Professional Education

  • Bachelor of Science, University Of Tokyo (2009)
  • Master of Science, University Of Tokyo (2011)
  • Doctor of Philosophy, University Of Tokyo (2014)

Stanford Advisors


All Publications

  • Structural insights into mu-opioid receptor activation NATURE Huang, W., Manglik, A., Venkatakrishnan, A. J., Laeremans, T., Feinberg, E. N., Sanborn, A. L., Kato, H. E., Livingston, K. E., Thorsen, T. S., Kling, R. C., Granier, S., Gmeiner, P., Husbands, S. M., Traynor, J. R., Weis, W. I., Steyaert, J., Dror, R. O., Kobilka, B. K. 2015; 524 (7565): 315-?
  • Molecular Dynamics of Channelrhodopsin at the Early Stages of Channel Opening PLOS ONE Takemoto, M., Kato, H. E., Koyama, M., Ito, J., Kamiya, M., Hayashi, S., Maturana, A. D., Deisseroth, K., Ishitani, R., Nureki, O. 2015; 10 (6)
  • Structural basis for Na+ transport mechanism by a light-driven Na+ pump NATURE Kato, H. E., Inoue, K., Abe-Yoshizumi, R., Kato, Y., Ono, H., Konno, M., Hososhima, S., Ishizuka, T., Hoque, M. R., Kunitomo, H., Ito, J., Yoshizawa, S., Yamashita, K., Takemoto, M., Nishizawa, T., Taniguchi, R., Kogure, K., Maturana, A. D., Iino, Y., Yawo, H., Ishitani, R., Kandori, H., Nureki, O. 2015; 521 (7550): 48-U347


    Krokinobacter eikastus rhodopsin 2 (KR2) is the first light-driven Na(+) pump discovered, and is viewed as a potential next-generation optogenetics tool. Since the positively charged Schiff base proton, located within the ion-conducting pathway of all light-driven ion pumps, was thought to prohibit the transport of a non-proton cation, the discovery of KR2 raised the question of how it achieves Na(+) transport. Here we present crystal structures of KR2 under neutral and acidic conditions, which represent the resting and M-like intermediate states, respectively. Structural and spectroscopic analyses revealed the gating mechanism, whereby the flipping of Asp116 sequesters the Schiff base proton from the conducting pathway to facilitate Na(+) transport. Together with the structure-based engineering of the first light-driven K(+) pumps, electrophysiological assays in mammalian neurons and behavioural assays in a nematode, our studies reveal the molecular basis for light-driven non-proton cation pumps and thus provide a framework that may advance the development of next-generation optogenetics.

    View details for DOI 10.1038/nature14322

    View details for Web of Science ID 000354040900029

    View details for PubMedID 25849775

  • Effective Application of Bicelles for Conformational Analysis of G Protein-Coupled Receptors by Hydrogen/Deuterium Exchange Mass Spectrometry JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY Nguyen Minh Duc, N. M., Du, Y., Thorsen, T. S., Lee, S. Y., Zhang, C., Kato, H., Kobilka, B. K., Chung, K. Y. 2015; 26 (5): 808-817


    G protein-coupled receptors (GPCRs) have important roles in physiology and pathology, and 40% of drugs currently on the market target GPCRs for the treatment of various diseases. Because of their therapeutic importance, the structural mechanism of GPCR signaling is of great interest in the field of drug discovery. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is a useful tool for analyzing ligand binding sites, the protein-protein interaction interface, and conformational changes of proteins. However, its application to GPCRs has been limited for various reasons, including the hydrophobic nature of GPCRs and the use of detergents in their preparation. In the present study, we tested the application of bicelles as a means of solubilizing GPCRs for HDX-MS studies. GPCRs (e.g., ?2-adrenergic receptor [?2AR], ?-opioid receptor, and protease-activated receptor 1) solubilized in bicelles produced better sequence coverage (greater than 90%) than GPCRs solubilized in n-dodecyl-?-D-maltopyranoside (DDM), suggesting that bicelles are a more effective method of solubilization for HDX-MS studies. The HDX-MS profile of ?2AR in bicelles showed that transmembrane domains (TMs) undergo lower deuterium uptake than intracellular or extracellular regions, which is consistent with the fact that the TMs are highly ordered and embedded in bicelles. The overall HDX-MS profiles of ?2AR solubilized in bicelles and in DDM were similar except for intracellular loop 3. Interestingly, we detected EX1 kinetics, an important phenomenon in protein dynamics, at the C-terminus of TM6 in ?2AR. In conclusion, we suggest the application of bicelles as a useful method for solubilizing GPCRs for conformational analysis by HDX-MS.

    View details for DOI 10.1007/s13361-015-1083-4

    View details for Web of Science ID 000352876100014

  • Structural basis for dynamic mechanism of nitrate/nitrite antiport by NarK NATURE COMMUNICATIONS Fukuda, M., Takeda, H., Kato, H. E., Doki, S., Ito, K., Maturana, A. D., Ishitani, R., Nureki, O. 2015; 6


    NarK belongs to the nitrate/nitrite porter (NNP) family in the major facilitator superfamily (MFS) and plays a central role in nitrate uptake across the membrane in diverse organisms, including archaea, bacteria, fungi and plants. Although previous studies provided insight into the overall structure and the substrate recognition of NarK, its molecular mechanism, including the driving force for nitrate transport, remained elusive. Here we demonstrate that NarK is a nitrate/nitrite antiporter, using an in vitro reconstituted system. Furthermore, we present the high-resolution crystal structures of NarK from Escherichia coli in the nitrate-bound occluded, nitrate-bound inward-open and apo inward-open states. The integrated structural, functional and computational analyses reveal the nitrate/nitrite antiport mechanism of NarK, in which substrate recognition is coupled to the transport cycle by the concomitant movement of the transmembrane helices and the key tyrosine and arginine residues in the substrate-binding site.

    View details for DOI 10.1038/ncomms8097

    View details for Web of Science ID 000355531600005

    View details for PubMedID 25959928

  • Atomistic design of microbial opsin-based blue-shifted optogenetics tools NATURE COMMUNICATIONS Kato, H. E., Kamiya, M., Sugo, S., Ito, J., Taniguchi, R., Orito, A., Hirata, K., Inutsuka, A., Yamanaka, A., Maturana, A. D., Ishitani, R., Sudo, Y., Hayashi, S., Nureki, O. 2015; 6


    Microbial opsins with a bound chromophore function as photosensitive ion transporters and have been employed in optogenetics for the optical control of neuronal activity. Molecular engineering has been utilized to create colour variants for the functional augmentation of optogenetics tools, but was limited by the complexity of the protein-chromophore interactions. Here we report the development of blue-shifted colour variants by rational design at atomic resolution, achieved through accurate hybrid molecular simulations, electrophysiology and X-ray crystallography. The molecular simulation models and the crystal structure reveal the precisely designed conformational changes of the chromophore induced by combinatory mutations that shrink its ?-conjugated system which, together with electrostatic tuning, produce large blue shifts of the absorption spectra by maximally 100 nm, while maintaining photosensitive ion transport activities. The design principle we elaborate is applicable to other microbial opsins, and clarifies the underlying molecular mechanism of the blue-shifted action spectra of microbial opsins recently isolated from natural sources.

    View details for DOI 10.1038/ncomms8177

    View details for Web of Science ID 000355536700004

    View details for PubMedID 25975962

  • Chimeras of Channelrhodopsin-1 and-2 from Chlamydomonas reinhardtii Exhibit Distinctive Light-induced Structural Changes from Channelrhodopsin-2 JOURNAL OF BIOLOGICAL CHEMISTRY Inaguma, A., Tsukamoto, H., Kato, H. E., Kimura, T., Ishizuka, T., Oishi, S., Yawo, H., Nureki, O., Furutani, Y. 2015; 290 (18): 11623-11634


    Channelrhodopsin-2 (ChR2) from the green alga Chlamydomonas reinhardtii functions as a light-gated cation channel that has been developed as an optogenetic tool to stimulate specific nerve cells in animals and control their behavior by illumination. The molecular mechanism of ChR2 has been extensively studied by a variety of spectroscopic methods, including light-induced difference Fourier transform infrared (FTIR) spectroscopy, which is sensitive to structural changes in the protein upon light activation. An atomic structure of channelrhodopsin was recently determined by x-ray crystallography using a chimera of channelrhodopsin-1 (ChR1) and ChR2. Electrophysiological studies have shown that ChR1/ChR2 chimeras are less desensitized upon continuous illumination than native ChR2, implying that there are some structural differences between ChR2 and chimeras. In this study, we applied light-induced difference FTIR spectroscopy to ChR2 and ChR1/ChR2 chimeras to determine the molecular basis underlying these functional differences. Upon continuous illumination, ChR1/ChR2 chimeras exhibited structural changes distinct from those in ChR2. In particular, the protonation state of a glutamate residue, Glu-129 (Glu-90 in ChR2 numbering), in the ChR chimeras is not changed as dramatically as in ChR2. Moreover, using mutants stabilizing particular photointermediates as well as time-resolved measurements, we identified some differences between the major photointermediates of ChR2 and ChR1/ChR2 chimeras. Taken together, our data indicate that the gating and desensitizing processes in ChR1/ChR2 chimeras are different from those in ChR2 and that these differences should be considered in the rational design of new optogenetic tools based on channelrhodopsins.

    View details for DOI 10.1074/jbc.M115.642256

    View details for Web of Science ID 000353719400037

    View details for PubMedID 25796616

  • Molecular Dynamics of Channelrhodopsin at the Early Stages of Channel Opening. PloS one Takemoto, M., Kato, H. E., Koyama, M., Ito, J., Kamiya, M., Hayashi, S., Maturana, A. D., Deisseroth, K., Ishitani, R., Nureki, O. 2015; 10 (6)


    Channelrhodopsin (ChR) is a light-gated cation channel that responds to blue light. Since ChR can be readily expressed in specific neurons to precisely control their activities by light, it has become a powerful tool in neuroscience. Although the recently solved crystal structure of a chimeric ChR, C1C2, provided the structural basis for ChR, our understanding of the molecular mechanism of ChR still remains limited. Here we performed electrophysiological analyses and all-atom molecular dynamics (MD) simulations, to investigate the importance of the intracellular and central constrictions of the ion conducting pore observed in the crystal structure of C1C2. Our electrophysiological analysis revealed that two glutamate residues, Glu122 and Glu129, in the intracellular and central constrictions, respectively, should be deprotonated in the photocycle. The simulation results suggested that the deprotonation of Glu129 in the central constriction leads to ion leakage in the ground state, and implied that the protonation of Glu129 is important for preventing ion leakage in the ground state. Moreover, we modeled the 13-cis retinal bound; i.e., activated C1C2, and performed MD simulations to investigate the conformational changes in the early stage of the photocycle. Our simulations suggested that retinal photoisomerization induces the conformational change toward channel opening, including the movements of TM6, TM7 and TM2. These insights into the dynamics of the ground states and the early photocycle stages enhance our understanding of the channel function of ChR.

    View details for DOI 10.1371/journal.pone.0131094

    View details for PubMedID 26114863

  • Crystallization and preliminary X-ray diffraction analysis of YidC, a membrane-protein chaperone and insertase from Bacillus halodurans. Acta crystallographica. Section F, Structural biology communications Kumazaki, K., Tsukazaki, T., Nishizawa, T., Tanaka, Y., Kato, H. E., Nakada-Nakura, Y., Hirata, K., Mori, Y., Suga, H., Dohmae, N., Ishitani, R., Nureki, O. 2014; 70: 1056-1060


    YidC, a member of the YidC/Oxa1/Alb3 family, inserts proteins into the membrane and facilitates membrane-protein folding in bacteria. YidC plays key roles in both Sec-mediated integration and Sec-independent insertion of membrane proteins. Here, Bacillus halodurans YidC2, which has five transmembrane helices conserved among the other family members, was identified as a target protein for structure determination by a fluorescent size-exclusion chromatography analysis. The protein was overexpressed, purified and crystallized in the lipidic cubic phase. The crystals diffracted X-rays to 2.4? resolution and belonged to space group P21, with unit-cell parameters a = 43.9, b = 60.6, c = 58.9?, ? = 100.3. The experimental phases were determined by the multiwavelength anomalous diffraction method using a mercury-derivatized crystal.

    View details for DOI 10.1107/S2053230X14012540

    View details for PubMedID 25084381

  • Water-Containing Hydrogen-Bonding Network in the Active Center of Channelrhodopsin JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Ito, S., Kato, H. E., Taniguchi, R., Iwata, T., Nureki, O., Kandori, H. 2014; 136 (9): 3475-3482


    Channelrhodopsin (ChR) functions as a light-gated ion channel in Chlamydomonas reinhardtii. Passive transport of cations by ChR is fundamentally different from the active transport by light-driven ion pumps such as archaerhodopsin, bacteriorhodopsin, and halorhodopsin. These microbial rhodopsins are important tools for optogenetics, where ChR is used to activate neurons by light, while the ion pumps are used for neural silencing. Ion-transport functions by these rhodopsins strongly depend on the specific hydrogen-bonding networks containing water near the retinal chromophore. In this work, we measured protein-bound water molecules in a chimeric ChR protein of ChR1 (helices A to E) and ChR2 (helices F and G) of Chlamydomonas reinhardtii using low-temperature FTIR spectroscopy at 77 K. We found that the active center of ChR possesses more water molecules (9 water vibrations) than those of other microbial (2-6 water vibrations) and animal (6-8 water vibrations) rhodopsins. We conclude that the protonated retinal Schiff base interacts with the counterion (Glu162) directly, without the intervening water molecule found in proton-pumping microbial rhodopsins. The present FTIR results and the recent X-ray structure of ChR reveal a unique hydrogen-bonding network around the active center of this light-gated ion channel.

    View details for DOI 10.1021/ja410836g

    View details for Web of Science ID 000332684700027

    View details for PubMedID 24512107

  • Structural basis for dynamic mechanism of proton-coupled symport by the peptide transporter POT PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Doki, S., Kato, H. E., Solcan, N., Iwaki, M., Koyama, M., Hattori, M., Iwase, N., Tsukazaki, T., Sugita, Y., Kandori, H., Newstead, S., Ishitani, R., Nureki, O. 2013; 110 (28): 11343-11348


    Proton-dependent oligopeptide transporters (POTs) are major facilitator superfamily (MFS) proteins that mediate the uptake of peptides and peptide-like molecules, using the inwardly directed H(+) gradient across the membrane. The human POT family transporter peptide transporter 1 is present in the brush border membrane of the small intestine and is involved in the uptake of nutrient peptides and drug molecules such as ?-lactam antibiotics. Although previous studies have provided insight into the overall structure of the POT family transporters, the question of how transport is coupled to both peptide and H(+) binding remains unanswered. Here we report the high-resolution crystal structures of a bacterial POT family transporter, including its complex with a dipeptide analog, alafosfalin. These structures revealed the key mechanistic and functional roles for a conserved glutamate residue (Glu310) in the peptide binding site. Integrated structural, biochemical, and computational analyses suggested a mechanism for H(+)-coupled peptide symport in which protonated Glu310 first binds the carboxyl group of the peptide substrate. The deprotonation of Glu310 in the inward open state triggers the release of the bound peptide toward the intracellular space and salt bridge formation between Glu310 and Arg43 to induce the state transition to the occluded conformation.

    View details for DOI 10.1073/pnas.1301079110

    View details for Web of Science ID 000321827000043

    View details for PubMedID 23798427

  • Structural basis for the drug extrusion mechanism by a MATE multidrug transporter NATURE Tanaka, Y., Hipolito, C. J., Maturana, A. D., Ito, K., Kuroda, T., Higuchi, T., Katoh, T., Kato, H. E., Hattori, M., Kumazaki, K., Tsukazaki, T., Ishitani, R., Suga, H., Nureki, O. 2013; 496 (7444): 247-?


    Multidrug and toxic compound extrusion (MATE) family transporters are conserved in the three primary domains of life (Archaea, Bacteria and Eukarya), and export xenobiotics using an electrochemical gradient of H(+) or Na(+) across the membrane. MATE transporters confer multidrug resistance to bacterial pathogens and cancer cells, thus causing critical reductions in the therapeutic efficacies of antibiotics and anti-cancer drugs, respectively. Therefore, the development of MATE inhibitors has long been awaited in the field of clinical medicine. Here we present the crystal structures of the H(+)-driven MATE transporter from Pyrococcus furiosus in two distinct apo-form conformations, and in complexes with a derivative of the antibacterial drug norfloxacin and three in vitro selected thioether-macrocyclic peptides, at 2.1-3.0 resolutions. The structures, combined with functional analyses, show that the protonation of Asp 41 on the amino (N)-terminal lobe induces the bending of TM1, which in turn collapses the N-lobe cavity, thereby extruding the substrate drug to the extracellular space. Moreover, the macrocyclic peptides bind the central cleft in distinct manners, which correlate with their inhibitory activities. The strongest inhibitory peptide that occupies the N-lobe cavity may pave the way towards the development of efficient inhibitors against MATE transporters.

    View details for DOI 10.1038/nature12014

    View details for Web of Science ID 000317346300047

    View details for PubMedID 23535598

  • Crystal structure of the channelrhodopsin light-gated cation channel NATURE Kato, H. E., Zhang, F., Yizhar, O., Ramakrishnan, C., Nishizawa, T., Hirata, K., Ito, J., Aita, Y., Tsukazaki, T., Hayashi, S., Hegemann, P., Maturana, A. D., Ishitani, R., Deisseroth, K., Nureki, O. 2012; 482 (7385): 369-U115


    Channelrhodopsins (ChRs) are light-gated cation channels derived from algae that have shown experimental utility in optogenetics; for example, neurons expressing ChRs can be optically controlled with high temporal precision within systems as complex as freely moving mammals. Although ChRs have been broadly applied to neuroscience research, little is known about the molecular mechanisms by which these unusual and powerful proteins operate. Here we present the crystal structure of a ChR (a C1C2 chimaera between ChR1 and ChR2 from Chlamydomonas reinhardtii) at 2.3? resolution. The structure reveals the essential molecular architecture of ChRs, including the retinal-binding pocket and cation conduction pathway. This integration of structural and electrophysiological analyses provides insight into the molecular basis for the remarkable function of ChRs, and paves the way for the precise and principled design of ChR variants with novel properties.

    View details for DOI 10.1038/nature10870

    View details for Web of Science ID 000300287100039

    View details for PubMedID 22266941

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