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

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

https://doi.org/10.1038/srep36628

Detector system of the single-crystal time-of-flight neutron diffractometer at J-PARC/MLF

Kawasaki, Takuro; Nakamura, Tatsuya; To, Kentaro; Hosoya, Takaaki*; Oikawa, Kenichi; Ohara, Takashi; Kiyanagi, Ryoji; Ebine, Masumi; Birumachi, Atsushi; Sakasai, Kaoru; et al.

Nuclear Instruments and Methods in Physics Research A, 735, p.444 - 451, 2014/01

https://doi.org/10.1016/j.nima.2013.09.057

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.

Direct observation of crystalline-state reactions by single crystal neutron diffraction analyses

Ohara, Takashi; Hosoya, Takaaki; Ohashi, Yuji*

Nihon Kessho Gakkai-Shi, 50(1), p.98 - 102, 2008/02

https://doi.org/10.5940/jcrsj.50.98

The exchange of some hydrogen atoms with the other hydrogen atoms in the crystalline-state reactions, in which the reaction proceeds with retention of the single crystal form, can be directory observed by single crystal neutron diffraction technique if only the transferred hydrogen atoms were replaced with deuterium atoms before the photoirradiation. The method was successfully applied in the photoisomerization of three kinds of cobalt complex crystals and the mechanism in each reaction has been made clear.

Neutron diffraction analysis of deuterium transfer in chiral -thiolactam formation in the crystalline state

Hosoya, Takaaki*; Uekusa, Hidehiro*; Ohashi, Yuji*; Ohara, Takashi; Tanaka, Ichiro*; Niimura, Nobuo*

Acta Crystallographica Section B; Structural Science, Crystal Engineering and Materials (Internet), 62(1), p.153 - 160, 2006/02

https://doi.org/10.1107/S0108768105038656

Since N,N-dibenzyl-1-cyclohexenecarbothioamide is photoisomerized to the optically active -thiolactam with the retention of the single-crystal form, the mechanism of chirality induction was identified by X-ray crystal structure analyses during the process of the reaction. In order to clarify the mechanism of hydrogen transfer in the reaction, the H atomsof the benzyl groups were replaced with deuterium atoms. The crystal structure after photoisomerization was analyzed by neutron diffraction. One of four deuterium atoms of the two benzyl groups is transferred to the C atom of the cyclohexene ring. The absolute configuration of the -CHD- group(chiral methylene) in the photoproduct r-thiolactam revealed that the deuterium atom occupies the equatorial position. This suggests that the deuterium atom is not transferred from the benzyl group of a neighbouring molecule, but from one of the benzyl groups within the molecule.

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 processing software for a TOF single crystal neutron diffractometer at J-PARC

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

no journal, , 

no abstracts in English