Prof. Takashi Ishikawa

photo of Takashi Ishikawa Group Leader
Cellular Structure Imaging

Paul Scherrer Institute
OFLB/010
5232 Villigen PSI
Switzerland

Telephone: +41 56 310 4217
E-mail: takashi.ishikawa@psi.ch





Research by Takashi Ishikawa

Our main focus is structural biology of eukaryotic flagella/cilia using electron cryo tomography and microscopy (cryo-EM). Cryo-EM provides images of biological macromolecules and organelles in intact hydrated states. Computational image analysis enables three-dimensional reconstruction. For highly symmetrical objects (2D crystal of membrane proteins, tubular crystals) atomic resolution could be reached. For non-crystalline macromolecules and macromolecular complexes, single particle analysis will be applied. In electron cryo-tomography images are acquired multiple times from an ice-embedded specimen tilted continuously in the microscope and merged into a 3D structure. This is a suitable method to analyze macromolecules forming complex and dynamic molecular networks in vivo.

We apply these methods to reveal the mechanism of flagellar/ciliary bending motion. In flagella/cilia, which consist of ~300 proteins, nine microtubule doublets are linked by dynein motor proteins. We are analyzing molecular arrangement of dynein and other proteins by electron tomography and refine high resolution structures by single particle analysis, developing methodologies. Eukaryotic flagella/cilia are bending organelles which drive cells forward or backward, or generate extracellular flows. They exist in sperms, tracheae (respiratory cilia), brain, embryo (nodal cilia) and many other organs. Therefore defects of flagella/cilia cause diseases (ciliopathy). Flagella/cilia are attractive in the view point of nanomachine development.

Flagella and cilia from various species and organisms share the “9+2” axonemal structure, in which nine microtubule doublets surround two singlet microtubules. Adjacent microtubule doublets slide past each other by ATP-driven power stroke of dynein motor proteins. Our research focuses the mechanism of force generation of dynein and the mechanism to integrate dynein power strokes into well-orchestrated bending motion of flagella/cilia. We employed technique of electron cryo-tomography (fig. 1) and 3D image analysis to answer these questions.

3D molecular architecture of outer and inner dynein arms from Chlamydomonas flagella

We extracted 96nm periodic fragments (subtomograms) from tomograms of flagella (fig. 1), aligned and averaged them three-dimensionally (fig. 2). The obtained 3D structure describes the molecular conformation and arrangement of dyneins and other molecules on the microtubule doublets. In the inner dynein arm (which determines the wave form) eight dyneins form a longitudinal array, while the outer arm (responsible for force generation and acceleration) consists of three dyneins stacking vertically. At ~35Å resolution, our averaged tomograms revealed 3D conformation of dynein (which consists of an AAA-ring (ring-shaped ATPase domain), a coiled-coil stalk and an N-terminal tail) in situ. N-terminal tails extend from AAA-rings toward the distal end (= plus end of the microtubule). By combining 3D structures of mutants which lack various dynein isoforms, we identified them in our 3D map (fig. 2).



References:
Bui, K.H., Sakakibara, H., Movassagh, T., Oiwa, K. and Ishikawa, T. (2008) “Molecular architecture of inner dynein arms in situ in Chlamydomonas flagella” J. Cell Biol., 183, 923-932. Ishikawa, T., Sakakibara, H., and Oiwa, K. (2007) “The architecture of outer dynein arms in situ” J. Mol. Biol. 368, 1249-1258.

Structural basis of dynein power stroke and flagellar/ciliary bending

Averaged tomograms of flagella in the presence and in the absence of nucleotides showed the conformational change of dyneins. In the presence of ADP.Vi (Vi: vanadate), which is non-hydrolysable ATP analogue and mimics the pre-power stroke state, the AAA-ring of dynein stays at the proximal (minus end of the microtubule) and the N-terminal tail gradually curves toward the microtubule. However, in the apo state (corresponding to the post-power stroke state), the ATPase head moves toward the distal (plus) end and the N-terminal tail sharply kinks toward the microtubule. This indicates the translational shift of dynein (not rotation), pulls the adjacent microtubule toward the distal end (fig. 3).



In the flagella in the presence of ADP.Vi, this conformational change occurs at about half of dyneins, while the other dyneins stay at the apo conformation, indicating cooperativity among dyneins prohibits other dyneins to change their conformations. Interestingly these two conformations do not appear randomly, but form cluster (fig. 4). This phenomenon provides one hypothesis of flagellar/ciliary bending: torsion is generated at interface between two clusters.



Reference:
Movassagh, T., Bui, K.H., Sakakibara, H., Oiwa, K. and Ishikawa, T. (2010) “Global conformational changes of dynein arms in flagella induced by nucleotides” Nat. Struct. Mol. Biol., 17, 761-767.

Asymmetry of dynein arrangement in Chlamydomonas flagella – mechanism of planar asymmetric bending

We found that the arrangement of inner arm dyneins is not perfectly symmetrical among nine microtubule doublets of the Chlamydomonas flagellum. Two microtubule doublets, which are apposed between two flagella of one Chlamydomonas cell, lacks a few inner arm dyneins (fig. 5), which will results in asymmetric force generation between the internal and external sides of flagellar bending. Our tomographic studies identified linkers which connect only doublets on the bending plane, suggesting the mechanism to limit the flagellar motion planar.



Reference:
Bui, K.H., Sakakibara, H., Movassagh, T., Oiwa, K. and Ishikawa, T. (2009) “Asymmetry of inner dynein arms and inter-doublet links in Chlamydomonas flagella” J. Cell Biol. 186, 437-446.

Our main projects

Bui, K.H. and Ishikawa, T. (2013) “3D structural analysis of flagella/cilia by cryo-electron tomography.” Methods Enzymol., 524, 305-323.

Bui, K.H., Toshiki, Y., Yamamoto, R., Kamiya, R. and Ishikawa, T. (2012) “Polarity and asymmetry in the arrangement of dynein and related structures in the Chlamydomonas axoneme.” J. Cell Biol., 198, 913-925.

Maheshwari, A. and Ishikawa, T. (2012) “Heterogeneity of dynein structure implies coordinated suppression of dynein motor activity in the axoneme.” J. Struct. Biol., 179, 235-241.

Ueno, H., Ishikawa, T., Bui, K.H., Gonda, K., Ishikawa, T. and Yamaguchi, T. (2012) “Mouse respiratory cilia with the asymmetric axonemal structure on sparsely distributed ciliary cells can generate overall directional flow.” Nanomedicine, 8, 1081-1087.

Pigino, G., Maheshwari, A., Bui, K.H., Shingyoji, C., Kamimura, S. and Ishikawa, T. (2012) “Comparative structural analysis of eukaryotic flagella and cilia from Chlamydomonas, Tetrahymena and sea urchins.” J. Struct. Biol., 178, 199-206.

Guichard, P., Desfosses, A., Maheshwari, A., Hachet, V., Dietrich, C., Brune, A., Ishikawa, T., Sachse, C. and Gonczy, P. (2012) “Cartwheel architecture of Trichonympha basal body.” Science, 337, 553.

Pigino, G., Bui, K.H., Maheshwari, A., Lupetti, P., Diener, D. and Ishikawa, T. (2011) “Cryoelectron tomography of radial spokes in cilia and flagella.” J. Cell Biol., 195, 673-687.

Bui, K.H., Pigino, G. and Ishikawa, T. (2011) “3D structural analysis of eukaryotic flagella/cilia by electron cryo-tomography” J. Synchrotron Radiation, 18, 2-5.

Movassagh, T., Bui, K.H., Sakakibara, H., Oiwa, K. and Ishikawa, T. (2010) “Global conformational changes of dynein arms in flagella induced by nucleotides” Nat. Struct. Mol. Biol., 17, 761-767.

Bui, K.H., Sakakibara, H., Movassagh, T., Oiwa, K. and Ishikawa, T. (2009) “Asymmetry of inner dynein arms and inter-doublet links in Chlamydomonas flagella” J. Cell Biol. 186, 437-446.

Bui, K.H., Sakakibara, H., Movassagh, T., Oiwa, K. and Ishikawa, T. (2008) “Molecular architecture of inner dynein arms in situ in Chlamydomonas flagella” J. Cell Biol., 183, 923-932.

Ishikawa, T., Sakakibara, H., and Oiwa, K. (2007) “The architecture of outer dynein arms in situ” J. Mol. Biol. 368, 1249-1258.

Reviews and book chapters

Ishikawa, T. (2014) “Protein tagging reveals new insights into signaling in flagella“ J. Cell Biol. 204, 631-633.

Ishikawa, T. (2012) “Structural biology of cytoplasmic and axonemal dyneins.“ J. Struct. Biol. 179, 229-234.

Pigino, G. and Ishikawa, T. (2012) “Axonemal radial spokes: 3D structure, function and assembly“ BioArchitecture, 2, 50-58.

Ishikawa, T. (2012) “3D structures of axonemes” in “Handbook of Dynein” edited by L. Amos and K. Hirose, Pan Stanford

Ishikawa, T. (2011) “Organization of dyneins and associated regulatory systems in the axoneme” in “Dyneins: Structure, biology and disease” edited by S. King, Elsevier

Collaborations with other groups

Liebi, M., Kuster, S., Kohlbrecher, J., Ishikawa, T., Fischer, P., Walde, P. and Windhab, E.L. (2013) “Cholesterol-diethylenetriaminepentaacetate complexd with thulium ions integrated into bicelles to increase their magnetic alignability.“ J. Phys. Chem. B., 117, 14743-14748.

Liebi, M., Kuster, S., Kohlbrecher, J., Ishikawa, T., Fischer, P., Walde, P. and Windhab, E.L. (2012) “Magnetically enhanced bicelles delivering switchable anisotropy in optical gels.“ ACS Appl. Mater Interfaces, 6, 1100-1105.

Liebi, M., Kohlbrecher, J., Ishikawa, T., Fischer, P., Walde, P. and Windhab, E.L. (2012) “Cholesterol increases the magnetic aligning of bicellar disks from an aqueous mixture of DMPC and DMPE-DTPA with complexed thulium ions.“ Langmuir, 28, 10905-10915.

Lowell, A.N., Qiao, H., Liu, T., Ishikawa, T., Zhang, H., Oriana, S., Wang, M., Ricciotti, E., FitzGerald, G.A., Zhou, R. and Yamakoshi, Y. (2012) “Functionalized low-density lipoprotein nanoparticles for in vivo enhancement of atherosclerosis on magnetic resonance images“ Bioconjug. Chem., 23, 2313-2319.

Tokutsu, R., Kato, N., Bui, K.H., Ishikawa, T. and Minagawa, J. (2012) “Revisiting the supramolecular organization of photosystem II in Chlamydomonas reinhardtii“ J. Biol. Chem., 287, 31574-31581.

Effantin, G., Ishikawa, T., De Donatis, G.M., Maurizi, M.R. and Steven, A.C. (2010) “Local and global mobility in th ClpA AAA+ chaperone detected by cryo-electron microscopy: functional connotations“ Structure, 18, 553-562.

Megli, P., Conte, E. and Ishikawa, T. (2010) “Cholesterol attenuates and prevents bilayer damage and breakdown in lipoperoxidized model membranes. A spin labeling EPR study“ Biochim. Biophys. Acta, 1808, 2267-2274.

Beck, P., Liebi, M., Kohlbrecher, J., Ishikawa, T., Ruegger, H., Zepik, H, Fischer, P., Walde, P. and Windhab, E. (2010) “Novel type of bicellar disks from a mixture of DMPC and DMPE-DTPA with complexed lanthanides“ Langmuir, 26, 5382-5387.

Bleicken, S., Classen, M., Padmavathi, P.V., Ishikawa, T., Zeth, K., Steinhoff, H.J. and Bordignon, E. (2010) “Molecular details of Bax activation, oligomerization and membrane insertion“ J. Biol. Chem. 285, 6636-6647.

Beck, P., Liebi, M., Kohlbrecher, J., Ishikawa, T., Ruegger, H., Zepik, H, Fischer, P., Walde, P. and Windhab, E. (2010) “Magnetic field alignable domains in phospholipid vesicle membranes containing lanthanides“ J. Phys. Chem. B 114, 174-186.

Guo, Z.W., Ruegger, H., Kissner, R., Ishikawa, T., Willeke, M. and Walde, P. (2009) “Vesicles as soft templates for the enzymatic polymerization on aniline“ Langmuir, 25, 11390-11405.

Kato, K., Walde, P., Koike, N., Ichikawa, S., Ishikawa, T., Nagayama, R., Ishihara, T., Tsuji, T., Shudou, M., Omokawa, Y., Kuroiwa, T. (2008) “Temperature-sensitive nonionic vesicles prepared from Span 80 (sorbitan monooleate)” Langmuir, 24, 10762-10770.

Nishiyama, M., Ishikawa, T., Rechsteiner, H. and Glockshuber, R. (2008) “Reconstruction of pilus assembly reveals a bacterial outer membrane catalyst” Science 320, 376-379.

Capone S., Walde P., Seebach D., Ishikawa T. and Caputo R. (2008) “pH-sensitive vesicles containing a lipidic beta-amino acid with two hydrophobic chains” Chem. Biodivers. 5, 16-30.

Zepik, H.H., Walde, P., and Ishikawa, T. (2008) “Vesicle formation from reactive surfactants“ Angew. Chem. Int. Ed. Engl. 47, 1323-1325.

Namani, T., Ishikawa, T., Morigaki, K. and Walde, P. (2007) “Vesicles from docosahexaenoic acid“ Colloids Surf. B Biointerfaces 54, 118-123.

Schaffitzel, C., Oswald, M., Berger, I., Ishikawa, T., Abrahams, J.P., Koerten, H.K., Koning, R.I. and Ban, N. (2006) “Structure of the E. coli signal recognition particle bound to a translating ribosome” Nature 444, 503-506.

List of Publications

2018

  • Botulinum Neurotoxin Diversity from a Gene-Centered View Benoit R
    Toxins 10, 310 (2018).
    DOI: 10.3390/toxins10080310
  • Development of Smart Optical Gels with Highly Magnetically Responsive Bicelles Isabettini S, Stucki S, Massabni S, Baumgartner ME, Reckey PQ, Kohlbrecher J, Ishikawa T, Windhab Erich J, Fischer P, Kuster S
    ACS APPLIED MATERIALS & INTERFACES 10, 8926 (2018).
    DOI: 10.1021/acsami.7b17134

2017

  • Crystal structure of the BoNT/A2 receptor-binding domain in complex with the luminal domain of its neuronal receptor SV2C Benoit RM, Schaerer MA, Wieser MM, Li X, Frey D, Kammerer RA
    Scientific Reports 7, 43588 (2017).
    DOI: 10.1038/srep43588
  • Mastering the magnetic susceptibility of magnetically responsive bicelles with 3?-amino-5-cholestene and complexed lanthanide ions Isabettini S, Liebi M, Kohlbrecher J, Ishikawa T, Fischer P, Windhab Erich J, Walde P, Kuster S
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS 19, 10820 (2017).
    DOI: 10.1039/C7CP01025G
  • Methods for Generating Highly Magnetically Responsive Lanthanide-Chelating Phospholipid Polymolecular Assemblies Isabettini S, Baumgartner Mirjam E, Reckey Pernille Q, Kohlbrecher J, Ishikawa T, Fischer P, Windhab Erich J, Kuster S
    LANGMUIR 33, 6363 (2017).
    DOI: 10.1021/acs.langmuir.7b00725
  • Molecular engineering of lanthanide ion chelating phospholipids generating assemblies with a switched magnetic susceptibility Isabettini S, Massabni S, Hodzic A, Durovic D, Kohlbrecher J, Ishikawa T, Fischer P, Windhab Erich J, Walde P, Kuster S
    Phys. Chem. Chem. Phys. 19, 20991 (2017).
    DOI: 10.1039/C7CP03994H
  • OMNY PIN - A versatile sample holder for tomographic measurements at room and cryogenic temperatures Holler M, Raabe J, Wepf R, Shahmoradian SH, Diaz A, Sarafimov B, Lachat T, Walther H, Vitins M
    REVIEW OF SCIENTIFIC INSTRUMENTS 88, 113701 (2017).
    DOI: 10.1063/1.4996092
  • Three-Dimensional Imaging of Biological Tissue by Cryo X-Ray Ptychography Shahmoradian SH, Tsai EHR, Diaz A, Guizar-Sicairos M, Raabe J, Spycher L, Britschgi M, Ruf A, Stahlberg H, Holler M
    Scientific Reports 7, 6291 (2017).
    DOI: 10.1038/s41598-017-05587-4
Top

2016

  • A simple and fast approach for missing-wedge invariant classification of subtomograms extracted from filamentous structures Obbineni J, Yamamoto R, Ishikawa T
    JOURNAL OF STRUCTURAL BIOLOGY , (2016).
    DOI: 10.1016/j.jsb.2016.08.003
  • Addendum to Three-dimensional mass density mapping of cellular ultrastructure by ptychographic X-ray nanotomography [J. Struct. Biol. 192 (2015) 461-469] Diaz A, Malkova B, Holler M, Guizar-Sicairos M, Lima E, Panneels V, Pigino G, Bittermann A, Wettstein L, Tomizaki T, Bunk O, Schertler G, Ishikawa T, Wepf R, Menzel A
    JOURNAL OF STRUCTURAL BIOLOGY 193, 83 (2016).
    DOI: 10.1016/j.jsb.2015.12.003
  • Biochemie und Molekularbiologie Christen P, Jaussi R, Benoit R
    Springer Verlag Berlin Heidelberg , (2016).
    DOI: 10.1007/978-3-662-46430-4_1
  • Control of the structural landscape and neuronal proteotoxicity of mutant Huntingtin by domains flanking the polyQ tract Shen K, Calamini B, Fauerbach J, Ma B, Shahmoradian S, Serrano Lachapel I, Chiu W, Lo D, Frydman J
    ELIFE 5, (2016).
    DOI: 10.7554/eLife.18065
  • Seamless Insert-Plasmid Assembly at High Efficiency and Low Cost Benoit RM, Ostermeier C, Geiser M, Li JSZ, Widmer H, Auer M
    PLOS ONE 11, e0153158 (2016).
    DOI: 10.1371/journal.pone.0153158
  • Structural basis for misregulation of kinesin KIF21A autoinhibition by CFEOM1 disease mutations Bianchi S, van Riel Wilhelmina E, Kraatz Sebastian HW, Olieric N, Frey D, Katrukha Eugene A, Jaussi R, Missimer J, Grigoriev I, Olieric V, Benoit Roger M, Steinmetz Michel O, Akhmanova A, Kammerer Richard A
    Scientific Reports 6, 30668 (2016).
    DOI: 10.1038/srep30668
  • TRiC subunits enhance BDNF axonal transport and rescue striatal atrophy in Huntington?s disease Zhao X, Chen X, Han E, Hu Y, Paik P, Ding Z, Overman J, Lau Alice L, Shahmoradian SH, Chiu W, Thompson Leslie M, Wu C, Mobley William C
    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 113, E5655 (2016).
    DOI: 10.1073/pnas.1603020113
  • Tailoring Bicelle Morphology and Thermal Stability with Lanthanide-Chelating Cholesterol Conjugates Isabettini S, Liebi M, Kohlbrecher J, Ishikawa T, Windhab Erich J, Fischer P, Walde P, Kuster S
    LANGMUIR 32 (35), 9005 (2016).
    DOI: 10.1021/acs.langmuir.6b01968
Top

2015

  • Bilayer Properties of 1,3-Diamidophospholipids Weinberger A, Tanasescu R, Stefaniu C, Fedotenko lllya A, Favarger F, Ishikawa T, Brezesinski G, Marques Carlos M, Zumbuehl A
    LANGMUIR 31, 1879 (2015).
    DOI: 10.1021/la5041745
  • Cryo-electron tomography of motile cilia and flagella Ishikawa T
    Cilia 4, 3 (2015).
    DOI: 10.1186/s13630-014-0012-7
  • RAFT synthesis of poly(vinylpyrrolidone) amine and preparation of a water-soluble C 60 -PVP conjugate Aroua S, Tiu Elisha Gabrielle V, Ayer M, Ishikawa T, Yamakoshi Y
    Polym. Chem. 6, 2616 (2015).
    DOI: 10.1039/C4PY01333F
  • Structure of the BoNT/A1 - receptor complex Benoit Roger M, Frey D, Wieser Mara M, Thieltges Katherine M, Jaussi R, Capitani G, Kammerer Richard A
    TOXICON 107, 25 (2015).
    DOI: 10.1016/j.toxicon.2015.08.002
  • Synthesis of Single Crystal Nanoreactor Materials with Multiple Catalytic Functions by Incipient Wetness Impregnation and Ion Exchange Fodor D, Ishikawa T, Krumeich F, van Bokhoven Jeroen A
    ADVANCED MATERIALS 27, 1919 (2015).
    DOI: 10.1002/adma.201404628
  • Three-dimensional mass density mapping of cellular ultrastructure by ptychographic X-ray nanotomography Diaz A, Malkova B, Holler M, Guizar-Sicairos M, Lima E, Panneels V, Pigino G, Bittermann A, Wettstein L, Tomizaki T, Bunk O, Schertler G, Ishikawa T, Wepf R, Menzel A
    JOURNAL OF STRUCTURAL BIOLOGY 192, 461 (2015).
    DOI: 10.1016/j.jsb.2015.10.008
  • alpha- and beta-Tubulin Lattice of the Axonemal Microtubule Doublet and Binding Proteins Revealed by Single Particle Cryo-Electron Microscopy and Tomography Maheshwari A, Obbineni J, Bui K, Shibata K, Toyoshima Yoko Y, Ishikawa T
    STRUCTURE 23, 1584 (2015).
    DOI: 10.1016/j.str.2015.06.017
Top

2014

  • Magnetically Enhanced Bicelles Delivering Switchable Anisotropy in Optical Gels Liebi M, Kuster S, Kohlbrecher J, Ishikawa T, Fischer P, Walde P, Windhab EJ
    ACS APPLIED MATERIALS & INTERFACES 6, 1100-1105 (2014).
    DOI: 10.1021/am4046469
  • Preparation of Primary Neurons for Visualizing Neurites in a Frozen-hydrated State Using Cryo-Electron Tomography Shahmoradian SH, Galiano Mauricio R, Wu C, Chen S, Rasband Matthew N, Mobley William C, Chiu W
    Journal of Visualized Experiments -, - (2014).
    DOI: 10.3791/50783
  • Protein tagging reveals new insights into signaling in flagella Ishikawa T
    The Journal of Cell Biology 204, 631 (2014).
    DOI: 10.1083/jcb.201401142
  • Structural basis for recognition of synaptic vesicle protein 2C by botulinum neurotoxin A Benoit Roger M, Frey Daniel, Hilbert Manuel, Kevenaar Josta T, Wieser Mara M, Stirnimann Christian U, McMillan David, Ceska Tom, Lebon Florence, Jaussi Rolf, Steinmetz Michel O, Schertler Gebhard F X, Hoogenraad Casper C, Capitani Guido, Kammerer Richard A
    NATURE 505, 108-+ (2014).
    DOI: 10.1038/nature12732
  • Structure of dimeric axonemal dynein in cilia suggests an alternative mechanism of force generation Ueno H, Bui K, Ishikawa T, Imai Y, Yamaguchi T, Ishikawa T
    Cytoskeleton 71, 412 (2014).
    DOI: 10.1002/cm.21180

2013

  • Anomalous signal from S atoms in protein crystallographic data from an X-ray free-electron laser Barends Thomas R M, Foucar Lutz, Shoeman Robert L, Bari Sadia, Epp Sascha W, Hartmann Robert, Hauser Gunter, Huth Martin, Kieser Christian, Lomb Lukas, Motomura Koji, Nagaya Kiyonobu, Schmidt Carlo, Strecker Rafael, Anielski Denis, Boll Rebecca, Erk Benjamin, Fukuzawa Hironobu, Hartmann Elisabeth, Hatsui Takaki, Holl Peter, Inubushi Yuichi, Ishikawa Tetsuya, Kassemeyer Stephan, Kaiser Christian, Koeck Frank, Kunishima Naoki, Kurka Moritz, Rolles Daniel, Rudek Benedikt, Rudenko Artem, Sato Takahiro, Schroeter Claus-Dieter, Soltau Heike, Strueder Lothar, Tanaka Tomoyuki, Togashi Tadashi, Tono Kensuke, Ullrich Joachim, Yase Satoshi, Wada Shin-ichi, Yao Makoto, Yabashi Makina, Ueda Kiyoshi, Schlichting Ilme
    ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY 69, 838-842 (2013).
    DOI: 10.1107/S0907444913002448
  • TRiC?s tricks inhibit huntingtin aggregation Shahmoradian S, Galaz-Montoya J, Schmid M, Cong Y, Ma B, Spiess C, Frydman J, Ludtke S, Chiu W
    ELIFE 2, - (2013).
    DOI: 10.7554/eLife.00710

2012

  • Comparative structural analysis of eukaryotic flagella and cilia from Chlamydomonas, Tetrahymena, and sea urchins Pigino G, Maheshwari A, Bui K, Shingyoji C, Kamimura S, Ishikawa T
    JOURNAL OF STRUCTURAL BIOLOGY 178, 199 (2012).
    DOI: 10.1016/j.jsb.2012.02.012
  • Functionalized Low-Density Lipoprotein Nanoparticles for in Vivo Enhancement of Atherosclerosis on Magnetic Resonance Images Lowell Andrew N, Qiao H, Liu T, Ishikawa T, Zhang H, Oriana S, Wang M, Ricciotti E, FitzGerald Garret A, Zhou R, Yamakoshi Y
    BIOCONJUGATE CHEMISTRY 23, 2313 (2012).
    DOI: 10.1021/bc300561e
  • Mouse respiratory cilia with the asymmetric axonemal structure on sparsely distributed ciliary cells can generate overall directional flow Ueno H, Ishikawa T, Bui K, Gonda K, Ishikawa T, Yamaguchi T
    Nanomedicine: Nanotechnology, Biology and Medicine 8, 1081 (2012).
    DOI: 10.1016/j.nano.2012.01.004
  • Polarity and asymmetry in the arrangement of dynein and related structures in the Chlamydomonas axoneme Bui K, Yagi T, Yamamoto R, Kamiya R, Ishikawa T
    The Journal of Cell Biology 198, 913 (2012).
    DOI: 10.1083/jcb.201201120
  • Revisiting the Supramolecular Organization of Photosystem II in Chlamydomonas reinhardtii Tokutsu R, Kato N, Bui KH, Ishikawa T, Minagawa J
    JOURNAL OF BIOLOGICAL CHEMISTRY 287, 31574 (2012).
    DOI: 10.1074/jbc.M111.331991
  • Supramolecular Non-Amyloid Intermediates in the Early Stages of ?-Synuclein Aggregation Fauerbach Jonathan A, Yushchenko Dmytro A, Shahmoradian Sarah H, Chiu W, Jovin Thomas M, Jares-Erijman Elizabeth A
    BIOPHYSICAL JOURNAL 102, 1127 (2012).
    DOI: 10.1016/j.bpj.2012.01.051
Top

2011

  • Cholesterol attenuates and prevents bilayer damage and breakdown in lipoperoxidized model membranes. A spin labeling EPR study Megli Francesco M, Conte E, Ishikawa T
    Biochimica et Biophysica Acta (BBA) - Biomembranes 1808, 2267 (2011).
    DOI: 10.1016/j.bbamem.2011.04.016
  • Cryoelectron tomography of radial spokes in cilia and flagella Pigino G, Bui K, Maheshwari A, Lupetti P, Diener D, Ishikawa T
    The Journal of Cell Biology 195, 673 (2011).
    DOI: 10.1083/jcb.201106125

2010

  • Nucleotide-induced global conformational changes of flagellar dynein arms revealed by in situ analysis Movassagh T, Bui K, Sakakibara H, Oiwa K, Ishikawa T
    NATURE STRUCTURAL & MOLECULAR BIOLOGY 17, 761 (2010).
    DOI: 10.1038/nsmb.1832
  • Three-dimensional structural analysis of eukaryotic flagella/cilia by electron cryo-tomography Bui K, Pigino G, Ishikawa T
    JOURNAL OF SYNCHROTRON RADIATION 18, 2 (2010).
    DOI: 10.1107/s0909049510036812

2009

  • Asymmetry of inner dynein arms and inter-doublet links in Chlamydomonas flagella Bui K, Sakakibara H, Movassagh T, Oiwa K, Ishikawa T
    The Journal of Cell Biology 186, 437 (2009).
    DOI: 10.1083/jcb.200903082
  • Terminal Adenosyl Transferase Activity of Posttranscriptional Regulator HuR Revealed by Confocal On-Bead Screening Meisner N, Hintersteiner M, Seifert J, Bauer R, Benoit R, Widmer A, Schindler T, Uhl V, Lang M, Gstach H, Auer M
    JOURNAL OF MOLECULAR BIOLOGY 386, 435 (2009).
    DOI: 10.1016/j.jmb.2008.12.020

2008

  • Molecular architecture of inner dynein arms in situ in Chlamydomonas reinhardtii flagella Bui K, Sakakibara H, Movassagh T, Oiwa K, Ishikawa T
    The Journal of Cell Biology 183, 923 (2008).
    DOI: 10.1083/jcb.200808050

2007

  • Early segregation of layered projections from the lateral superior olivary nucleus to the central nucleus of the inferior colliculus in the neonatal cat Gabriele Mark L, Shahmoradian SH, French Christopher C, Henkel Craig K, McHaffie John G
    BRAIN RESEARCH 1173, 66 (2007).
    DOI: 10.1016/j.brainres.2007.07.055
  • Structure of the E. coli signal recognition particle bound to a translating ribosome Schaffitzel C, Oswald M, Berger I, Ishikawa T, Abrahams J, Koerten Henk K, Koning Roman I, Ban N
    NATURE 448, 1076 (2007).
    DOI: 10.1038/nature06169

2006

  • An improved method for fast, robust, and seamless integration of DNA fragments into multiple plasmids Benoit RM, Wilhelm RN, Scherer-Becker D, Ostermeier C
    PROTEIN EXPRESSION AND PURIFICATION 45, 66-71 (2006).
    DOI: 10.1016/j.pep.2005.09.022
  • Structure of the E. coli signal recognition particle bound to a translating ribosome Schaffitzel C, Oswald M, Berger I, Ishikawa T, Abrahams J, Koerten Henk K, Koning Roman I, Ban N
    NATURE 444, 503 (2006).
    DOI: 10.1038/nature05182

Publications (before 2005)

Ishikawa, T., Cheng, N., Liu, X., Korn, E.D. and Steven, A.C. (2004) “Subdomain organization of the Acanthamoeba myosin IC tail from cryo-electron microscopy” Proc. Natl. Acad. Sci. USA 101, 12189-12194.

Ishikawa, T., Maurizi, M.R. and Steven, A.C. (2004) “The N-terminal substrate-binding domain of ClpA unfoldase is highly mobile and extends axially from the distal surface of ClpAP protease” J. Struct. Biol. 146, 180-188.

Zakalskiy, A., Hoegenauer, G., Ishikawa, T., Wehrschuetz-Sigl, E., Wendler, F., Teis, D. Zisser, D., Steven, A.C. and Bergler, H. (2002) “Structural and enzymatic properties of the AAA Protein Drg1p from Saccharomyces cerevisiae. Decoupling of intracellular function from ATPase activity and hexamerization” J. Biol. Chem. 277, 26788-26795.

Miyanishi, T., Ishikawa, T., Hayashibara, T., Maita, T. and Wakabayashi, T. (2002) “The two actin-binding regions on the myosin heads of cardiac muscle” Biochemistry 41, 5429-5438.

Ishikawa, T., Beuron, F., Kessel, M., Wickner, S., Maurizi, M.R. and Steven, A.C. (2001) “Translocation pathway of protein substrates in ClpAP protease” Proc. Natl. Acad. Sci. USA 98, 4328-33.

Narita, A., Yasunaga, T., Ishikawa, T., Mayanagi, K. and Wakabayashi, T. (2001) “Ca(2+)-induced switching of troponin and tropomyosin on actin filaments as revealed by electron cryo-microscopy” J. Mol. Biol. 308, 241-261.

Singh, S.K., Rozycki, J., Ortega, J., Ishikawa, T., Lo, J., Steven, A.C. and Maurizi, M.R. (2001) “Functional domains of the ClpA and ClpX molecular chaperones identified by limited proteolysis and deletion analysis” J. Biol. Chem. 276, 29420-29429.

Ishikawa, T., Maurizi, M.R., Belnap, D.M. and Steven, A.C. (2000) “Docking of components in a bacterial complex” Nature 408, 667-668.

Ortega, J., Singh, S.K., Ishikawa, T., Maurizi, M.R. and Steven, A.C. (2000) “Visualization of substrate binding and translocation by the ATP-dependent protease,ClpXP” Mol. Cell 6, 1515-1521.

Ishikawa, T. and Wakabayashi, T. (1999) “Calcium-induced changes in the location and conformation of troponin in skeletal muscle thin filaments” J. Biochem. (Tokyo) 126, 200-211.

Mayanagi, K., Ishikawa, T., Toyoshima, C., Inoue, Y. and Nakazato, K. (1998) “Three- Dimensional Electron Microscopy of the Photosystem II Core Complex” J. Struct. Biol. 123, 211-224.

Kikkawa, M., Ishikawa, T., Wakabayashi, T. and Hirokawa, N. (1995) “Threedimensional structure of the kinesin head-microtubule complex” Nature 376, 274-277.

Ishikawa, T. and Wakabayashi, T. (1995) “Proposal of alignment-independent classification of electron microscopic images with helical symmetry and its application to reconstituted thin filament of skeletal muscle” Ultramicroscopy 57, 91-101.

Ishikawa, T. and Wakabayashi, T. (1994) “Calcium induced change in three-dimesional structure of thin filaments of rabbit skeletal muscle as revealed by cryo-elecron miscroscopy” Biochem. Biophys. Res. Commun. 203, 951-958.

Kikkawa, M., Ishikawa, T., Nakata, T., Wakabayashi, T. and Hirokawa, N. (1994) “Direct visualization of the microtubule lattice seam both in vitro and in vivo” J. Cell Biol. 127, 1965-1971.

Group Members


Photo of Takashi Ishikawa Ishikawa, Takashi Prof.
Group Leader
Telephone: +41 56 310 4217
E-mail: takashi.ishikawa@psi.ch
Photo of Roger Benoit Benoit, Roger Dr.
Scientist
Telephone: +41 56 310 4703
E-mail: roger.benoit@psi.ch
Photo of Sarah Shahmoradian Shahmoradian, Sarah Dr.
Scientist
Telephone: +41 56 310 3309
E-mail: sarah.shahmoradian@psi.ch
Photo of Iman Rostami Rostami, Iman Dr.
Postdoc
Telephone: +41 56 310 3309
E-mail: iman.rostami@psi.ch
Photo of Tobias Bierig Bierig, Tobias
Ph.D. Student
Telephone: +41 56 310 5246
E-mail: tobias.bierig@psi.ch
Photo of Gabriella Collu Collu, Gabriella
Ph.D. Student
Telephone: +41 56 310 4591
E-mail: gabriella.collu@psi.ch
Photo of Valtteri Johannes Järvinen Järvinen, Valtteri Johannes
Ph.D. Student
Telephone: +41 56 310 4240
E-mail: valtteri.jaervinen@psi.ch
Photo of Hung Tri Tran Tran, Hung Tri
Ph.D. Student
Telephone: +41 56 310 3309
E-mail: hung-tri.tran@psi.ch

Former Members


Huy Bui, Khanh Dr.
Postdoc

Maheshwari, Aditi
PhD Student

Malkova, Barbora Dr.
Postdoc

Movassagh, Tandis
PhD Student

Obbineni, Jagan Mohan
Ph.D. Student

Pigino, Gaia Dr.
Postdoc

Poghosyan, Poghosyan
PhD Student

Shaik, Farooque Razvi Dr.
Postdoc

Ueno, Hironori Dr.
Postdoc