop a method for deriving the non-linear force-extension relationship from optical trap data. For the kinesin heads, cargo, and microscope stage we formulate a three dimensional Brownian Dynamics model that takes into account excluded volume interactions. To efficiently compute statistics from the model, an algorithm is proposed which uses a two step protocol that separates the simulation of the mechanical features of the model from the chemical kinetics of the model. Using this approach for a bead transported by the motor, the force dependent average velocity and randomness parameter are computed and compared with the experimental data.
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Affiliation(s)
- Paul J Atzberger
- Department of Mathematics, Rensselaer Polytechnic Institute, Amos Eaton Hall, Troy, NY 12180, USA.
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46
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Marx A, Müller J, Mandelkow EM, Hoenger A, Mandelkow E. Interaction of kinesin motors, microtubules, and MAPs. J Muscle Res Cell Motil 2005; 27:125-37. [PMID: 16362723 DOI: 10.1007/s10974-005-9051-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2005] [Accepted: 11/18/2005] [Indexed: 11/30/2022]
Abstract
Kinesins are a family of microtubule-dependent motor proteins that carry cargoes such as vesicles, organelles, or protein complexes along microtubules. Here we summarize structural studies of the "conventional" motor protein kinesin-1 and its interactions with microtubules, as determined by X-ray crystallography and cryo-electron microscopy. In particular, we consider the docking between the kinesin motor domain and tubulin subunits and summarize the evidence that kinesin binds mainly to beta tubulin with the switch-2 helix close to the intradimer interface between alpha and beta tubulin.
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Affiliation(s)
- A Marx
- Max-Planck-Unit for Structural Molecular Biology, Notkestrasse 85, 22607, Hamburg, Germany
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47
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Santos JE, Franosch T, Parmeggiani A, Frey E. Renewal processes and fluctuation analysis of molecular motor stepping. Phys Biol 2005; 2:207-22. [PMID: 16224126 DOI: 10.1088/1478-3975/2/3/008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We present a systematic method of analysis of experiments performed with single motor proteins. The use of such a method should allow a more detailed description of the motor's chemical cycle through the precise fitting of the experimental data. We model the dynamics of a processive or rotary molecular motor using a renewal process, in line with the work initiated by Svoboda, Mitra and Block. We apply a functional technique to compute different types of multiple-time correlation function of the renewal process, which have applications to bead-assay experiments performed both with processive molecular motors, such as myosin V and kinesin, and rotary motors, such as F1-ATPase.
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Affiliation(s)
- Jaime E Santos
- Hahn-Meitner Institut, Abteilung Theorie, Glienicker Str. 100, D-14109 Berlin, Germany
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48
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Vent J, Wyatt TA, Smith DD, Banerjee A, Ludueña RF, Sisson JH, Hallworth R. Direct involvement of the isotype-specific C-terminus of beta tubulin in ciliary beating. J Cell Sci 2005; 118:4333-41. [PMID: 16159957 PMCID: PMC1992443 DOI: 10.1242/jcs.02550] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In previous studies in Drosophila, Nielsen et al. hypothesized that the beta tubulin C-terminal axonemal motif ;EGEFXXX', where X is an acidic amino acid, is required for ciliary function and assembly (Nielsen et al., 2001, Curr. Biol. 11, 529-533). This motif is present in some but not all mammalian beta tubulin isotypes. We therefore investigated whether this motif is important in ciliary function in mammals. In a preparation of isolated, ATP-reactivated bovine tracheal cilia, we found that monoclonal antibodies directed against the C-terminus of betaI, betaIV and betaV tubulin blocked ciliary beating in a concentration dependent manner. Antibodies against other epitopes of beta tubulin were ineffective, as were antibodies against alpha tubulin. Peptides consisting of the axonemal motif and motif-like sequences of these isotypes blocked ciliary beating. These results suggest that the axonemal motif sequences of betaI, betaIV and betaV tubulin are essential for ciliary function. Peptides consisting of corresponding C-terminal sequences in alpha tubulin isotypes were also ineffective in blocking ciliary beating, which suggests that the C-terminus of alpha tubulin is not directly involved in cilia function in mammals.
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Affiliation(s)
- Julia Vent
- Department of Biomedical Sciences, Creighton University, Omaha, Nebraska 68178, USA.
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49
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Rosenfeld SS, Xing J, Jefferson GM, King PH. Docking and rolling, a model of how the mitotic motor Eg5 works. J Biol Chem 2005; 280:35684-95. [PMID: 16115880 DOI: 10.1074/jbc.m506561200] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Whereas kinesin I is designed to transport cargoes long distances in isolation, a closely related kinesin motor, Eg5, is designed to generate a sustained opposing force necessary for proper mitotic spindle formation. Do the very different roles for these evolutionarily related motors translate into differences in how they generate movement? We have addressed this question by examining when in the ATPase cycle the Eg5 motor domain and neck linker move through the use of a series of novel spectroscopic probes utilizing fluorescence resonance energy transfer, and we have compared our results to kinesin I. Our results are consistent with a model in which movement in Eg5 occurs in two sequential steps, an ATP-dependent docking of the neck linker, followed by a rotation or "rolling" of the entire motor domain on the microtubule surface that occurs with ATP hydrolysis. These two forms of movement are consistent with the functions of a motor designed to generate sustained opposing force, and hence, our findings support the argument that the mechanochemical features of a molecular motor are shaped more by the demands placed on it than by its particular family of origin.
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Affiliation(s)
- Steven S Rosenfeld
- Department of Neurology, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA.
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50
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Miranda JJL, De Wulf P, Sorger PK, Harrison SC. The yeast DASH complex forms closed rings on microtubules. Nat Struct Mol Biol 2005; 12:138-43. [PMID: 15640796 DOI: 10.1038/nsmb896] [Citation(s) in RCA: 219] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2004] [Accepted: 01/03/2005] [Indexed: 01/24/2023]
Abstract
The Saccharomyces cerevisiae DASH complex is an essential microtubule-binding component of the kinetochore. We coexpressed all ten subunits of this assembly in Escherichia coli and purified a single complex, a approximately 210-kDa heterodecamer with an apparent stoichiometry of one copy of each subunit. The hydrodynamic properties of the recombinant assembly are indistinguishable from those of the native complex in yeast extracts. The structure of DASH alone and bound to microtubules was visualized by EM. The free heterodecamer is relatively globular. In the presence of microtubules, DASH oligomerizes to form rings and paired helices that encircle the microtubules. We discuss potential roles for such collar-like structures in maintaining microtubule attachment and spindle integrity during chromosome segregation.
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Affiliation(s)
- J J L Miranda
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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