A Technique for determining the deuterium/hydrogen contrast map in neutron macromolecular crystallography

Chatake, Toshiyuki*; Fujiwara, Satoru

Acta Crystallographica Section D; Structural Biology (Internet), 72(1), p.71 - 82, 2016/01

https://doi.org/10.1107/S2059798315021269

An Approach to DNA crystallization using the thermal reversible process of DNA duplexes

Chatake, Toshiyuki*; Sazaki, Gen*; Kikko, Tatsuhiko*; Fujiwara, Satoru; Ishikawa, Takuya*; Matsumoto, Osamu*; Morimoto, Yukio*

Crystal Growth & Design, 10(3), p.1090 - 1095, 2010/03

https://doi.org/10.1021/cg9007075

We propose a technique for DNA crystallization using the thermal reversible process of DNA: a conversion between a double-stranded DNA (dsDNA) and two single-stranded DNAs (ssDNAs) with temperatures. We investigated the solubility of the crystals of a DNA hexamer d(CGCGCG) and their melting temperature, at which the thermal conversion occurs. The results obtained suggest that the conversion from a dsDNA to ssDNAs results in an increase in solubility. It was shown that using this temperature-controlled technique, high-grade single crystals of the DNA hexamer could be obtained from a small amount of DNA samples. This easy-to-apply technique would be superior to the conventional vapor diffusion technique in that it allows the solubility of DNA crystals to be controlled with no need for expensive setups.

A Neutron crystallographic analysis of a cubic porcine insulin at pD 6.6

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

Chemical Physics, 345(2-3), p.152 - 158, 2008/04

https://doi.org/10.1016/j.chemphys.2007.06.053

Orientations of water molecules surrounding B-DNA observed by neutron crystallographic analysis

Arai, Shigeki; Chatake, Toshiyuki*; Niimura, Nobuo

Nihon Kessho Gakkai-Shi, 48(2), p.133 - 139, 2006/04

https://doi.org/10.5940/jcrsj.48.133

It has long been suspected that the structure and function of a DNA duplex can be strongly dependent on its degree of hydration. By neutron diffraction experiments, we have succeeded in determining most of the hydrogen (H) and deuterium (D) atomic positions in the d(CCATTAATGG) duplex. Moreover, the D positions in 27 DO molecules have been determined. In particular, the complex water network in the minor groove has been observed in detail. By a combined structural analysis using 2.0 AA resolution X-ray and 3.0 AA resolution neutron data, it is clear that the spine of hydration is built up, not only by a simple hexagonal hydration pattern (as reported in prior X-ray studies), but also by many other water bridges hydrogen-bonded to the DNA strands. The complexity of the hydration pattern in the minor groove is derived from an extraordinary variety of orientations displayed by the water molecules.

Complicated water orientations in the minor groove of the B-DNA decamer d(CCATTAATGG) observed by neutron diffraction measurements

Arai, Shigeki; Chatake, Toshiyuki*; Ohara, Takashi; Kurihara, Kazuo; Tanaka, Ichiro*; Suzuki, Nobuhiro*; Fujimoto, Zui*; Mizuno, Hiroshi*; Niimura, Nobuo

Nucleic Acids Research, 33(9), p.3017 - 3024, 2005/05

https://doi.org/10.1093/nar/gki616

It has long been suspected that the structure and function of a DNA duplex can be strongly dependent on its degree of hydration. By neutron diffraction experiments, we have succeeded in determining most of the hydrogen (H) and deuterium (D) atomic positions in the d(CCATTAATGG) duplex. Moreover, the D positions in 27 DO molecules have been determined. In particular, the complex water network in the minor groove has been observed in detail. By a combined structural analysis using 2.0 Å resolution X-ray and 3.0 Å resolution neutron data, it is clear that the spine of hydration is built up, not only by a simple hexagonal hydration pattern (as reported in prior X-ray studies), but also by many other water bridges hydrogen-bonded to the DNA strands. The complexity of the hydration pattern in the minor groove is derived from an extraordinary variety of orientations displayed by the water molecules.

A Neutron crystallographic analysis of a rubredoxin mutant at 1.6 resolution

Chatake, Toshiyuki*; Kurihara, Kazuo; Tanaka, Ichiro*; Tsyba, I.*; Bau, R.*; Jenney, F. E. Jr.*; Adams, M. W. W.*; Niimura, Nobuo

Acta Crystallographica Section D, 60(8), p.1364 - 1373, 2004/08

https://doi.org/10.1107/S090744490401176X

A neutron diffraction study has been carried out at 1.6 resolution on a mutant rubredoxin from using the BIX-3 single-crystal diffractometer at the JRR-3 reactor of JAERI. In order to study the unusual thermostability of rubredoxin from , the hydrogen-bonding patterns were compared between the native and a 'triple-mutant' variant where three residues were changed so that they are identical to those in a mesophilic rubredoxin. In the present study, some minor changes were found between the wild-type and mutant proteins in the hydrogen-bonding patterns of the Trp3/Tyr3 region. The H/D-exchange ratios in the protein were also studied. The results suggest that the backbone amide bonds near the four Cys residues of the FeS redox center are most resistant to H/D exchange. In addition, the 1.6 resolution of the present neutron structure determination has revealed a more detailed picture than previously available of some portions of the water structure, including ordered and disordered O-D bonds.

More rapid evaluation of biomacromolecular crystals for diffraction experiments

Arai, Shigeki; Chatake, Toshiyuki; Suzuki, Nobuhiro*; Mizuno, Hiroshi*; Niimura, Nobuo

Acta Crystallographica Section D, 60(6), p.1032 - 1039, 2004/06

https://doi.org/10.1107/S0907444904006559

The parameters used for evaluating biomacromolecular crystal quality (, /(), maximum resolution and mosaicity) strongly depend on the diffraction experimental conditions. In this paper we describe the distinctive features of the relative Wilson plot method, and we show that the overall B-factor obtained from this plot is given as a more appropriate to characterize protein crystals. The relative Wilson plot has been applied to the characterization of crystals of a B-DNA decamer d(CCATTAATGG), and crystals of the proteins DsrD (dissimilatory sulfite reductase D) and hen egg-white lysozyme (HEWL) which we have studied by neutron diffraction. We have found that the crystal qualities of the B-DNA decamer and DsrD significantly depend on the regions of the crystallization phase diagram from which samples were taken. However, in the case of HEWL, crystal quality appears to be independent on the region of the crystallization phase diagram.

Crystallization and preliminary neutron analysis of the dissimilatory sulfite reductase D (DsrD) protein from the sulfate-reducing bacterium

Chatake, Toshiyuki; Mizuno, Nobuhiro*; Voordown, G.*; Higuchi, Yoshiki*; Arai, Shigeki; Tanaka, Ichiro; Niimura, Nobuo

Acta Crystallographica Section D, 59(Part2), p.2306 - 2309, 2003/12

https://doi.org/10.1107/S0907444903020596

Issimilatory sulfite reductase D (DsrD) from has been crystallized for a neutron diffraction study. The initial crystals obtained were too small for the neutron experiment. In order to obtain a larger crystal (1 mm), a combination of two techniques was used to find the optimum crystallization conditions: a crystallization phase diagram, followed by crystal-quality assessment via X-ray diffraction. Using conditions determined in this manner, a large single crystal (1.7 mm) of the DsrD protein was subsequently grown in DO solution by the macro-seeding technique. The neutron diffraction experiment was carried out using the BIX-3 diffractometer at the Japan Atomic Energy Research Institute (JAERI), and the diffraction data up to 2.4 AA resolution could be collected from this crystal.

Hydration in proteins observed by high-resolution neutron crystallography

Chatake, Toshiyuki; Ostermann, A.; Kurihara, Kazuo; Parak, F.*; Niimura, Nobuo

Proteins: Structure, Function, and Bioinformatics, 50(3), p.516 - 523, 2003/02

https://doi.org/10.1002/prot.10303

no abstracts in English

A High-performance neutron diffractometer for biological crystallography (BIX-3)

Tanaka, Ichiro; Kurihara, Kazuo; Chatake, Toshiyuki; Niimura, Nobuo

Journal of Applied Crystallography, 35(Part1), p.34 - 40, 2002/02

A high performance neutron diffractometer for biological crystallography (BIX-3) has been constructed at JRR-3M in Japan Atomic Energy Research Institute (JAERI) in order to determine the hydrogen positions in biological macromolecules. It uses several recent technical innovations, such as a neutron imaging plate and an elastically bent silicon monochromator developed by the authors. These have made it possible to realize a compact vertical arrangement of the diffractometer. Diffraction data have been collected from the proteins rubredoxin and myoglobin in about one month, to a resolution of 1.5, good enough to identify the hydrogen atoms with high accuracy. By adopting a crystal-step scan method for measuring Bragg diffraction intensities, the signal to noise ratio was much better than that of the Laue method. This shows that BIX-3 is one of the best-performing machines for neutron protein crystallography in the world currently.