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

https://doi.org/10.1107/S2059798318012081

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

https://doi.org/10.3390/qubs1030009

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.

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

https://doi.org/10.5940/jcrsj.57.297

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.

Single crystal diffractometers at J-PARC

Kusaka, Katsuhiro*; Ohara, Takashi; Yamada, Taro*; Kiyanagi, Ryoji

Hamon, 25(2), p.171 - 178, 2015/00

https://doi.org/10.5611/hamon.25.2_171

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

https://doi.org/10.1007/s10969-014-9170-5

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 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.

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

https://doi.org/10.1107/S090904951302075X

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 for four months. The neutron crystal structure solved at 2.0 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.

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

https://doi.org/10.1016/j.jsb.2011.12.022

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

https://doi.org/10.1248/yakushi.130.665

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 . It is expected to measure more than 100 samples per year if they have 2 mm in crystal volume, and to measure even around 0.1 mm 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 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.

Current status of the data-processing software for iBIX, a TOF single crystal neutron diffractometer at J-PARC

Ohara, Takashi; Kusaka, Katsuhiro*; Hosoya, Takaaki*; Kurihara, Kazuo; Niimura, Nobuo*; Tanaka, Ichiro*; Suzuki, Jiro*; Nakatani, Takeshi; Otomo, Toshiya*; Seki, Akiyuki; et al.

no journal, , 

no abstracts in English

Development of a data reduction software for iBIX

Ohara, Takashi; Kusaka, Katsuhiro*; Hosoya, Takaaki; Kurihara, Kazuo; Tomoyori, Katsuaki*; Niimura, Nobuo*; Tanaka, Ichiro*; Suzuki, Jiro*; Nakatani, Takeshi; Otomo, Toshiya*; et al.

no journal, , 

For a single crystal diffractometer, a data reduction software which extracts a HKLF list from the raw data is one of the most important components. We are now developing a new data reduction software for a new single crystal neutron diffractometer, "IBARAKI Biological Crystal Diffractometer (iBIX)", which is now constructing at the MLF of J-PARC.