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1. Full Text Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL
by Suga, Michihiro and Akita, Fusamichi and Sugahara, Michihiro and Kubo, Minoru and Nakajima, Yoshiki and Nakane, Takanori and Yamashita, Keitaro and Umena, Yasufumi and Nakabayashi, Makoto and Yamane, Takahiro and Nakano, Takamitsu and Suzuki, Mamoru and Masuda, Tetsuya and Inoue, Shigeyuki and Kimura, Tetsunari and Nomura, Takashi and Yonekura, Shinichiro and Yu, Long-Jiang and Sakamoto, Tomohiro and Motomura, Taiki and Chen, Jing-Hua and Kato, Yuki and Noguchi, Takumi and Tono, Kensuke and Joti, Yasumasa and Kameshima, Takashi and Hatsui, Takaki and Nango, Eriko and Tanaka, Rie and Naitow, Hisashi and Matsuura, Yoshinori and Yamashita, Ayumi and Yamamoto, Masaki and Nureki, Osamu and Yabashi, Makina and Ishikawa, Tetsuya and Iwata, So and Shen, Jian-Ren
Nature, ISSN 0028-0836, 03/2017, Volume 543, Issue 7643, pp. 131 - 135
Photosystem II (PSII) is a huge membrane-protein complex consisting of 20 different subunits with a total molecular mass of 350 kDa for a monomer. It catalyses... 
OXYGEN-EVOLVING COMPLEX | PROTON RELEASE | MECHANISM | MULTIDISCIPLINARY SCIENCES | PHOTOSYSTEM-II | X-RAY-DIFFRACTION | PHOTOSYNTHETIC WATER OXIDATION | STATE | INFRARED DETECTION | OXIDIZING COMPLEX | BINDING | Protons | Temperature | Nonheme Iron Proteins - metabolism | Electron Transport - radiation effects | Cyanobacteria - chemistry | Crystallography - methods | Oxygen - metabolism | Fourier Analysis | Time Factors | Lasers | Light | Oxygen - chemistry | Water - chemistry | Nonheme Iron Proteins - chemistry | Biocatalysis - radiation effects | Water - metabolism | Models, Molecular | Nonheme Iron Proteins - radiation effects | Manganese - chemistry | Photosystem II Protein Complex - metabolism | Manganese - metabolism | Photosystem II Protein Complex - radiation effects | Photosystem II Protein Complex - chemistry | Oxygen - radiation effects | Electrons | Chemical bonds | Physiological aspects | Photosystem II | Structure | Photosynthesis research | Membrane proteins | Datasets | Ligands | Fourier transforms | Binding sites
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2. Full Text Human mitotic chromosomes consist predominantly of irregularly folded nucleosome fibres without a 30‐nm chromatin structure
by Nishino, Yoshinori and Eltsov, Mikhail and Joti, Yasumasa and Ito, Kazuki and Takata, Hideaki and Takahashi, Yukio and Hihara, Saera and Frangakis, Achilleas S and Imamoto, Naoko and Ishikawa, Tetsuya and Maeshima, Kazuhiro
The EMBO Journal, ISSN 0261-4189, 04/2012, Volume 31, Issue 7, pp. 1644 - 1653
How a long strand of genomic DNA is compacted into a mitotic chromosome remains one of the basic questions in biology. The nucleosome fibre, in which DNA is... 
X‐ray sacattering | fractal structure | 30‐nm chromatin fibre | cryo‐EM | chromosome structure | Chromosome structure | X-ray sacattering | 30-nm chromatin fibre | cryo-EM | CONDENSIN-II | PARTICLE | CRYOELECTRON MICROSCOPY | BIOCHEMISTRY & MOLECULAR BIOLOGY | X-RAY-DIFFRACTION | MODEL | GENOME | CELL BIOLOGY | SUPERSTRUCTURE | HIGHER-ORDER STRUCTURE | CELL | Chromatin - ultrastructure | Mitosis | Nucleosomes - chemistry | Humans | Scattering, Small Angle | Chromosomes, Human - ultrastructure | Protein Folding | Chromosomes, Human - chemistry | Cryoelectron Microscopy | X-Ray Diffraction | HeLa Cells | Nucleosomes - ultrastructure | Chromatin - chemistry | Chromatin | Molecular structure | Molecular biology | Chromosomes | Genomics
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3. Full Text Imaging live cell in micro-liquid enclosure by X-ray laser diffraction
by Kimura, Takashi and Joti, Yasumasa and Shibuya, Akemi and Song, Changyong and Kim, Sangsoo and Tono, Kensuke and Yabashi, Makina and Tamakoshi, Masatada and Moriya, Toshiyuki and Oshima, Tairo and Ishikawa, Tetsuya and Bessho, Yoshitaka and Nishino, Yoshinori
Nature Communications, ISSN 2041-1723, 01/2014, Volume 5, Issue 1, p. 3052
Emerging X-ray free-electron lasers with femtosecond pulse duration enable single-shot snapshot imaging almost free from sample damage by outrunning major... 
SPECIMENS | BACTERIA | MULTIDISCIPLINARY SCIENCES | FREE-ELECTRON LASER | CRYSTALLOGRAPHY | WHOLE | ATOMIC-RESOLUTION | SCATTERING | Actinobacteria - cytology | Scattering, Radiation | Animals | X-Ray Diffraction - methods | Lasers | Imaging, Three-Dimensional - methods
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4. Full Text Grease matrix as a versatile carrier of proteins for serial crystallography
by Sugahara, Michihiro and Mizohata, Eiichi and Nango, Eriko and Suzuki, Mamoru and Tanaka, Tomoyuki and Masuda, Tetsuya and Tanaka, Rie and Shimamura, Tatsuro and Tanaka, Yoshiki and Suno, Chiyo and Ihara, Kentaro and Pan, Dongqing and Kakinouchi, Keisuke and Sugiyama, Shigeru and Murata, Michio and Inoue, Tsuyoshi and Tono, Kensuke and Song, Changyong and Park, Jaehyun and Kameshima, Takashi and Hatsui, Takaki and Joti, Yasumasa and Yabashi, Makina and Iwata, S
Nature Methods, ISSN 1548-7091, 11/2014, Volume 12, Issue 1, pp. 61 - 63
Serial femtosecond X-ray crystallography (SFX) has revolutionized atomic-resolution structural investigation by expanding applicability to micrometer-sized... 
Crystallography, X-Ray - methods | Aldose-Ketose Isomerases - chemistry | Lubricants | Fatty Acid Binding Protein 3 | Lasers | Muramidase - chemistry | Plant Proteins - chemistry | Crystallization | Fatty Acid-Binding Proteins - chemistry | Mineral Oil | Proteins - chemistry | STRUCTURAL BIOLOGY | FEMTOSECOND CRYSTALLOGRAPHY | FREE-ELECTRON LASER | CRYSTALS | DIFFRACTION DATA | RHEUMATOLOGY | SOFTWARE | Proteins | Usage | Lubrication and lubricants | Research | Structure | Crystallography | Methods
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5. Full Text Nucleosomal arrays self‐assemble into supramolecular globular structures lacking 30‐nm fibers
by Maeshima, Kazuhiro and Rogge, Ryan and Tamura, Sachiko and Joti, Yasumasa and Hikima, Takaaki and Szerlong, Heather and Krause, Christine and Herman, Jake and Seidel, Erik and DeLuca, Jennifer and Ishikawa, Tetsuya and Hansen, Jeffrey C
The EMBO Journal, ISSN 0261-4189, 05/2016, Volume 35, Issue 10, pp. 1115 - 1132
The existence of a 30‐nm fiber as a basic folding unit for DNA packaging has remained a topic of active discussion. Here, we characterize the supramolecular... 
X‐ray scattering | analytical ultracentrifugation | microscopy | nucleosomal array | 10‐nm chromatin fiber | 10-nm chromatin fiber | X-ray scattering | CHROMATIN FIBER | PROTEIN | CRYOELECTRON MICROSCOPY | BIOCHEMISTRY & MOLECULAR BIOLOGY | X-RAY-DIFFRACTION | SEDIMENTATION-VELOCITY ANALYSIS | TAIL DOMAIN | CELL BIOLOGY | ORGANIZATION | HUMAN GENOME | N-TERMINI | LINKER HISTONES | Magnesium Chloride - pharmacology | Micrococcal Nuclease - metabolism | Humans | Nucleosomes - drug effects | Nucleosomes - metabolism | DNA - metabolism | HeLa Cells | Molecular structure | Chromatin | Chromatin, Epigenetics, Genomics & Functional Genomics
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6. Full Text A three-dimensional movie of structural changes in bacteriorhodopsin
by Nango, E and Royant, A and Kubo, M and Nakane, T and Wickstrand, C and Kimura, T and Tanaka, T and Tono, K and Song, CY and Tanaka, R and Arima, T and Yamashita, A and Kobayashi, J and Hosaka, T and Mizohata, E and Nogly, P and Sugahara, M and Nam, D and Nomura, T and Shimamura, T and Im, D and Fujiwara, T and Yamanaka, Y and Jeon, B and Nishizawa, T and Oda, K and Fukuda, M and Andersson, R and Bath, P and Dods, R and Davidsson, J and Matsuoka, S and Kawatake, S and Murata, M and Nureki, O and Owada, S and Kameshima, T and Hatsui, T and Joti, Y and Schertler, G and Yabashi, M and Bondar, AN and Standfuss, J and Neutze, R and Iwata, S and Teknisk-naturvetenskapliga vetenskapsområdet and Institutionen för kemi - Ångström and Uppsala universitet and Kemiska sektionen and Fysikalisk kemi
SCIENCE, ISSN 0036-8075, 12/2016, Volume 354, Issue 6319, pp. 1552 - 1557
Bacteriorhodopsin (bR) is a light-driven proton pump and a model membrane transport protein. We used time-resolved serial femtosecond crystallography at an... 
ANGSTROM RESOLUTION | M-STATE | CRYSTAL-STRUCTURE | MULTIDISCIPLINARY SCIENCES | PHOTOACTIVE YELLOW PROTEIN | SCHIFF-BASE | X-RAY-RADIATION | L-INTERMEDIATE | WATER-MOLECULES | L-PHOTOINTERMEDIATE | VECTORIAL PROTON TRANSPORT | Cytoplasm - chemistry | Protons | Protein Conformation, alpha-Helical | Lasers | Retinaldehyde - chemistry | Bacteriorhodopsins - ultrastructure | Imaging, Three-Dimensional | Spectrum Analysis | Bacteriorhodopsins - chemistry | Crystallography | Motion Pictures | Bacteriorhodopsin | Protein structure prediction | Structure | Methods | Proteins | Membranes | Microorganisms | Crystal structure | Femtosecond | Free electron lasers | X-rays | Nanostructure | Transport | Life Sciences | Biomolecules | Biochemistry, Molecular Biology | Biological Sciences | Biofysik | Naturvetenskap | Biokemi och molekylärbiologi | Biologiska vetenskaper | Biochemistry and Molecular Biology | Natural Sciences | Biophysics
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7. Full Text Ion-ion interactions in the denatured state contribute to the stabilization of CutA1 proteins
by Yutani, Katsuhide and Matsuura, Yoshinori and Naitow, Hisashi and Joti, Yasumasa
Scientific Reports, ISSN 2045-2322, 12/2018, Volume 8, Issue 1, pp. 7613 - 9
In order to elucidate features of the denatured state ensembles that exist in equilibrium with the native state under physiological conditions, we performed... 
ELECTROSTATIC INTERACTIONS | UNFOLDED-STATE | PYRROLIDONE CARBOXYL PEPTIDASE | THERMOPHILIC PROTEINS | RESIDUAL STRUCTURE | MULTIDISCIPLINARY SCIENCES | CHARGE-CHARGE INTERACTIONS | DYNAMICS | HYPERTHERMOPHILE | PYROCOCCUS-HORIKOSHII | THERMUS-THERMOPHILUS | Hyperthermophiles | Disulfide bonds | Entropy | Hydrophobicity | Simulation | Denaturation
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8. Full Text X-ray free electron laser single-particle analysis for biological systems
by Miyashita, Osamu and Joti, Yasumasa
Current Opinion in Structural Biology, ISSN 0959-440X, 04/2017, Volume 43, pp. 163 - 169
The X-ray free electron laser (XFEL) is a new light source that can produce coherent, ultra-brilliant, femtosecond X-ray pulses. This X-ray beam provides new... 
PHASE RETRIEVAL | DIFFRACTION PATTERNS | BIOCHEMISTRY & MOLECULAR BIOLOGY | CLASSIFICATION | CRYSTALLOGRAPHY | SOFTWARE | CELL BIOLOGY | Lasers | Molecular Imaging - instrumentation | X-Rays | Molecular Imaging - methods | Imaging, Three-Dimensional | Equipment Design | Electrons | Free electron lasers
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9. Full Text A beam branching method for timing and spectral characterization of hard X-ray free-electron lasers
by Katayama, Tetsuo and Owada, Shigeki and Togashi, Tadashi and Ogawa, Kanade and Karvinen, Petri and Vartiainen, Ismo and Eronen, Anni and David, Christian and Sato, Takahiro and Nakajima, Kyo and Joti, Yasumasa and Yumoto, Hirokatsu and Ohashi, Haruhiko and Yabashi, Makina
Structural Dynamics, ISSN 2329-7778, 05/2016, Volume 3, Issue 3, pp. 034301 - 034301-14
We report a method for achieving advanced photon diagnostics of x-ray free-electron lasers (XFELs) under a quasi-noninvasive condition by using a... 
SINGLE | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | DYNAMICS | CHEMISTRY, PHYSICAL | TIME | ABSORPTION | RADIATION | SCATTERING
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10. Full Text Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography
by Yohta Fukuda and Ka Man Tse and Takanori Nakane and 中根 崇智 and Toru Nakatsu and Mamoru Suzuki and Michihiro Sugahara and Shigeyuki Inoue and Tetsuya Masuda and Fumiaki Yumoto and Naohiro Matsugaki and Eriko Nango and Kensuke Tono and Yasumasa Joti and Takashi Kameshima and Changyong Song and Takaki Hatsui and Makina Yabashi and Osamu Nureki and Michael E. P. Murphy and Tsuyoshi Inoue and So Iwata and Eiichi Mizohata and 溝端 栄一
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 3/2016, Volume 113, Issue 11, pp. 2928 - 2933
Proton-coupled electron transfer (PCET), a ubiquitous phenomenon in biological systems, plays an essential role in copper nitrite reductase (CuNiR), the key... 
ACTIVE-SITE | MULTIDISCIPLINARY SCIENCES | bioinorganic chemistry | NITROGEN-CYCLE | X-RAY-DIFFRACTION | RHODOBACTER-SPHAEROIDES | free electron laser | SAD phasing | damage-free structure | ELECTRON-TRANSFER | TYPE-2 COPPER SITE | HIGH-RESOLUTION | SPECTROSCOPIC CHARACTERIZATION | copper | ALCALIGENES-FAECALIS | CATALYTIC PATHWAY | Protons | Bacterial Proteins - chemistry | Molecular Sequence Data | Nitrites - metabolism | Alcaligenes faecalis - genetics | Structure-Activity Relationship | Mutation, Missense | Recombinant Fusion Proteins - metabolism | Crystallography, X-Ray - methods | Alcaligenes faecalis - enzymology | Copper - chemistry | Crystallography, X-Ray - instrumentation | Nitrite Reductases - chemistry | Catalysis | Binding Sites | Nitrite Reductases - genetics | Amino Acid Sequence | Oxidation-Reduction | Bacterial Proteins - genetics | Models, Molecular | Recombinant Fusion Proteins - chemistry | Point Mutation | Hydrogen Bonding | Bacterial Proteins - metabolism | Protein Conformation | Amino Acid Substitution | Nitrite Reductases - metabolism | Nitrites | Oxidation-reduction reaction | Chemical properties | Electron transport | Observations | Crystallography | Identification and classification | Methods | Biological Sciences
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11. Full Text Thermodynamics of protein denaturation at temperatures over 100°C: CutA1 mutant proteins substituted with hydrophobic and charged residues
by Matsuura, Yoshinori and Takehira, Michiyo and Joti, Yasumasa and Ogasahara, Kyoko and Tanaka, Tomoyuki and Ono, Naoko and Kunishima, Naoki and Yutani, Katsuhide
Scientific Reports, ISSN 2045-2322, 10/2015, Volume 5, Issue 1, p. 15545
Although the thermodynamics of protein denaturation at temperatures over 100 °C is essential for the rational design of highly stable proteins, it is not... 
Thermodynamics | Mutant Proteins - chemistry | Escherichia coli - metabolism | Protein Denaturation | Escherichia coli Proteins - genetics | Hydrophobic and Hydrophilic Interactions | Escherichia coli Proteins - metabolism | Mutant Proteins - metabolism | Hot Temperature | Escherichia coli Proteins - chemistry | Proteins | Protein denaturation | Hydrophobicity | Enthalpy
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12. Full Text Monte Carlo study for optimal conditions in single-shot imaging with femtosecond x-ray laser pulses
by Park, Jaehyun and Joti, Yasumasa and Ishikawa, Tetsuya and Song, Changyong
Applied Physics Letters, ISSN 0003-6951, 12/2013, Volume 103, Issue 26, p. 264101
Intense x-ray pulses from x-ray free electron lasers (XFELs) enable the unveiling of atomic structure in material and biological specimens via ultrafast... 
FREE-ELECTRON LASER | PHYSICS, APPLIED | Femtosecond | X ray lasers | Particle injection | Computer simulation | Free electron lasers | Atomic structure | Monte Carlo simulation | Biological materials | FREE ELECTRON LASERS | VELOCITY | X RADIATION | MONTE CARLO METHOD | PARTICLES | CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS | BEAMS | X-RAY LASERS | MEMBRANES | OPTIMIZATION | COMPUTERIZED SIMULATION | PULSES
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13. Full Text A soft X‐ray free‐electron laser beamline at SACLA: the light source, photon beamline and experimental station
by Owada, Shigeki and Togawa, Kazuaki and Inagaki, Takahiro and Hara, Toru and Tanaka, Takashi and Joti, Yasumasa and Koyama, Takahisa and Nakajima, Kyo and Ohashi, Haruhiko and Senba, Yasunori and Togashi, Tadashi and Tono, Kensuke and Yamaga, Mitsuhiro and Yumoto, Hirokatsu and Yabashi, Makina and Tanaka, Hitoshi and Ishikawa, Tetsuya
Journal of Synchrotron Radiation, ISSN 1600-5775, 01/2018, Volume 25, Issue 1, pp. 282 - 288
The design and performance of a soft X‐ray free‐electron laser (FEL) beamline of the SPring‐8 Compact free‐electron LAser (SACLA) are described. The SPring‐8... 
soft X‐ray | free‐electron laser | beamline instrumentation | free-electron laser | soft X-ray | SPECTROMETER | PHYSICS, APPLIED | COHERENT | INTENSE | RADIATION | INSTRUMENTS & INSTRUMENTATION | PHOTOABSORPTION | OPERATION | WAVELENGTH | EXTREME-ULTRAVIOLET | ABSORPTION | OPTICS | SCATTERING | Free electron lasers | Electron beams | X rays | Lasers | Soft x rays | Laser beams | Linear accelerators | Electrons
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