1
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Sumiyoshi R, Yamagishi M, Furuta A, Nishizaka T, Furuta K, Cross RA, Yajima J. Tether-scanning the kinesin motor domain reveals a core mechanical action. Proc Natl Acad Sci U S A 2024; 121:e2403739121. [PMID: 39012822 DOI: 10.1073/pnas.2403739121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 06/17/2024] [Indexed: 07/18/2024] Open
Abstract
Natural kinesin motors are tethered to their cargoes via short C-terminal or N-terminal linkers, whose docking against the core motor domain generates directional force. It remains unclear whether linker docking is the only process contributing directional force or whether linker docking is coupled to and amplifies an underlying, more fundamental force-generating mechanical cycle of the kinesin motor domain. Here, we show that kinesin motor domains tethered via double-stranded DNAs (dsDNAs) attached to surface loops drive robust microtubule (MT) gliding. Tethering using dsDNA attached to surface loops disconnects the C-terminal neck-linker and the N-terminal cover strand so that their dock-undock cycle cannot exert force. The most effective attachment positions for the dsDNA tether are loop 2 or loop 10, which lie closest to the MT plus and minus ends, respectively. In three cases, we observed minus-end-directed motility. Our findings demonstrate an underlying, potentially ancient, force-generating core mechanical action of the kinesin motor domain, which drives, and is amplified by, linker docking.
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Affiliation(s)
- Rieko Sumiyoshi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan
| | - Masahiko Yamagishi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan
- Komaba Institute for Science, The University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan
| | - Akane Furuta
- Kobe Frontier Research Center, National Institute of Information and Communications Technology, Kobe, Hyogo 651-2492, Japan
| | - Takayuki Nishizaka
- Department of Physics, Gakushuin University, Toshima-ku, Tokyo 171-8588, Japan
| | - Ken'ya Furuta
- Kobe Frontier Research Center, National Institute of Information and Communications Technology, Kobe, Hyogo 651-2492, Japan
| | - Robert A Cross
- Centre for Mechanochemical Cell Biology, Warwick Medical School, Gibbet Hill, Coventry CV4 7AL, United Kingdom
| | - Junichiro Yajima
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan
- Komaba Institute for Science, The University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan
- Research Center for Complex Systems Biology, Universal Biology Institute, The University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan
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2
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Anchoring geometry is a significant factor in determining the direction of kinesin-14 motility on microtubules. Sci Rep 2022; 12:15417. [PMID: 36104376 PMCID: PMC9474454 DOI: 10.1038/s41598-022-19589-4] [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: 06/03/2022] [Accepted: 08/31/2022] [Indexed: 11/25/2022] Open
Abstract
Kinesin-14 microtubule-based motors have an N-terminal tail attaching the catalytic core to its load and usually move towards microtubule minus ends, whilst most other kinesins have a C-terminal tail and move towards plus ends. Loss of conserved sequences external to the motor domain causes kinesin-14 to switch to plus-end motility, showing that an N-terminal attachment is compatible with plus-end motility. However, there has been no systematic study on the role of attachment position in minus-end motility. We therefore examined the motility of monomeric kinesin-14s differing only in their attachment point. We find that a C-terminal attachment point causes kinesin-14s to become plus-end-directed, with microtubule corkscrewing rotation direction and pitch in motility assays similar to that of kinesin-1, suggesting that both C-kinesin kinesins-14 and N-kinesin kinesin-1 share a highly conserved catalytic core function with an intrinsic plus-end bias. Thus, an N-terminal attachment is one of the requirements for minus-end motility in kinesin-14.
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3
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Raudaskoski M. Kinesin Motors in the Filamentous Basidiomycetes in Light of the Schizophyllum commune Genome. J Fungi (Basel) 2022; 8:jof8030294. [PMID: 35330296 PMCID: PMC8950801 DOI: 10.3390/jof8030294] [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: 02/12/2022] [Revised: 03/03/2022] [Accepted: 03/08/2022] [Indexed: 12/10/2022] Open
Abstract
Kinesins are essential motor molecules of the microtubule cytoskeleton. All eukaryotic organisms have several genes encoding kinesin proteins, which are necessary for various cell biological functions. During the vegetative growth of filamentous basidiomycetes, the apical cells of long leading hyphae have microtubules extending toward the tip. The reciprocal exchange and migration of nuclei between haploid hyphae at mating is also dependent on cytoskeletal structures, including the microtubules and their motor molecules. In dikaryotic hyphae, resulting from a compatible mating, the nuclear location, synchronous nuclear division, and extensive nuclear separation at telophase are microtubule-dependent processes that involve unidentified molecular motors. The genome of Schizophyllum commune is analyzed as an example of a species belonging to the Basidiomycota subclass, Agaricomycetes. In this subclass, the investigation of cell biology is restricted to a few species. Instead, the whole genome sequences of several species are now available. The analyses of the mating type genes and the genes necessary for fruiting body formation or wood degrading enzymes in several genomes of Agaricomycetes have shown that they are controlled by comparable systems. This supports the idea that the genes regulating the cell biological process in a model fungus, such as the genes encoding kinesin motor molecules, are also functional in other filamentous Agaricomycetes.
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Affiliation(s)
- Marjatta Raudaskoski
- Molecular Plant Biology, Department of Life Technologies, University of Turku, 20014 Turku, Finland
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4
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Morikawa M, Jerath NU, Ogawa T, Morikawa M, Tanaka Y, Shy ME, Zuchner S, Hirokawa N. A neuropathy-associated kinesin KIF1A mutation hyper-stabilizes the motor-neck interaction during the ATPase cycle. EMBO J 2022; 41:e108899. [PMID: 35132656 PMCID: PMC8886545 DOI: 10.15252/embj.2021108899] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 11/09/2022] Open
Abstract
The mechanochemical coupling of ATPase hydrolysis and conformational dynamics in kinesin motors facilitates intramolecular interaction cycles between the kinesin motor and neck domains, which are essential for microtubule-based motility. Here, we characterized a charge-inverting KIF1A-E239K mutant that we identified in a family with axonal-type Charcot-Marie-Tooth disease and also in 24 cases in human neuropathies including spastic paraplegia and hereditary sensory and autonomic neuropathy. We show that Glu239 in the β7 strand is a key residue of the motor domain that regulates the motor-neck interaction. Expression of the KIF1A-E239K mutation has decreased ability to complement Kif1a+/- neurons, and significantly decreases ATPase activity and microtubule gliding velocity. X-ray crystallography shows that this mutation causes an excess positive charge on β7, which may electrostatically interact with a negative charge on the neck. Quantitative mass spectrometric analysis supports that the mutation hyper-stabilizes the motor-neck interaction at the late ATP hydrolysis stage. Thus, the negative charge of Glu239 dynamically regulates the kinesin motor-neck interaction, promoting release of the neck from the motor domain upon ATP hydrolysis.
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Affiliation(s)
- Manatsu Morikawa
- Department of Cell Biology and AnatomyGraduate School of MedicineThe University of TokyoTokyoJapan
| | - Nivedita U Jerath
- Department of NeurologyCarver College of MedicineUniversity of IowaIowa CityIAUSA,Neuromuscular DivisionAdventHealth OrlandoWinter ParkFLUSA
| | - Tadayuki Ogawa
- Department of Cell Biology and AnatomyGraduate School of MedicineThe University of TokyoTokyoJapan,Research Center for Advanced Medical ScienceDokkyo Medical UniversityMibuJapan
| | - Momo Morikawa
- Department of Cell Biology and AnatomyGraduate School of MedicineThe University of TokyoTokyoJapan,Department of Anatomy and NeuroscienceFaculty of MedicineUniversity of TsukubaTsukubaJapan
| | - Yosuke Tanaka
- Department of Cell Biology and AnatomyGraduate School of MedicineThe University of TokyoTokyoJapan
| | - Michael E Shy
- Department of NeurologyCarver College of MedicineUniversity of IowaIowa CityIAUSA
| | - Stephan Zuchner
- Department of Human Genetics and Hussman Institute for Human GenomicsMiller School of MedicineUniversity of MiamiMiamiFLUSA
| | - Nobutaka Hirokawa
- Department of Cell Biology and AnatomyGraduate School of MedicineThe University of TokyoTokyoJapan
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5
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Neijenhuis T, van Keulen SC, Bonvin AMJJ. Interface refinement of low- to medium-resolution Cryo-EM complexes using HADDOCK2.4. Structure 2022; 30:476-484.e3. [PMID: 35216656 DOI: 10.1016/j.str.2022.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 11/25/2021] [Accepted: 01/28/2022] [Indexed: 10/19/2022]
Abstract
A wide range of cellular processes requires the formation of multimeric protein complexes. The rise of cryo-electron microscopy (cryo-EM) has enabled the structural characterization of these protein assemblies. The density maps produced can, however, still suffer from limited resolution, impeding the process of resolving structures at atomic resolution. In order to solve this issue, monomers can be fitted into low- to medium-resolution maps. Unfortunately, the models produced frequently contain atomic clashes at the protein-protein interfaces (PPIs), as intermolecular interactions are typically not considered during monomer fitting. Here, we present a refinement approach based on HADDOCK2.4 to remove intermolecular clashes and optimize PPIs. A dataset of 14 cryo-EM complexes was used to test eight protocols. The best-performing protocol, consisting of a semi-flexible simulated annealing refinement with centroid restraints on the monomers, was able to decrease intermolecular atomic clashes by 98% without significantly deteriorating the quality of the cryo-EM density fit.
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Affiliation(s)
- Tim Neijenhuis
- Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Science for Life, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Siri C van Keulen
- Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Science for Life, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Alexandre M J J Bonvin
- Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Science for Life, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands.
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6
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Yamagishi M, Maruyama Y, Sugawa M, Yajima J. Characterization of the motility of monomeric kinesin-5/Cin8. Biochem Biophys Res Commun 2021; 555:115-120. [PMID: 33845395 DOI: 10.1016/j.bbrc.2021.03.134] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 03/24/2021] [Indexed: 12/30/2022]
Abstract
Cin8, the Saccharomyces cerevisiae kinesin-5, has an essential role in mitosis. In in vitro motility assays, tetrameric and dimeric Cin8 constructs showed bidirectional motility in response to ionic strength or Cin8 motor density. However, whether property-switching directionality is present in a monomeric form of Cin8 is unknown. Here we engineered monomeric Cin8 constructs with and without the Cin8-specific ∼99 residues in the loop 8 domain and examined the directionality of these constructs using an in vitro polarity-marked microtubule gliding assay within the range of the motor density or ionic strength. We found that both monomeric constructs showed only plus end-directed activity over the ranges measured, which suggested that minus end-directed motility driven by Cin8 is necessary for at least dimeric forms. Using an in vitro microtubule corkscrewing assay, we also found that monomeric Cin8 corkscrewed microtubules around their longitudinal axes with a constant left-handed pitch. Overall, our results imply that plus-end-directed and left-handed motor activity comprise the intrinsic properties of the Cin8 motor domain as with other monomeric N-kinesins.
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Affiliation(s)
- Masahiko Yamagishi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Yohei Maruyama
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Mitsuhiro Sugawa
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan; Komaba Institute for Science, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Junichiro Yajima
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan; Komaba Institute for Science, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan; Research Center for Complex Systems Biology, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan.
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7
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Maruyama Y, Sugawa M, Yamaguchi S, Davies T, Osaki T, Kobayashi T, Yamagishi M, Takeuchi S, Mishima M, Yajima J. CYK4 relaxes the bias in the off-axis motion by MKLP1 kinesin-6. Commun Biol 2021; 4:180. [PMID: 33568771 PMCID: PMC7876049 DOI: 10.1038/s42003-021-01704-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 01/14/2021] [Indexed: 12/18/2022] Open
Abstract
Centralspindlin, a complex of the MKLP1 kinesin-6 and CYK4 GAP subunits, plays key roles in metazoan cytokinesis. CYK4-binding to the long neck region of MKLP1 restricts the configuration of the two MKLP1 motor domains in the centralspindlin. However, it is unclear how the CYK4-binding modulates the interaction of MKLP1 with a microtubule. Here, we performed three-dimensional nanometry of a microbead coated with multiple MKLP1 molecules on a freely suspended microtubule. We found that beads driven by dimeric MKLP1 exhibited persistently left-handed helical trajectories around the microtubule axis, indicating torque generation. By contrast, centralspindlin, like monomeric MKLP1, showed similarly left-handed but less persistent helical movement with occasional rightward movements. Analysis of the fluctuating helical movement indicated that the MKLP1 stochastically makes off-axis motions biased towards the protofilament on the left. CYK4-binding to the neck domains in MKLP1 enables more flexible off-axis motion of centralspindlin, which would help to avoid obstacles along crowded spindle microtubules. Analysing the 3D movement of MKLP1 motors, Maruyama et al. find that dimeric C. elegans MKLP1 drives a left-handed helical motion around the microtubule with minimum protofilament switching to the right side whereas less persistent motions are driven by monomers or by heterotetramers with CYK4. These findings suggest how obstacles along crowded spindle microtubules may be avoided by CYK4 binding to MKLP1.
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Affiliation(s)
- Yohei Maruyama
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Mitsuhiro Sugawa
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, Japan.,Komaba Institute for Science, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Shin Yamaguchi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Tim Davies
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK.,Department of Biosciences, Durham University, Durham, UK
| | - Toshihisa Osaki
- Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Takuya Kobayashi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Masahiko Yamagishi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, Japan.,Komaba Institute for Science, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Shoji Takeuchi
- Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo, Japan.,Research Center for complex Systems Biology, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Masanori Mishima
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK.
| | - Junichiro Yajima
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, Japan. .,Komaba Institute for Science, The University of Tokyo, Meguro-ku, Tokyo, Japan. .,Research Center for complex Systems Biology, The University of Tokyo, Meguro-ku, Tokyo, Japan.
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8
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How Kinesin-1 Utilize the Energy of Nucleotide: The Conformational Changes and Mechanochemical Coupling in the Unidirectional Motion of Kinesin-1. Int J Mol Sci 2020; 21:ijms21186977. [PMID: 32972035 PMCID: PMC7555842 DOI: 10.3390/ijms21186977] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/12/2020] [Accepted: 09/21/2020] [Indexed: 12/23/2022] Open
Abstract
Kinesin-1 is a typical motile molecular motor and the founding member of the kinesin family. The most significant feature in the unidirectional motion of kinesin-1 is its processivity. To realize the fast and processive movement on the microtubule lattice, kinesin-1 efficiently transforms the chemical energy of nucleotide binding and hydrolysis to the energy of mechanical movement. The chemical and mechanical cycle of kinesin-1 are coupled to avoid futile nucleotide hydrolysis. In this paper, the research on the mechanical pathway of energy transition and the regulating mechanism of the mechanochemical cycle of kinesin-1 is reviewed.
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9
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Yamagishi M, Fujimura S, Sugawa M, Nishizaka T, Yajima J. N‐terminal β‐strand of single‐headed kinesin‐1 can modulate the off‐axis force‐generation and resultant rotation pitch. Cytoskeleton (Hoboken) 2020; 77:351-361. [DOI: 10.1002/cm.21630] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/08/2020] [Accepted: 08/20/2020] [Indexed: 02/04/2023]
Affiliation(s)
- Masahiko Yamagishi
- Department of Life Sciences, Graduate School of Arts and Sciences The University of Tokyo Tokyo Japan
- Komaba Institute for Science The University of Tokyo Tokyo Japan
| | | | - Mitsuhiro Sugawa
- Department of Life Sciences, Graduate School of Arts and Sciences The University of Tokyo Tokyo Japan
- Komaba Institute for Science The University of Tokyo Tokyo Japan
| | | | - Junichiro Yajima
- Department of Life Sciences, Graduate School of Arts and Sciences The University of Tokyo Tokyo Japan
- Komaba Institute for Science The University of Tokyo Tokyo Japan
- Research Center for Complex Systems Biology The University of Tokyo Tokyo Japan
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10
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Swentowsky KW, Gent JI, Lowry EG, Schubert V, Ran X, Tseng KF, Harkess AE, Qiu W, Dawe RK. Distinct kinesin motors drive two types of maize neocentromeres. Genes Dev 2020; 34:1239-1251. [PMID: 32820038 PMCID: PMC7462060 DOI: 10.1101/gad.340679.120] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 07/28/2020] [Indexed: 12/26/2022]
Abstract
A maize chromosome variant called abnormal chromosome 10 (Ab10) converts knobs on chromosome arms into neocentromeres, causing their preferential segregation to egg cells in a process known as meiotic drive. We previously demonstrated that the gene Kinesin driver (Kindr) on Ab10 encodes a kinesin-14 required to mobilize neocentromeres made up of the major tandem repeat knob180. Here we describe a second kinesin-14 gene, TR-1 kinesin (Trkin), that is required to mobilize neocentromeres made up of the minor tandem repeat TR-1. Trkin lies in a 4-Mb region of Ab10 that is not syntenic with any other region of the maize genome and shows extraordinary sequence divergence from Kindr and other kinesins in plants. Despite its unusual structure, Trkin encodes a functional minus end-directed kinesin that specifically colocalizes with TR-1 in meiosis, forming long drawn out neocentromeres. TRKIN contains a nuclear localization signal and localizes to knobs earlier in prophase than KINDR. The fact that TR-1 repeats often co-occur with knob180 repeats suggests that the current role of the TRKIN/TR-1 system is to facilitate the meiotic drive of the KINDR/knob180 system.
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Affiliation(s)
- Kyle W Swentowsky
- Department of Plant Biology, University of Georgia, Athens Georgia 30602, USA
| | - Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens Georgia 30602, USA
| | - Elizabeth G Lowry
- Department of Plant Biology, University of Georgia, Athens Georgia 30602, USA
| | - Veit Schubert
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466 Seeland, Germany
| | - Xia Ran
- Department of Physics, Oregon State University, Corvallis, Oregon 97331, USA.,Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, USA
| | - Kuo-Fu Tseng
- Department of Physics, Oregon State University, Corvallis, Oregon 97331, USA.,Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, USA
| | - Alex E Harkess
- Department of Plant Biology, University of Georgia, Athens Georgia 30602, USA
| | - Weihong Qiu
- Department of Physics, Oregon State University, Corvallis, Oregon 97331, USA.,Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, USA
| | - R Kelly Dawe
- Department of Plant Biology, University of Georgia, Athens Georgia 30602, USA.,Department of Genetics, University of Georgia, Athens Georgia 30602, USA
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11
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Matsuda K, Sugawa M, Yamagishi M, Kodera N, Yajima J. Visualizing dynamic actin cross‐linking processes driven by the actin‐binding protein anillin. FEBS Lett 2019; 594:1237-1247. [DOI: 10.1002/1873-3468.13720] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/26/2019] [Accepted: 12/09/2019] [Indexed: 01/16/2023]
Affiliation(s)
- Kyohei Matsuda
- Department of Life Sciences Graduate School of Arts and Sciences The University of Tokyo Japan
| | - Mitsuhiro Sugawa
- Department of Life Sciences Graduate School of Arts and Sciences The University of Tokyo Japan
- Komaba Institute for Science The University of Tokyo Japan
| | - Masahiko Yamagishi
- Department of Life Sciences Graduate School of Arts and Sciences The University of Tokyo Japan
- Komaba Institute for Science The University of Tokyo Japan
| | - Noriyuki Kodera
- Nano Life Science Institute (WPI‐NanoLSI) Kanazawa University Japan
| | - Junichiro Yajima
- Department of Life Sciences Graduate School of Arts and Sciences The University of Tokyo Japan
- Komaba Institute for Science The University of Tokyo Japan
- Research Center for Complex Systems Biology The University of Tokyo Japan
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12
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Interactions between motor domains in kinesin-14 Ncd - a molecular dynamics study. Biochem J 2019; 476:2449-2462. [PMID: 31416830 DOI: 10.1042/bcj20190484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/11/2019] [Accepted: 08/15/2019] [Indexed: 11/17/2022]
Abstract
Minus-end directed, non-processive kinesin-14 Ncd is a dimeric protein with C-terminally located motor domains (heads). Generation of the power-stroke by Ncd consists of a lever-like rotation of a long superhelical 'stalk' segment while one of the kinesin's heads is bound to the microtubule. The last ∼30 amino acids of Ncd head play a crucial but still poorly understood role in this process. Here, we used accelerated molecular dynamics simulations to explore the conformational dynamics of several systems built upon two crystal structures of Ncd, the asymmetrical T436S mutant in pre-stroke/post-stroke conformations of two partner subunits and the symmetrical wild-type protein in pre-stroke conformation of both subunits. The results revealed a new conformational state forming following the inward motion of the subunits and stabilized with several hydrogen bonds to residues located on the border or within the C-terminal linker, i.e. a modeled extension of the C-terminus by residues 675-683. Forming of this new, compact Ncd conformation critically depends on the length of the C-terminus extending to at least residue 681. Moreover, the associative motion leading to the compact conformation is accompanied by a partial lateral rotation of the stalk. We propose that the stable compact conformation of Ncd may represent an initial state of the working stroke.
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13
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Structural basis for power stroke vs. Brownian ratchet mechanisms of motor proteins. Proc Natl Acad Sci U S A 2019; 116:19777-19785. [PMID: 31506355 DOI: 10.1073/pnas.1818589116] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Two mechanisms have been proposed for the function of motor proteins: The power stroke and the Brownian ratchet. The former refers to generation of a large downhill free energy gradient over which the motor protein moves nearly irreversibly in making a step, whereas the latter refers to biasing or rectifying the diffusive motion of the motor. Both mechanisms require input of free energy, which generally involves the processing of an ATP (adenosine 5'-triphosphate) molecule. Recent advances in experiments that reveal the details of the stepping motion of motor proteins, together with computer simulations of atomistic structures, have provided greater insights into the mechanisms. Here, we compare the various models of the power stroke and the Brownian ratchet that have been proposed. The 2 mechanisms are not mutually exclusive, and various motor proteins employ them to different extents to perform their biological function. As examples, we discuss linear motor proteins Kinesin-1 and myosin-V, and the rotary motor F1-ATPase, all of which involve a power stroke as the essential element of their stepping mechanism.
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14
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Shigematsu H, Imasaki T, Doki C, Sumi T, Aoki M, Uchikubo-Kamo T, Sakamoto A, Tokuraku K, Shirouzu M, Nitta R. Structural insight into microtubule stabilization and kinesin inhibition by Tau family MAPs. J Cell Biol 2018; 217:4155-4163. [PMID: 30275105 PMCID: PMC6279373 DOI: 10.1083/jcb.201711182] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 07/02/2018] [Accepted: 09/11/2018] [Indexed: 11/22/2022] Open
Abstract
The Tau family of microtubule-associated proteins promote microtubule stabilization or regulate microtubule-based motility. Shigematsu et al. visualized MAP4 and microtubules complexed with kinesin-1 by cryo-EM, which suggests a structural basis of microtubule stabilization and kinesin inhibition by Tau family MAPs. The Tau family microtubule-associated proteins (MAPs) promote microtubule stabilization and regulate microtubule-based motility. They share the C-terminal microtubule-binding domain, which includes three to five tubulin-binding repeats. Different numbers of repeats formed by alternative splicing have distinct effects on the activities of these proteins, and the distribution of these variants regulates fundamental physiological phenomena in cells. In this study, using cryo-EM, we visualized the MAP4 microtubule complex with the molecular motor kinesin-1. MAP4 bound to the C-terminal domains of tubulins along the protofilaments stabilizes the longitudinal contacts of the microtubule. The strongest bond of MAP4 was found around the intertubulin–dimer interface such that MAP4 coexists on the microtubule with kinesin-1 bound to the intratubulin–dimer interface as well. MAP4, consisting of five repeats, further folds and accumulates above the intertubulin–dimer interface, interfering with kinesin-1 movement. Therefore, these cryo-EM studies reveal new insight into the structural basis of microtubule stabilization and inhibition of kinesin motility by the Tau family MAPs.
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Affiliation(s)
- Hideki Shigematsu
- RIKEN Center for Life Science Technologies, Yokohama, Japan.,RIKEN SPring-8 Center, Hyogo, Japan
| | - Tsuyoshi Imasaki
- Division of Structural Medicine and Anatomy, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Japan.,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Saitama, Japan
| | - Chihiro Doki
- Division of Applied Science and Engineering, Course of Biosystem, Graduate School of Muroran Institute of Technology, Muroran, Japan
| | - Takuya Sumi
- Division of Structural Medicine and Anatomy, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Mari Aoki
- RIKEN Center for Life Science Technologies, Yokohama, Japan.,RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Tomomi Uchikubo-Kamo
- RIKEN Center for Life Science Technologies, Yokohama, Japan.,RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Ayako Sakamoto
- RIKEN Center for Life Science Technologies, Yokohama, Japan.,RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Kiyotaka Tokuraku
- Division of Applied Science and Engineering, Course of Biosystem, Graduate School of Muroran Institute of Technology, Muroran, Japan
| | - Mikako Shirouzu
- RIKEN Center for Life Science Technologies, Yokohama, Japan.,RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Ryo Nitta
- RIKEN Center for Life Science Technologies, Yokohama, Japan .,Division of Structural Medicine and Anatomy, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Japan
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15
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Gicking AM, Swentowsky KW, Dawe RK, Qiu W. Functional diversification of the kinesin‐14 family in land plants. FEBS Lett 2018; 592:1918-1928. [DOI: 10.1002/1873-3468.13094] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 04/24/2018] [Accepted: 05/05/2018] [Indexed: 01/01/2023]
Affiliation(s)
| | | | - R. Kelly Dawe
- Department of Plant Biology University of Georgia Athens GA USA
- Department of Genetics University of Georgia Athens GA USA
| | - Weihong Qiu
- Department of Physics Oregon State University Corvallis OR USA
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16
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Nitta R, Imasaki T, Nitta E. Recent progress in structural biology: lessons from our research history. Microscopy (Oxf) 2018; 67:4996565. [PMID: 29771342 DOI: 10.1093/jmicro/dfy022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 04/25/2018] [Indexed: 11/13/2022] Open
Abstract
The recent 'resolution revolution' in structural analyses of cryo-electron microscopy (cryo-EM) has drastically changed the research strategy for structural biology. In addition to X-ray crystallography and nuclear magnetic resonance spectroscopy, cryo-EM has achieved the structural analysis of biological molecules at near-atomic resolution, resulting in the Nobel Prize in Chemistry 2017. The effect of this revolution has spread within the biology and medical science fields affecting everything from basic research to pharmaceutical development by visualizing atomic structure. As we have used cryo-EM as well as X-ray crystallography since 2000 to elucidate the molecular mechanisms of the fundamental phenomena in the cell, here we review our research history and summarize our findings. In the first half of the review, we describe the structural mechanisms of microtubule-based motility of molecular motor kinesin by using a joint cryo-EM and X-ray crystallography method. In the latter half, we summarize our structural studies on transcriptional regulation by X-ray crystallography of in vitro reconstitution of a multi-protein complex.
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Affiliation(s)
- Ryo Nitta
- Division of Structural Medicine and Anatomy, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan
- RIKEN Center for Life Science Technologies, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Tsuyoshi Imasaki
- Division of Structural Medicine and Anatomy, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan
- RIKEN Center for Life Science Technologies, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Eriko Nitta
- Division of Structural Medicine and Anatomy, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan
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17
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Kato Y, Miyakawa T, Tanokura M. Overview of the mechanism of cytoskeletal motors based on structure. Biophys Rev 2018; 10:571-581. [PMID: 29235081 PMCID: PMC5899727 DOI: 10.1007/s12551-017-0368-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 11/19/2017] [Indexed: 12/31/2022] Open
Abstract
In the last two decades, a wealth of structural and functional knowledge has been obtained for the three major cytoskeletal motor proteins, myosin, kinesin and dynein, which we review here. The cytoskeletal motor proteins myosin and kinesin are structurally similar in the core architecture of their motor domains and have similar force-producing mechanisms that are coupled with the chemical cycles of ATP binding, hydrolysis, Pi release and subsequent ADP release. The force is generated through conformational changes in the motor domain during Pi release and ATP binding in myosin and kinesin, respectively, and then converted into the rotation of the lever arm or neck linker (referred to as a power stroke) through the common structural pathways. On the other hand, the dynein cytoskeletal motor is an AAA+ protein and has a different structure and power stroke mechanism from those of myosins and kinesins. The linker protruding from the AAA+ ring of dynein swings according to the ATPase states, which, presumably, generates force to carry cargos within a cell. The communication mechanism between the track-binding and ATPase domains of dynein is unique because the two helices that presumably slide with respect to each other work as coordinators for these domains. Details of the mechanism underlying the power stroke and interdomain communication were revealed through recent progress in the structural studies of myosin, kinesin and dynein.
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Affiliation(s)
- Yusuke Kato
- Institute for Enzyme Research, Tokushima University, Tokushima, Japan
| | - Takuya Miyakawa
- Laboratory of Basic Science on Healthy Longevity, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Masaru Tanokura
- Laboratory of Basic Science on Healthy Longevity, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
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18
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Furuta K, Furuta A. Re-engineering of protein motors to understand mechanisms biasing random motion and generating collective dynamics. Curr Opin Biotechnol 2017; 51:39-46. [PMID: 29179022 DOI: 10.1016/j.copbio.2017.11.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 11/12/2017] [Accepted: 11/14/2017] [Indexed: 11/25/2022]
Abstract
A considerable amount of insight into the mechanisms of protein-based biomolecular motors has been accumulated over decades of research. However, our knowledge about the design principles of these motors is still limited. Even less is known about the design of multi-motor systems that perform various functions within the cell. Here we focus on constructive (or synthetic) approaches to biomolecular motors that could make a breakthrough in our understanding. Recent achievements include studies at different hierarchical levels of complexity: re-engineering of individual motors, construction of multi-motor systems, and generation of large-scale complex behaviour. We then propose a strategy where the collective behaviour can be repeatedly tested upon modifying individual motors, which may provide important clues about how biomolecular motors and their systems are designed.
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Affiliation(s)
- Ken'ya Furuta
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe, Hyogo 651-2492, Japan.
| | - Akane Furuta
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe, Hyogo 651-2492, Japan
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19
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Hwang W, Lang MJ, Karplus M. Kinesin motility is driven by subdomain dynamics. eLife 2017; 6:28948. [PMID: 29111975 PMCID: PMC5718755 DOI: 10.7554/elife.28948] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 11/03/2017] [Indexed: 12/13/2022] Open
Abstract
The microtubule (MT)-associated motor protein kinesin utilizes its conserved ATPase head to achieve diverse motility characteristics. Despite considerable knowledge about how its ATPase activity and MT binding are coupled to the motility cycle, the atomic mechanism of the core events remain to be found. To obtain insights into the mechanism, we performed 38.5 microseconds of all-atom molecular dynamics simulations of kinesin-MT complexes in different nucleotide states. Local subdomain dynamics were found to be essential for nucleotide processing. Catalytic water molecules are dynamically organized by the switch domains of the nucleotide binding pocket while ATP is torsionally strained. Hydrolysis products are 'pulled' by switch-I, and a new ATP is 'captured' by a concerted motion of the α0/L5/switch-I trio. The dynamic and wet kinesin-MT interface is tuned for rapid interactions while maintaining specificity. The proposed mechanism provides the flexibility necessary for walking in the crowded cellular environment. Motor proteins called kinesins perform a number of different roles inside cells, including transporting cargo and organizing filaments called microtubules to generate the force needed for a cell to divide. Kinesins move along the microtubules, with different kinesins moving in different ways: some ‘walk’, some jump, and some destroy the microtubule as they travel along it. All kinesins power their movements using the same molecule as fuel – adenosine triphosphate, known as ATP for short. Energy stored in ATP is released by a chemical reaction known as hydrolysis, which uses water to break off specific parts of the ATP molecule. The site to which ATP binds in a kinesin has a similar structure to the ATP binding site of many other proteins that use ATP. However, little was known about the way in which kinesin uses ATP as a fuel, including how ATP binds to kinesin and is hydrolyzed, and how the products of hydrolysis are released. These events are used to power the motor protein. Hwang et al. have used powerful computer simulation methods to examine in detail how ATP interacts with kinesin whilst moving across a microtubule. The simulations suggest that regions (or 'domains') of kinesin near the ATP binding site move around to help in processing ATP. These kinesin domains trap a nearby ATP molecule from the environment and help to deliver water molecules to ATP for hydrolysis. Hwang et al. also found that the domain motion subsequently helps in the release of the hydrolysis products by kinesin. The domains around the ATP pocket vary among the kinesins and these differences may enable kinesins to fine-tune how they use ATP to move. Further investigations will help us understand why different kinesin families behave differently. They will also contribute to exploring how kinesin inhibitors might be used as anti-cancer drugs.
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Affiliation(s)
- Wonmuk Hwang
- Department of Biomedical Engineering, Texas A&M University, College Station, United States.,Department of Materials Science & Engineering, Texas A&M University, College Station, United States.,School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Korea
| | - Matthew J Lang
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, United States.,Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, United States
| | - Martin Karplus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States.,Laboratoire de Chimie Biophysique, ISIS, Université de Strasbourg, Strasbourg, France
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20
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Li L, Jia Z, Peng Y, Godar S, Getov I, Teng S, Alper J, Alexov E. Forces and Disease: Electrostatic force differences caused by mutations in kinesin motor domains can distinguish between disease-causing and non-disease-causing mutations. Sci Rep 2017; 7:8237. [PMID: 28811629 PMCID: PMC5557957 DOI: 10.1038/s41598-017-08419-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 07/10/2017] [Indexed: 01/09/2023] Open
Abstract
The ability to predict if a given mutation is disease-causing or not has enormous potential to impact human health. Typically, these predictions are made by assessing the effects of mutation on macromolecular stability and amino acid conservation. Here we report a novel feature: the electrostatic component of the force acting between a kinesin motor domain and tubulin. We demonstrate that changes in the electrostatic component of the binding force are able to discriminate between disease-causing and non-disease-causing mutations found in human kinesin motor domains using the receiver operating characteristic (ROC). Because diseases may originate from multiple effects not related to kinesin-microtubule binding, the prediction rate of 0.843 area under the ROC plot due to the change in magnitude of the electrostatic force alone is remarkable. These results reflect the dependence of kinesin’s function on motility along the microtubule, which suggests a precise balance of microtubule binding forces is required.
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Affiliation(s)
- Lin Li
- Department of Physics and Astronomy, Clemson University, Clemson, SC, 29634, USA
| | - Zhe Jia
- Department of Physics and Astronomy, Clemson University, Clemson, SC, 29634, USA
| | - Yunhui Peng
- Department of Physics and Astronomy, Clemson University, Clemson, SC, 29634, USA
| | - Subash Godar
- Department of Physics and Astronomy, Clemson University, Clemson, SC, 29634, USA
| | - Ivan Getov
- Department of Chemical Engineering, Clemson University, Clemson, SC, 29634, USA
| | - Shaolei Teng
- Department of Biology, Howard University, Washington, DC, 20059, USA
| | - Joshua Alper
- Department of Physics and Astronomy, Clemson University, Clemson, SC, 29634, USA.
| | - Emil Alexov
- Department of Physics and Astronomy, Clemson University, Clemson, SC, 29634, USA.
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21
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She ZY, Yang WX. Molecular mechanisms of kinesin-14 motors in spindle assembly and chromosome segregation. J Cell Sci 2017; 130:2097-2110. [DOI: 10.1242/jcs.200261] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
ABSTRACT
During eukaryote cell division, molecular motors are crucial regulators of microtubule organization, spindle assembly, chromosome segregation and intracellular transport. The kinesin-14 motors are evolutionarily conserved minus-end-directed kinesin motors that occur in diverse organisms from simple yeasts to higher eukaryotes. Members of the kinesin-14 motor family can bind to, crosslink or slide microtubules and, thus, regulate microtubule organization and spindle assembly. In this Commentary, we present the common subthemes that have emerged from studies of the molecular kinetics and mechanics of kinesin-14 motors, particularly with regard to their non-processive movement, their ability to crosslink microtubules and interact with the minus- and plus-ends of microtubules, and with microtubule-organizing center proteins. In particular, counteracting forces between minus-end-directed kinesin-14 and plus-end-directed kinesin-5 motors have recently been implicated in the regulation of microtubule nucleation. We also discuss recent progress in our current understanding of the multiple and fundamental functions that kinesin-14 motors family members have in important aspects of cell division, including the spindle pole, spindle organization and chromosome segregation.
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Affiliation(s)
- Zhen-Yu She
- The Sperm Laboratory, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wan-Xi Yang
- The Sperm Laboratory, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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