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Journal Articles

Status of the neutron time-of-flight single-crystal diffraction data-processing software STARGazer

Yano, Naomine*; Yamada, Taro*; Hosoya, Takaaki*; Ohara, Takashi; Tanaka, Ichiro*; Niimura, Nobuo*; Kusaka, Katsuhiro*

Acta Crystallographica Section D; Structural Biology (Internet), 74(11), p.1041 - 1052, 2018/11

 Times Cited Count:10 Percentile:74.46(Biochemical Research Methods)

Journal Articles

Structure analysis and derivation of deformed electron density distribution of polydiacetylene giant single crystal by the combination of X-ray and neutron diffraction data

Tashiro, Koji*; Kusaka, Katsuhiro*; Hosoya, Takaaki*; Ohara, Takashi; Hanesaka, Makoto*; Yoshizawa, Yoshinori*; Yamamoto, Hiroko*; Niimura, Nobuo*; Tanaka, Ichiro*; Kurihara, Kazuo*; et al.

Macromolecules, 51(11), p.3911 - 3922, 2018/06

 Times Cited Count:3 Percentile:14.64(Polymer Science)

Journal Articles

Materials and Life Science Experimental Facility (MLF) at the Japan Proton Accelerator Research Complex, 2; Neutron scattering instruments

Nakajima, Kenji; Kawakita, Yukinobu; Ito, Shinichi*; Abe, Jun*; Aizawa, Kazuya; Aoki, Hiroyuki; Endo, Hitoshi*; Fujita, Masaki*; Funakoshi, Kenichi*; Gong, W.*; et al.

Quantum Beam Science (Internet), 1(3), p.9_1 - 9_59, 2017/12

The neutron instruments suite, installed at the spallation neutron source of the Materials and Life Science Experimental Facility (MLF) at the Japan Proton Accelerator Research Complex (J-PARC), is reviewed. MLF has 23 neutron beam ports and 21 instruments are in operation for user programs or are under commissioning. A unique and challenging instrumental suite in MLF has been realized via combination of a high-performance neutron source, optimized for neutron scattering, and unique instruments using cutting-edge technologies. All instruments are/will serve in world-leading investigations in a broad range of fields, from fundamental physics to industrial applications. In this review, overviews, characteristic features, and typical applications of the individual instruments are mentioned.

Journal Articles

Application of profile fitting method to neutron time-of-flight protein single crystal diffraction data collected at the iBIX

Yano, Naomine*; Yamada, Taro*; Hosoya, Takaaki*; Ohara, Takashi; Tanaka, Ichiro*; Kusaka, Katsuhiro*

Scientific Reports (Internet), 6, p.36628_1 - 36628_9, 2016/12

 Times Cited Count:11 Percentile:66.99(Multidisciplinary Sciences)

Journal Articles

Two protonation states and structural features of a bilin reductase PcyA revealed by neutron crystallography

Unno, Masayoshi*; Sugishima, Masakazu*; Wada, Kei*; Hagiwara, Yoshinori*; Kusaka, Katsuhiro*; Tamada, Taro; Fukuyama, Keiichi*

Nihon Kessho Gakkai-Shi, 57(5), p.297 - 303, 2015/10

Bilin compounds are fundamentally important for oxygenic photosynthetic organisms, because they are utilized as pigments for photosynthesis (phycobilins) and photoreceptors (phytochromobilin). Phycocyanobilin (PCB), a phycobilin, comprises the chromophore of algal phytochromes and the core phycobiliprotein antennae of cyanobacteria and red algae. PCB is biosynthesized by a member of the ferredoxin-dependent bilin reductase family, phycocyanobilin:ferredoxin oxidoreductase (PcyA). In the present study, we determined the neutron crystal structure of PcyA in complex with its substrate biliverdin (BV). This neutron structure revealed the protonation state of BV and the surrounding residues. We found that two forms of BV, neutral BV and protonated BVH$$^{+}$$, were coupled with the two conformation/protonation states of the essential residue Asp105. Further, His88 and His74 near BV were singly protonated and were connected with an intervening hydronium ion. Neutron analysis also revealed how X-ray irradiation of the PcyA-BV crystal altered the structure of the PcyA-BV complex.

Journal Articles

Insights into the proton transfer mechanism of a bilin reductase PcyA following neutron crystallography

Unno, Masayoshi*; Ishikawa, Kumiko*; Kusaka, Katsuhiro*; Tamada, Taro; Hagiwara, Yoshinori*; Sugishima, Masakazu*; Wada, Kei*; Yamada, Taro*; Tomoyori, Katsuaki; Hosoya, Takaaki*; et al.

Journal of the American Chemical Society, 137(16), p.5452 - 5460, 2015/04

 Times Cited Count:25 Percentile:65.65(Chemistry, Multidisciplinary)

Phycocyanobilin, a light-harvesting and photoreceptor pigment in higher plants, algae, and cyanobacteria, is synthesized from biliverdin IX$$alpha$$ (BV) by phycocyanobilin:ferredoxin oxidoreductase (PcyA) via two steps of two-proton-coupled two-electron reduction. We determined the neutron structure of PcyA from cyanobacteria complexed with BV, revealing the exact location of the hydrogen atoms involved in catalysis. Notably, approximately half of the BV bound to PcyA was BVH$$^{+}$$, a state in which all four pyrrole nitrogen atoms were protonated. The protonation states of BV complemented the protonation of adjacent Asp105. The "axial "water molecule that interacts with the neutral pyrrole nitrogen of the A-ring was identified. His88 N$$delta$$ was protonated to form a hydrogen bond with the lactam O atom of the BV A-ring. His88 and His74 were linked by hydrogen bonds via H$$_{3}$$O$$^{+}$$. These results imply that Asp105, His88, and the axial water molecule contribute to proton transfer during PcyA catalysis.

Journal Articles

Accurate structure analyses of polymer crystals on the basis of wide-angle X-ray and neutron diffractions

Tashiro, Koji*; Hanesaka, Makoto*; Yamamoto, Hiroko*; Wasanasuk, K.*; Jayaratri, P.*; Yoshizawa, Yoshinori*; Tanaka, Ichiro*; Niimura, Nobuo*; Kusaka, Katsuhiro*; Hosoya, Takaaki*; et al.

Kobunshi Rombunshu, 71(11), p.508 - 526, 2014/11

 Times Cited Count:5 Percentile:21.37(Polymer Science)

The crystal structure analysis of various polymer substances has been reviewed on the basis of wide-angle high-energy X-ray and neutron diffraction data. The progress in structural analytical techniques of polymer crystals have been reviewed at first. The structural models proposed so far were reinvestigated and new models have been proposed for various kinds of polymer crystals including polyethylene, poly(vinyl alcohol), poly(lactic acid) and its stereocomplex etc. The hydrogen atomic positions were also clarified by the quantitative analysis of wide-angle neutron diffraction data, from which the physical properties of polymer crystals have been evaluated theoretically. The bonded electron density distribution has been estimated for a polydiacetylene single crystal on the basis of the so-called X-N method or by the combination of structural information derived from X-ray and neutron diffraction data analysis. Some comments have been added about future developments in the field of structure-property relationship determination.

Journal Articles

Evaluation of intensity and pulse width of different moderators for designing a new diffractometer for protein crystals with large unit cells in J-PARC/MLF

Tomoyori, Katsuaki; Kusaka, Katsuhiro*; Yamada, Taro*; Tamada, Taro

Journal of Structural and Functional Genomics, 15(3), p.131 - 135, 2014/09

We plan to design a high-resolution biomacromolecule neutron time-of-flight diffractometer, which allows us to collect data from crystals with unit cells above 250 ${AA}$ in the Materials and Life Science Experimental Facility at the Japan Proton Accelerator Research Complex. This new diffractometer can be used for a detailed analysis of large proteins such as membrane proteins and supermolecular complex. A quantitative comparison of the intensity and pulse width of a decoupled moderator (DM) against a coupled moderator (CM) considering the pulse width time resolution indicated that the DM satisfies the criteria for our diffractometer rather than the CM. The results suggested that a characteristic feature of the DM, i.e., narrow pulse width with a short tail, is crucial for the separation of Bragg reflections from crystals with large unit cells. On the other hand, it should be noted that the weak signals from the DM are buried under the high-level background caused by the incoherent scattering of hydrogen atoms, especially, in the case of large unit cells. We propose a profile-fitting integration method combined with the energy loss functions and a background subtraction method achieved by employing the Statistics-sensitive Nonlinear Iterative Peak-clipping algorithm.

Journal Articles

Evaluation of performance for IBARAKI biological crystal diffractometer iBIX with new detectors

Kusaka, Katsuhiro*; Hosoya, Takaaki*; Yamada, Taro*; Tomoyori, Katsuaki; Ohara, Takashi; Katagiri, Masaki*; Kurihara, Kazuo; Tanaka, Ichiro*; Niimura, Nobuo*

Journal of Synchrotron Radiation, 20(6), p.994 - 998, 2013/11

 Times Cited Count:32 Percentile:85.22(Instruments & Instrumentation)

The IBARAKI biological crystal diffractometer, iBIX, is a high-performance time-of-flight neutron single-crystal diffractometer for elucidating mainly the hydrogen, protonation and hydration structures of biological macromolecules in various life processes. Since the end of 2008, iBIX has been available to user's experiments supported by Ibaraki University. Since August 2012, an upgrade of the 14-existing detectors has begun and 16 new detectors have been installed for iBIX. The total measurement efficiency of the present diffractometer has been impoved by one order of magnitude from the previous one with the increasing of accelerator power. In December 2012, commissioning of the new detectors was successful, and collection of the diffraction dataset of ribonucrease A as a standard protein was attempted in order to estimate the performance of the upgraded iBIX in comparison with previous results. The resolution of diffraction data, equivalence among intensities of symmetry-related reflections and reliability of the refined structure have been improved dramatically. iBIX is expected to be one of the highest-performance neutron single-crystal diffractometers for biological macromolecules in the world.

Journal Articles

Hydrogen-bond network and pH sensitivity in human transthyretin

Yokoyama, Takeshi*; Mizuguchi, Mineyuki*; Nabeshima, Yuko*; Kusaka, Katsuhiro*; Yamada, Taro*; Hosoya, Takaaki*; Ohara, Takashi; Kurihara, Kazuo; Tanaka, Ichiro*; Niimura, Nobuo*

Journal of Synchrotron Radiation, 20(6), p.834 - 837, 2013/11

 Times Cited Count:6 Percentile:26.18(Instruments & Instrumentation)

Transthyretin (TTR) is a tetrameric protein. TTR misfolding and aggregation are associated with human amyloid diseases. Dissociation of the TTR tetramer is believed to be the rate-limiting step in the amyloid fibril formation cascade. Low pH is known to promote dissociation into monomer and the formation of amyloid fibrils. In order to reveal the molecular mechanisms underlying pH sensitivity and structural stabilities of TTR, neutron diffraction studies were conducted using the IBARAKI Biological Crystal Diffractometer with the time-of-flight method. Crystals for the neutron diffraction experiments were grown up to 2.5 mm$$^{3}$$ for four months. The neutron crystal structure solved at 2.0 ${AA}$ revealed the protonation states of His88 and the detailed hydrogen-bond network depending on the protonation states of His88. This hydrogen-bond network is involved in monomer-monomer and dimer-dimer interactions, suggesting that the double protonation of His88 by acidification breaks the hydrogen-bond network and causes the destabilization of the TTR tetramer. Structural comparison with the X-ray crystal structure at acidic pH identified the three amino acid residues responsible for the pH sensitivity of TTR. Our neutron model provides insights into the molecular stability related to amyloidosis.

Journal Articles

Structure of morpholinium tribromoplumbate C$$_{4}$$H$$_{8}$$ONH$$_{2}$$PbBr$$_{3}$$ studied using single-crystal neutron diffraction

Kawasaki, Takuro; Takahashi, Miwako*; Ohara, Takashi*; Tanaka, Ichiro*; Kusaka, Katsuhiro*; Hosoya, Takaaki*; Yamada, Taro*; Kurihara, Kazuo

Journal of the Physical Society of Japan, 81(9), p.094602_1 - 094602_6, 2012/09

 Times Cited Count:6 Percentile:44.66(Physics, Multidisciplinary)

Journal Articles

Hydrogen-bond network and pH sensitivity in transthyretin; Neutron crystal structure of human transthyretin

Yokoyama, Takeshi*; Mizuguchi, Mineyuki*; Nabeshima, Yuko*; Kusaka, Katsuhiro*; Yamada, Taro*; Hosoya, Takaaki*; Ohara, Takashi*; Kurihara, Kazuo; Tomoyori, Katsuaki*; Tanaka, Ichiro*; et al.

Journal of Structural Biology, 177(2), p.283 - 290, 2012/02

 Times Cited Count:43 Percentile:83.49(Biochemistry & Molecular Biology)

Journal Articles

Neutron structure analysis using the IBARAKI biological crystal diffractometer (iBIX) at J-PARC

Tanaka, Ichiro*; Kusaka, Katsuhiro*; Hosoya, Takaaki*; Niimura, Nobuo*; Ohara, Takashi*; Kurihara, Kazuo; Yamada, Taro*; Onishi, Yuki*; Tomoyori, Katsuaki*; Yokoyama, Takeshi*

Acta Crystallographica Section D, 66(11), p.1194 - 1197, 2010/11

 Times Cited Count:46 Percentile:94.58(Biochemical Research Methods)

The IBARAKI Biological Crystal Diffractometer (iBIX), a new diffractometer for protein crystallography at the next-generation neutron source at J-PARC (Japan Proton Accelerator Research Complex), has been constructed and has been operational since December 2008. Preliminary structure analyses of organic crystals showed that iBIX has high performance even at 120 kW operation and the first full data set is being collected from a protein crystal.

Journal Articles

Beginning of open use of a New Biological Neutron Diffractometer (iBIX) in J-PARC

Tanaka, Ichiro*; Kusaka, Katsuhiro*; Hosoya, Takaaki*; Ohara, Takashi*; Kurihara, Kazuo; Niimura, Nobuo*

Yakugaku Zasshi, 130(5), p.665 - 670, 2010/05

 Times Cited Count:0 Percentile:0.02(Pharmacology & Pharmacy)

Ibaraki Prefectural Government together with Ibaraki University and Japan Atomic Energy Agency (JAEA) has almost finished constructing a time-of-flight (TOF) neutron diffractometer for biological macromolecules for industrial use at J-PARC, IBARAKI Biological Crystal Diffractometer (iBIX). Since 2009, Ibaraki University has been asked to operate this machine in order for users to do experiments by Ibaraki Prefecture. The diffractometer is designed to cover sample crystals which have their cell edges up to around 150 ${AA}$. It is expected to measure more than 100 samples per year if they have 2 mm$$^{3}$$ in crystal volume, and to measure even around 0.1 mm$$^{3}$$ in crystal volume of biological samples. The efficiency of iBIX is also expected about 100 times larger than those of the present high performance diffractometers at JRR-3 in JAEA when 1MW power realizes in J-PARC. Since December 2008, iBIX has been open to users and several proteins and organic compounds were tested under 20 kW proton power of J-PARC. It was found that one of their proteins was diffracted up to 1.4 ${AA}$ in d-spacing, which was nearly comparable resolution to that of BIX-3 in JRR-3 when used the same crystal as at iBIX for reasonable exposure time. In May 2009, 14 detector units were set up. By the end of fiscal year 2009, the basic part of data reduction software will be finished and an equipment blowing low temperature gas to the sample will be installed with the cooperation of JAEA.

Oral presentation

Current status of the neutron biological diffractometer in J-PARC

Tanaka, Ichiro*; Ohara, Takashi; Kurihara, Kazuo; Kusaka, Katsuhiro; Ozeki, Tomoji*; Niimura, Nobuo*

no journal, , 

Ibaraki Prefectural Government in Japan has started to construct a neutron diffractometer for biological macromolecules for industrial use at J-PARC. The diffractometer is designed to cover the sample crystals which have their cell edges less than 135 ${AA}$. It is expected to measure 100 samples per year if they have 2mm$$^{3}$$ in crystal volume. The efficiency is more than 50 times larger than the present high performance diffractometers, BIX-3 and BIX-4 in JRR-3 reactor, in JAERI. To realize this performance, three important and key items should be developed; an detector, neutron optics, and a software in data reduction. The current status of these developments will be reported with the latest parameters of this diffractometer.

Oral presentation

Ibaraki biological crystal diffractometer in J-PARC (BIX-P1); Optimization of design parameters

Kusaka, Katsuhiro; Ohara, Takashi; Tanaka, Ichiro*; Niimura, Nobuo*; Ozeki, Tomoji*; Kurihara, Kazuo; Aizawa, Kazuya; Morii, Yukio; Arai, Masatoshi; Ebata, Kazuhiro*; et al.

no journal, , 

The TOF neutron biological diffractometer in J-PARC proposed by Ibaraki prefectural government is designed to cover the samples have their cell edges up to 135A, and to realize the efficiency is more than 50 times larger than the present high performance diffractometer, BIX-4. To achieve this performance, the diffractometer will be installed on a coupled moderator has more intense peak but wider pulse shape. The overlapping of Bragg spots along the time-axis expected should be considered for the determination of optic parameters and it is necessary to de-convolute the overlapped spots with higher accuracy. The original simulation programs of TOF diffraction data were developed to obtain information of spot-overlapping, completeness of Bragg spots and spot profiles along time-axis. In this paper, the consideration of important designed parameters focused on biological macromolecular and the strategy of de-convoluting overlapped spots will be reported based on the simulation results.

Oral presentation

Design of the neutron optics for Ibaraki biomolecular diffractometer

Ohara, Takashi; Kurihara, Kazuo; Kusaka, Katsuhiro; Hosoya, Takaaki; Tanaka, Ichiro*; Niimura, Nobuo*; Ozeki, Tomoji*; Aizawa, Kazuya; Morii, Yukio; Arai, Masatoshi; et al.

no journal, , 

no abstracts in English

Oral presentation

Neutron diffraction study of cubic insulin at two different pDs

Ishikawa, Takuya*; Tanaka, Ichiro*; Chatake, Toshiyuki*; Kurihara, Kazuo; Onishi, Yuki*; Kusaka, Katsuhiro; Tamada, Taro; Kuroki, Ryota; Niimura, Nobuo*

no journal, , 

It is known that the protonation status of amino acid side chains can strongly affect the biological function and stability of a protein. It is often hard to estimate it because it depends also on the local environment of the side chain. Neutron diffraction is a powerful tool to observe hydrogen atoms because of its strong interaction with hydrogen. Thus, a neutron study of cubic insulin at pD 6 has been carried out using the BIX-4 diffractometer (JRR-3, JAEA) and the result was compared with the previous neutron study at pD 9 (Maeda, et al. 2004) and by X-ray at pH 6 (Diao, 2003). A large single crystal of cubic insulin was prepared based on the crystallization phase diagram. The crystal diffracted to 2.5 ${AA}$ resolution. It was found that only N$$_{pi}$$ of His 5 in the B-chain is protonated whereas both N$$_{pi}$$ and N$$_{tau}$$ of His10 in the B-chain is protonated at pD 6 and the results at pD 9 are also the same (the pK of histidine side chains in the free form is around 6.0). These indicate that neutron diffraction study is useful to determine the protonation status of a protein.

Oral presentation

Current status of IBARAKI biological diffractometer in J-PARC; Optimization of design parameters

Kusaka, Katsuhiro; Ohara, Takashi; Tanaka, Ichiro*; Niimura, Nobuo*; Kurihara, Kazuo; Hosoya, Takaaki; Ozeki, Tomoji*; Aizawa, Kazuya; Morii, Yukio; Arai, Masatoshi; et al.

no journal, , 

Ibaraki prefecture has started to construct IBARAKI biological crystal diffractometer for industrial use at MLF, J-PARC. It is designed to achieve the efficiency which is more than 50 times larger than the present high performance diffractometer BIX-4. To realize this performance, the diffractometer will be installed on a coupled moderator has more intense peak but wider pulse shape than a decoupled one. It is expected that some neighbor Bragg spots will overlap partially each other along the time axis. The overlapping of Bragg spots should be considered for optimization of design parameters and it is necessary to de-convolute the overlapped spots. The three original simulation programs of TOF diffraction data with designed parameters of the diffractometer were developed to obtain information of spot-overlapping, completeness of Bragg spots and spot profiles along the time axis. The consideration of important designed parameters will be reported based on the simulation results.

Oral presentation

Optimization of designparameters for Ibaraki Biological diffractometer in J-PARC by simulations of TOF diffraction data

Kusaka, Katsuhiro; Ohara, Takashi; Tanaka, Ichiro*; Niimura, Nobuo*; Kurihara, Kazuo; Hosoya, Takaaki; Ozeki, Tomoji*; Aizawa, Kazuya; Morii, Yukio; Arai, Masatoshi; et al.

no journal, , 

no abstracts in English

43 (Records 1-20 displayed on this page)