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Chiba K, Matsui T, Chatake T, Ohhara T, Tanaka I, Yutani K, Niimura N. Site-specific relaxation of peptide bond planarity induced by electrically attracted proton/deuteron observed by neutron crystallography. Protein Sci 2023; 32:e4765. [PMID: 37624071 PMCID: PMC10510461 DOI: 10.1002/pro.4765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 07/25/2023] [Accepted: 08/19/2023] [Indexed: 08/26/2023]
Abstract
In structural biology, peptide bonds, fundamental linkages between hundreds of amino acids, of which a protein molecule is composed, have been commonly treated as a plane structure just as Linus Pauling et al. proposed. In this paper, a site-specific peptide bond relaxation mechanism by deuterons whose localization has been suggested by neutron crystallography is proposed. Such deuteron was observed as an arm of neutron scattering length density protruding from the carbonyl oxygen atoms in the main chain in the omit map drawn by neutron crystallography of human lysozyme. Our comprehensive study using x-ray and neutron diffraction and 15 N chemical shifts of individual amide nitrogen atoms within the same peptide bond strongly suggests the relaxation of the electronic resonance structure because of site-specific modulation by protons/deuterons localized on the electron orbital of the carbonyl oxygen. All experimental data used in this examination were obtained at room temperature, which is preferable for enzymatic activity. Such a close interaction between the electron resonance structure of a peptide bond and the exchangeable protons/deuterons well agreed with that observed in an intermediate state in an amide hydrolytic reaction simulated by the ab-initio calculation including water molecules.
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Affiliation(s)
- Kaori Chiba
- Advanced Science Research Centre, JAERITokaiIbarakiJapan
- Department of Industrial EngineeringNational Institute of Technology, Ibaraki CollegeHitachinakaIbarakiJapan
| | - Takuro Matsui
- Advanced Science Research Centre, JAERITokaiIbarakiJapan
| | - Toshiyuki Chatake
- Advanced Science Research Centre, JAERITokaiIbarakiJapan
- Institute for Integrated Radiation and Nuclear ScienceKyoto UniversitySennanOsakaJapan
| | - Takashi Ohhara
- Advanced Science Research Centre, JAERITokaiIbarakiJapan
- Neutron Science Section, J‐PARC CenterJapan Atomic Energy AgencyTokaiIbarakiJapan
| | - Ichiro Tanaka
- Advanced Science Research Centre, JAERITokaiIbarakiJapan
- Graduate School of Science and EngineeringIbaraki UniversityHitachiIbarakiJapan
- Frontier Research Center for Applied Atomic SciencesIbaraki UniversityHitachiIbarakiJapan
| | | | - Nobuo Niimura
- Advanced Science Research Centre, JAERITokaiIbarakiJapan
- Frontier Research Center for Applied Atomic SciencesIbaraki UniversityHitachiIbarakiJapan
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Chatake T, Tanaka I, Kusaka K, Fujiwara S. Protonation states of hen egg-white lysozyme observed using D/H contrast neutron crystallography. ACTA CRYSTALLOGRAPHICA SECTION D STRUCTURAL BIOLOGY 2022; 78:770-778. [DOI: 10.1107/s2059798322004521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/29/2022] [Indexed: 11/10/2022]
Abstract
Hen egg-white lysozyme (HEWL) is an enzymatic protein with two acidic amino acids, Glu35 and Asp52, in its active site. Glu35 acts as a proton donor to the substrate and Asp52 interacts with the positively charged substrate, suggesting different protonation states of these residues. However, neutron crystallographic studies thus far have not provided a consistent picture of the protonation states of these residues. Only one study succeeded in observing the active protonation states of Glu35 and Asp52 in the triclinic crystal system. However, their active states in the most widely studied tetragonal crystal system are still unknown. The application of the D/H contrast technique in neutron crystallography improves the ability to locate exchangeable D/H atoms in proteins. In the present study, D2O and H2O solvent crystals were prepared. Each neutron data set was collected for only five days by combining a time-of-flight diffractometer (iBIX) and the spallation neutron source at the Japan Proton Accelerator Research Complex. The D/H contrast map provided better visualization of the D/H atoms in HEWL than the conventional neutron scattering length density map. The neutron D/H contrast map demonstrated the alternative protonation of the OE1 and OE2 atoms in the carboxyl group of Glu35. This alternative protonation occurs in the absence of a substrate, where high selectivity of the protonation site does not occur. In this case, only the OE1—HE1 bond attacks the substrate in an equilibrium between OE1—HE1 and OE2—HE2, or the H+ ion of the OE2—HE2 bond moves to the OE1 atom just before or after substrate binding to initiate the catalytic reaction. In contrast, the carboxyl group of Asp52 is not protonated. Protonation of the carboxyl group was not observed for other Asp and Glu residues. These results are consistent with results from NMR spectroscopy and explain the protonation states at the active site in the apo form of HEWL.
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Kono F, Kurihara K, Tamada T. Current status of neutron crystallography in structural biology. Biophys Physicobiol 2022; 19:1-10. [PMID: 35666700 PMCID: PMC9135615 DOI: 10.2142/biophysico.bppb-v19.0009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 03/29/2022] [Indexed: 12/01/2022] Open
Abstract
Hydrogen atoms and hydration water molecules in proteins are essential for many biochemical processes, especially enzyme catalysis. Neutron crystallography enables direct observation of hydrogen atoms, and reveals molecular recognition through hydrogen bonding and catalytic reactions involving proton-coupled electron transfer. The use of neutron crystallography is still limited for proteins, but its popularity is increasing owing to an increase in the number of diffractometers for structural biology at neutron facilities and advances in sample preparation. According to the characteristics of the neutrons, monochromatic or quasi-Laue methods and the time-of-flight method are used in nuclear reactors and pulsed spallation sources, respectively, to collect diffraction data. Growing large crystals is an inevitable problem in neutron crystallography for structural biology, but sample deuteration, especially protein perdeuteration, is effective in reducing background levels, which shortens data collection time and decreases the crystal size required. This review also introduces our recent neutron structure analyses of copper amine oxidase and copper-containing nitrite reductase. The neutron structure of copper amine oxidase gives detailed information on the protonation state of dissociable groups, such as the quinone cofactor, which are critical for catalytic reactions. Electron transfer via a hydrogen-bond jump and a hydroxide ion ligation in copper-containing nitrite reductase are clarified, and these observations are consistent with the results from the quantum chemical calculations. This review article is an extended version of the Japanese article, Elucidation of Enzymatic Reaction Mechanism by Neutron Crystallography, published in SEIBUTSU-BUTSURI Vol. 61, p.216–222 (2021).
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Affiliation(s)
- Fumiaki Kono
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology
| | - Kazuo Kurihara
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology
| | - Taro Tamada
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology
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Kono F, Tamada T. Neutron crystallography for the elucidation of enzyme catalysis. Curr Opin Struct Biol 2021; 71:36-42. [PMID: 34214927 DOI: 10.1016/j.sbi.2021.05.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/08/2021] [Accepted: 05/22/2021] [Indexed: 11/26/2022]
Abstract
Hydrogen atoms and hydration water molecules in proteins are indispensable for many biochemical processes, especially enzymatic catalysis. The locations of hydrogen atoms in proteins are usually predicted based on X-ray structures, but it is still very difficult to know the ionization states of the catalytic residues, the hydration structure of the protein, and the characteristics of hydrogen-bonding interactions. Neutron crystallography allows the direct observation of hydrogen atoms that play crucial roles in molecular recognition and the catalytic reactions of enzymes. In this review, we present the current status of neutron crystallography in structural biology and recent neutron structural analyses of three enzymes: ascorbate peroxidase, the main protease of severe acute respiratory syndrome coronavirus 2, and copper-containing nitrite reductase.
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Affiliation(s)
- Fumiaki Kono
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Taro Tamada
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan.
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Tashiro K, Kusaka K, Yamamoto H, Hanesaka M. Introduction of Disorder in the Crystal Structures of Atactic Poly(vinyl Alcohol) and Its Iodine Complex To Solve a Dilemma between X-ray and Neutron Diffraction Data Analyses. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c00839] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Kohji Tashiro
- Department of Future Industry-oriented Basic Science and Materials, Graduate School of Engineering, Toyota Technological Institute, Tempaku, Nagoya 468-8511, Japan
| | - Katsuhiro Kusaka
- Department of Biomolecular Functional Engineering, College of Engineering, Ibaraki University, Naka-Narisawa 4-12-1, Hitachi, Ibaraki 316-8511, Japan
| | - Hiroko Yamamoto
- Aichi Synchrotron Radiation Center, Aichi Science and Technology Foundation, 250-3 Minami-yamaguchi, Seto 489-0965, Japan
| | - Makoto Hanesaka
- Department of Future Industry-oriented Basic Science and Materials, Graduate School of Engineering, Toyota Technological Institute, Tempaku, Nagoya 468-8511, Japan
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Abstract
Neutron and X-ray crystallography are complementary to each other. While X-ray scattering is directly proportional to the number of electrons of an atom, neutrons interact with the atomic nuclei themselves. Neutron crystallography therefore provides an excellent alternative in determining the positions of hydrogens in a biological molecule. In particular, since highly polarized hydrogen atoms (H+) do not have electrons, they cannot be observed by X-rays. Neutron crystallography has its own limitations, mainly due to inherent low flux of neutrons sources, and as a consequence, the need for much larger crystals and for different data collection and analysis strategies. These technical challenges can however be overcome to yield crucial structural insights about protonation states in enzyme catalysis, ligand recognition, as well as the presence of unusual hydrogen bonds in proteins.
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Abstract
The IBARAKI Biological Crystal Diffractometer (iBIX) has been available for use at MLF (Material and Life Science Facility) in J-PARC (Japan Proton Accelerator Research Complex) since 2008. The development in state-of-the-art detector systems could enable iBIX to become one of the highest-performance neutron single-crystal diffractometers in the world. Here, together with other various developments, such as data reduction software, crystal growth, and new techniques in measurement coupled analysis, we provided new hydrogen and water structural data of several proteins and macromolecules. Although the proton power at MLF has not yet reached its planned maximum (1MW), a more powerful neutron source will be soon needed for neutron protein crystallography. A future idea is also proposed and discussed in this article.
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Yano N, Yamada T, Hosoya T, Ohhara T, Tanaka I, Niimura N, Kusaka K. Status of the neutron time-of-flight single-crystal diffraction data-processing software STARGazer. Acta Crystallogr D Struct Biol 2018; 74:1041-1052. [PMID: 30387763 PMCID: PMC6213574 DOI: 10.1107/s2059798318012081] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 08/24/2018] [Indexed: 11/10/2022] Open
Abstract
The STARGazer data-processing software is used for neutron time-of-flight (TOF) single-crystal diffraction data collected using the IBARAKI Biological Crystal Diffractometer (iBIX) at the Japan Proton Accelerator Research Complex (J-PARC). This software creates hkl intensity data from three-dimensional (x, y, TOF) diffraction data. STARGazer is composed of a data-processing component and a data-visualization component. The former is used to calculate the hkl intensity data. The latter displays the three-dimensional diffraction data with searched or predicted peak positions and is used to determine and confirm integration regions. STARGazer has been developed to make it easier to use and to obtain more accurate intensity data. For example, a profile-fitting method for peak integration was developed and the data statistics were improved. STARGazer and its manual, containing installation and data-processing components, have been prepared and provided to iBIX users. This article describes the status of the STARGazer data-processing software and its data-processing algorithms.
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Affiliation(s)
- Naomine Yano
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Taro Yamada
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Takaaki Hosoya
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
- College of Engineering, Ibaraki University, 4-12-1 Nakanarusawa, Hitachi, Ibaraki 316-8511, Japan
| | - Takashi Ohhara
- Neutron Science Section, J-PARC Center, Japan Atomic Energy Agency, 2-4 Shirakata-Shirane, Tokai, Ibaraki 319-1195, Japan
| | - Ichiro Tanaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
- College of Engineering, Ibaraki University, 4-12-1 Nakanarusawa, Hitachi, Ibaraki 316-8511, Japan
| | - Nobuo Niimura
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Katsuhiro Kusaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
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Tashiro K, Kusaka K, Hosoya T, Ohhara T, Hanesaka M, Yoshizawa Y, Yamamoto H, Niimura N, Tanaka I, Kurihara K, Kuroki R, Tamada T. Structure Analysis and Derivation of Deformed Electron Density Distribution of Polydiacetylene Giant Single Crystal by the Combination of X-ray and Neutron Diffraction Data. Macromolecules 2018. [DOI: 10.1021/acs.macromol.8b00650] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kohji Tashiro
- Department of Future Industry-Oriented Basic Science and Materials, Toyota Technological Institute, Tempaku, Nagoya 468-8511, Japan
| | - Katsuhiro Kusaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Tokai, Naka-gun, Ibaraki 319-1106, Japan
| | - Takaaki Hosoya
- Department of Biomolecular Functional Engineering, College of Engineering, Ibaraki University, Hitachi 316-8511, Japan
| | - Takashi Ohhara
- Research Unit for Quantum Beam Science Initiative, Japan Atomic Energy Agency, Tokai, Naka-gun, Ibaraki 319-1195, Japan
| | - Makoto Hanesaka
- Department of Future Industry-Oriented Basic Science and Materials, Toyota Technological Institute, Tempaku, Nagoya 468-8511, Japan
| | - Yoshinori Yoshizawa
- Department of Future Industry-Oriented Basic Science and Materials, Toyota Technological Institute, Tempaku, Nagoya 468-8511, Japan
| | - Hiroko Yamamoto
- Aichi Synchrotron Radiation Center, Aichi Science and Technology Foundation, 250-3 minamiyamaguchi, Seto 489-0965, Japan
| | - Nobuo Niimura
- Department of Biomolecular Functional Engineering, College of Engineering, Ibaraki University, Hitachi 316-8511, Japan
| | - Ichiro Tanaka
- Department of Biomolecular Functional Engineering, College of Engineering, Ibaraki University, Hitachi 316-8511, Japan
| | - Kazuo Kurihara
- Research Unit for Quantum Beam Science Initiative, Japan Atomic Energy Agency, Tokai, Naka-gun, Ibaraki 319-1195, Japan
| | - Ryota Kuroki
- Research Unit for Quantum Beam Science Initiative, Japan Atomic Energy Agency, Tokai, Naka-gun, Ibaraki 319-1195, Japan
| | - Taro Tamada
- Research Unit for Quantum Beam Science Initiative, Japan Atomic Energy Agency, Tokai, Naka-gun, Ibaraki 319-1195, Japan
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Kurihara K, Hirano Y, Oikawa K, Harada M, Nakamura T, Tamada T. Instrument and shielding design of a neutron diffractometer at J-PARC for protein crystallography covering crystals with large unit-cell volume. J Appl Crystallogr 2018. [DOI: 10.1107/s1600576718004673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Structural information on hydrogen atoms and hydration water molecules obtained by neutron protein crystallography is expected to contribute to the elucidation and improvement of protein function. However, many proteins, especially membrane proteins and protein complexes, have large molecular weights and the unit cells of their crystals have large volumes, which are out of the range of unit-cell volumes measurable by conventional diffractometers because a large unit-cell volume causes difficulty in separating Bragg peaks close to each other in the spatial and time dimensions in diffraction images. Therefore, a new diffractometer has been designed at the Japan Accelerator Research Complex (J-PARC), which can measure crystals with a large unit-cell volume. The proposed diffractometer uses a large camera distance (L
2 = 800 mm) and more than 40 novel large-area detectors (larger than 320 × 320 mm). In addition, a decoupled hydrogen moderator, which has a narrow pulse width, is selected as the neutron source. This diffractometer is estimated to be able to measure crystals with a lattice length of 250 Å along each axis at d
min = 2.0 Å. Ellipsoidal and curved shapes were introduced in the vertical and horizontal guide designs, respectively, providing an estimated neutron flux of 6 × 105 n s−1 mm−2 in the wavelength range 1.5–5.5 Å.
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11
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Neutron macromolecular crystallography. Emerg Top Life Sci 2018; 2:39-55. [DOI: 10.1042/etls20170083] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/12/2017] [Accepted: 12/19/2017] [Indexed: 01/02/2023]
Abstract
Neutron diffraction techniques permit direct determination of the hydrogen (H) and deuterium (D) positions in crystal structures of biological macromolecules at resolutions of ∼1.5 and 2.5 Å, respectively. In addition, neutron diffraction data can be collected from a single crystal at room temperature without radiation damage issues. By locating the positions of H/D-atoms, protonation states and water molecule orientations can be determined, leading to a more complete understanding of many biological processes and drug-binding. In the last ca. 5 years, new beamlines have come online at reactor neutron sources, such as BIODIFF at Heinz Maier-Leibnitz Zentrum and IMAGINE at Oak Ridge National Laboratory (ORNL), and at spallation neutron sources, such as MaNDi at ORNL and iBIX at the Japan Proton Accelerator Research Complex. In addition, significant improvements have been made to existing beamlines, such as LADI-III at the Institut Laue-Langevin. The new and improved instrumentations are allowing sub-mm3 crystals to be regularly used for data collection and permitting the study of larger systems (unit-cell edges >100 Å). Owing to this increase in capacity and capability, many more studies have been performed and for a wider range of macromolecules, including enzymes, signalling proteins, transport proteins, sugar-binding proteins, fluorescent proteins, hormones and oligonucleotides; of the 126 structures deposited in the Protein Data Bank, more than half have been released since 2013 (65/126, 52%). Although the overall number is still relatively small, there are a growing number of examples for which neutron macromolecular crystallography has provided the answers to questions that otherwise remained elusive.
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Biological Structures. NEUTRON SCATTERING - APPLICATIONS IN BIOLOGY, CHEMISTRY, AND MATERIALS SCIENCE 2017. [DOI: 10.1016/b978-0-12-805324-9.00001-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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O'Dell WB, Bodenheimer AM, Meilleur F. Neutron protein crystallography: A complementary tool for locating hydrogens in proteins. Arch Biochem Biophys 2016; 602:48-60. [DOI: 10.1016/j.abb.2015.11.033] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/12/2015] [Accepted: 11/16/2015] [Indexed: 10/22/2022]
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Ohhara T, Kiyanagi R, Oikawa K, Kaneko K, Kawasaki T, Tamura I, Nakao A, Hanashima T, Munakata K, Moyoshi T, Kuroda T, Kimura H, Sakakura T, Lee CH, Takahashi M, Ohshima KI, Kiyotani T, Noda Y, Arai M. SENJU: a new time-of-flight single-crystal neutron diffractometer at J-PARC. J Appl Crystallogr 2016; 49:120-127. [PMID: 26937237 PMCID: PMC4762571 DOI: 10.1107/s1600576715022943] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 11/30/2015] [Indexed: 11/10/2022] Open
Abstract
SENJU is a new single-crystal time-of-flight neutron diffractometer installed at BL18 at the Materials and Life Science Experimental Facility of the Japan Accelerator Research Complex (J-PARC). The diffractometer was designed for precise crystal and magnetic structure analyses under multiple extreme sample environments such as low temperature, high pressure and high magnetic field, and for diffraction measurements of small single crystals down to 0.1 mm3 in volume. SENJU comprises three choppers, an elliptical shape straight supermirror guide, a vacuum sample chamber and 37 scintillator area detectors. The moderator-to-sample distance is 34.8 m, and the sample-to-detector distance is 800 mm. The wavelength of incident neutrons is 0.4-4.4 Å (first frame). Because short-wavelength neutrons are available and the large solid angle around the sample position is covered by the area detectors, a large reciprocal space can be simultaneously measured. Furthermore, the vacuum sample chamber and collimator have been designed to produce a very low background level. Thus, the measurement of a small single crystal is possible. As sample environment devices, a newly developed cryostat with a two-axis (ω and φ axes) goniometer and some extreme environment devices, e.g. a vertical-field magnet, high-temperature furnace and high-pressure cell, are available. The structure analysis of a sub-millimetre size (0.1 mm3) single organic crystal, taurine, and a magnetic structure analysis of the antiferromagnetic phase of MnF2 have been performed. These results demonstrate that SENJU can be a powerful tool to promote materials science research.
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Affiliation(s)
- Takashi Ohhara
- Neutron Science Section, J-PARC Center, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai, Ibaraki 319-1195, Japan
| | - Ryoji Kiyanagi
- Neutron Science Section, J-PARC Center, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai, Ibaraki 319-1195, Japan
| | - Kenichi Oikawa
- Neutron Science Section, J-PARC Center, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai, Ibaraki 319-1195, Japan
| | - Koji Kaneko
- Neutron Science Section, J-PARC Center, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai, Ibaraki 319-1195, Japan
| | - Takuro Kawasaki
- Neutron Science Section, J-PARC Center, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai, Ibaraki 319-1195, Japan
| | - Itaru Tamura
- Neutron Science Section, J-PARC Center, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai, Ibaraki 319-1195, Japan
| | - Akiko Nakao
- Research Center for Neutron Science and Technology, Comprehensive Research Organization for Science and Society, IQBRC Building, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Takayasu Hanashima
- Research Center for Neutron Science and Technology, Comprehensive Research Organization for Science and Society, IQBRC Building, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Koji Munakata
- Research Center for Neutron Science and Technology, Comprehensive Research Organization for Science and Society, IQBRC Building, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Taketo Moyoshi
- Research Center for Neutron Science and Technology, Comprehensive Research Organization for Science and Society, IQBRC Building, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Tetsuya Kuroda
- Research Center for Neutron Science and Technology, Comprehensive Research Organization for Science and Society, IQBRC Building, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Hiroyuki Kimura
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Terutoshi Sakakura
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Chang-Hee Lee
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
- Neutron Science Division, Korea Atomic Energy Research Institute, 111 Daedeok-Daero 989 Beon-Gil, Yuseong-Gu, Daejeon, Republic of Korea
| | - Miwako Takahashi
- Institute of Materials Science, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
| | - Ken-ichi Ohshima
- Institute of Materials Science, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
| | - Tamiko Kiyotani
- Department of Pharmacy, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
| | - Yukio Noda
- Neutron Science Section, J-PARC Center, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai, Ibaraki 319-1195, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Masatoshi Arai
- Neutron Science Section, J-PARC Center, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai, Ibaraki 319-1195, Japan
- European Spallation Source ESS AB, PO Box 176, SE-221 00, Lund, Sweden
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Abstract
The hydration shells surrounding nucleic acids and hydrogen-bonding networks involving water molecules and nucleic acids are essential interactions for the structural stability and function of nucleic acids. Water molecules in the hydration shells influence various conformations of DNA and RNA by specific hydrogen-bonding networks, which often contribute to the chemical reactivity and molecular recognition of nucleic acids. However, X-ray crystallography could not provide a complete description of structural information with respect to hydrogen bonds. Indeed, X-ray crystallography is a powerful tool for determining the locations of water molecules, i.e., the location of the oxygen atom of H2O; however, it is very difficult to determine the orientation of the water molecules, i.e., the orientation of the two hydrogen atoms of H2O, because X-ray scattering from the hydrogen atom is very small.Neutron crystallography is a specialized tool for determining the positions of hydrogen atoms. Neutrons are not diffracted by electrons, but are diffracted by atomic nuclei; accordingly, neutron scattering lengths of hydrogen and its isotopes are comparable to those of non-hydrogen atoms. Therefore, neutron crystallography can determine both of the locations and orientations of water molecules. This chapter describes the current status of neutron nucleic acid crystallographic research as well as the basic principles of neutron diffraction experiments performed on nucleic acid crystals: materials, crystallization, diffraction experiments, and structure determination.
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Affiliation(s)
- Toshiyuki Chatake
- Research Reactor Institute, Kyoto University, 2, Asashironishi, Kumatori, Osaka, 590-0494, Japan,
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16
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Chatake T, Fujiwara S. A technique for determining the deuterium/hydrogen contrast map in neutron macromolecular crystallography. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:71-82. [DOI: 10.1107/s2059798315021269] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Accepted: 11/09/2015] [Indexed: 11/10/2022]
Abstract
A difference in the neutron scattering length between hydrogen and deuterium leads to a high density contrast in neutron Fourier maps. In this study, a technique for determining the deuterium/hydrogen (D/H) contrast map in neutron macromolecular crystallography is developed and evaluated using ribonuclease A. The contrast map between the D2O-solvent and H2O-solvent crystals is calculated in real space, rather than in reciprocal space as performed in previous neutron D/H contrast crystallography. The present technique can thus utilize all of the amplitudes of the neutron structure factors for both D2O-solvent and H2O-solvent crystals. The neutron D/H contrast maps clearly demonstrate the powerful detectability of H/D exchange in proteins. In fact, alternative protonation states and alternative conformations of hydroxyl groups are observed at medium resolution (1.8 Å). Moreover, water molecules can be categorized into three types according to their tendency towards rotational disorder. These results directly indicate improvement in the neutron crystal structure analysis. This technique is suitable for incorporation into the standard structure-determination process used in neutron protein crystallography; consequently, more precise and efficient determination of the D-atom positions is possible using a combination of this D/H contrast technique and standard neutron structure-determination protocols.
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Blakeley MP, Hasnain SS, Antonyuk SV. Sub-atomic resolution X-ray crystallography and neutron crystallography: promise, challenges and potential. IUCRJ 2015; 2:464-74. [PMID: 26175905 PMCID: PMC4491318 DOI: 10.1107/s2052252515011239] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 06/09/2015] [Indexed: 05/20/2023]
Abstract
The International Year of Crystallography saw the number of macromolecular structures deposited in the Protein Data Bank cross the 100000 mark, with more than 90000 of these provided by X-ray crystallography. The number of X-ray structures determined to sub-atomic resolution (i.e. ≤1 Å) has passed 600 and this is likely to continue to grow rapidly with diffraction-limited synchrotron radiation sources such as MAX-IV (Sweden) and Sirius (Brazil) under construction. A dozen X-ray structures have been deposited to ultra-high resolution (i.e. ≤0.7 Å), for which precise electron density can be exploited to obtain charge density and provide information on the bonding character of catalytic or electron transfer sites. Although the development of neutron macromolecular crystallography over the years has been far less pronounced, and its application much less widespread, the availability of new and improved instrumentation, combined with dedicated deuteration facilities, are beginning to transform the field. Of the 83 macromolecular structures deposited with neutron diffraction data, more than half (49/83, 59%) were released since 2010. Sub-mm(3) crystals are now regularly being used for data collection, structures have been determined to atomic resolution for a few small proteins, and much larger unit-cell systems (cell edges >100 Å) are being successfully studied. While some details relating to H-atom positions are tractable with X-ray crystallography at sub-atomic resolution, the mobility of certain H atoms precludes them from being located. In addition, highly polarized H atoms and protons (H(+)) remain invisible with X-rays. Moreover, the majority of X-ray structures are determined from cryo-cooled crystals at 100 K, and, although radiation damage can be strongly controlled, especially since the advent of shutterless fast detectors, and by using limited doses and crystal translation at micro-focus beams, radiation damage can still take place. Neutron crystallography therefore remains the only approach where diffraction data can be collected at room temperature without radiation damage issues and the only approach to locate mobile or highly polarized H atoms and protons. Here a review of the current status of sub-atomic X-ray and neutron macromolecular crystallography is given and future prospects for combined approaches are outlined. New results from two metalloproteins, copper nitrite reductase and cytochrome c', are also included, which illustrate the type of information that can be obtained from sub-atomic-resolution (∼0.8 Å) X-ray structures, while also highlighting the need for complementary neutron studies that can provide details of H atoms not provided by X-ray crystallography.
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Affiliation(s)
- Matthew P. Blakeley
- Large-Scale Structures Group, Institut Laue-Langevin, 71 Avenue des Martyrs, Grenoble 38000, France
| | - Samar S. Hasnain
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZX, UK
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZX, UK
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Golden EA, Vrielink A. Looking for Hydrogen Atoms: Neutron Crystallography Provides Novel Insights Into Protein Structure and Function. Aust J Chem 2014. [DOI: 10.1071/ch14337] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Neutron crystallography allows direct localization of hydrogen positions in biological macromolecules. Within enzymes, hydrogen atoms play a pivotal role in catalysis. Recent advances in instrumentation and sample preparation have helped to overcome the difficulties of performing neutron diffraction experiments on protein crystals. The application of neutron macromolecular crystallography to a growing number of proteins has yielded novel structural insights. The ability to accurately position water molecules, hydronium ions, and hydrogen atoms within protein structures has helped in the study of low-barrier hydrogen bonds and hydrogen-bonding networks. The determination of protonation states of protein side chains, substrates, and inhibitors in the context of the macromolecule has provided important insights into enzyme chemistry and ligand binding affinities, which can assist in the design of potent therapeutic agents. In this review, we give an overview of the method and highlight advances in knowledge attained through the application of neutron protein crystallography.
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Meilleur F, Munshi P, Robertson L, Stoica AD, Crow L, Kovalevsky A, Koritsanszky T, Chakoumakos BC, Blessing R, Myles DAA. The IMAGINE instrument: first neutron protein structure and new capabilities for neutron macromolecular crystallography. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2157-60. [DOI: 10.1107/s0907444913019604] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 07/15/2013] [Indexed: 11/11/2022]
Abstract
The first high-resolution neutron protein structure of perdeuterated rubredoxin fromPyrococcus furiosus(PfRd) determined using the new IMAGINE macromolecular neutron crystallography instrument at the Oak Ridge National Laboratory is reported. Neutron diffraction data extending to 1.65 Å resolution were collected from a relatively small 0.7 mm3PfRd crystal using 2.5 d (60 h) of beam time. The refined structure contains 371 out of 391, or 95%, of the D atoms of the protein and 58 solvent molecules. The IMAGINE instrument is designed to provide neutron data at or near atomic resolution (1.5 Å) from crystals with volume <1.0 mm3and with unit-cell edges <100 Å. Beamline features include novel elliptical focusing mirrors that deliver neutrons into a 2.0 × 3.2 mm focal spot at the sample position with full-width vertical and horizontal divergences of 0.5 and 0.6°, respectively. Variable short- and long-wavelength cutoff optics provide automated exchange between multiple-wavelength configurations (λmin= 2.0, 2.8, 3.3 Å to λmax= 3.0, 4.0, 4.5, ∼20 Å). These optics produce a more than 20-fold increase in the flux density at the sample and should help to enable more routine collection of high-resolution data from submillimetre-cubed crystals. Notably, the crystal used to collect thesePfRd data was 5–10 times smaller than those previously reported.
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Lee CH, Noda Y, Ishikawa Y, Kim SA, Moon M, Kimura H, Watanabe M, Dohi Y. Development and applications of a new neutron single-crystal diffractometer based on a two-dimensional large-area curved position-sensitive detector. J Appl Crystallogr 2013; 46:697-708. [PMID: 23682194 PMCID: PMC3654314 DOI: 10.1107/s002188981300681x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Accepted: 03/11/2013] [Indexed: 11/22/2022] Open
Abstract
A new reactor-based neutron single-crystal diffractometer was developed based on a large-area curved position-sensitive detector with a delay-line readout method. The instrumentation details are presented, including diffractometer construction, measurement method, raw data treatment and calibration, and various applications for structural studies are given to exploit the strengths of the diffractometer. A new single-crystal neutron diffractometer based on a large-area curved two-dimensional position-sensitive detector (C-2DPSD) has been developed. The diffractometer commissioning is almost complete, together with development of the measurement methodology and the raw data processing software package, the Reciprocal Analyzer, and the instrument is now ready to be launched for users. Position decoding of the C-2DPSD is via a delay-line readout method with an effective angular range of 110 × 54° in the horizontal and vertical directions, respectively, with a nominal radius of curvature of 530 mm. The diffractometer is equipped with a Ge(311) mosaic monochromator and two supermirror vacuum guide paths, one before and one after the monochromator position. The commissioning incorporates corrections and calibration of the instrument using an NaCl crystal, various applications such as crystallographic and magnetic structure measurements, a crystallinity check on large crystals, and a study on the composition or dopant content of a mixed crystal of (TmxYb1−x)Mn2O5. The installation of the diffractometer and the measurement method, the calibration procedure and results, the raw data treatment and visualization, and several applications using the large C-2DPSD-based diffractometer are reported.
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Affiliation(s)
- Chang-Hee Lee
- Neutron Science Division, Korea Atomic Energy Research Institute, Daejeon, Republic of Korea ; Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Japan
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Kim SA, Lee CH, Moon MK, Cho SJ, Yoon TS, Noda Y, Ishikawa Y. Bio-Diffractometers at HANARO. ACTA ACUST UNITED AC 2013. [DOI: 10.1080/10448632.2013.777646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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22
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Langan P, Evans BR, Foston M, Heller WT, O'Neill H, Petridis L, Pingali SV, Ragauskas AJ, Smith JC, Urban VS, Davison BH. Neutron Technologies for Bioenergy Research. Ind Biotechnol (New Rochelle N Y) 2012. [DOI: 10.1089/ind.2012.0012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Paul Langan
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN
- Center for Structural Molecular Biology, Oak Ridge National Laboratory, Oak Ridge, TN
| | - Barbara R. Evans
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN
| | - Marcus Foston
- Institute of Paper Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA
| | - William T. Heller
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN
| | - Hugh O'Neill
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN
- Center for Structural Molecular Biology, Oak Ridge National Laboratory, Oak Ridge, TN
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN
| | - Loukas Petridis
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN
| | - Sai Venkatesh Pingali
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN
- Center for Structural Molecular Biology, Oak Ridge National Laboratory, Oak Ridge, TN
| | - Arthur J. Ragauskas
- Institute of Paper Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA
| | - Jeremy C. Smith
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN
| | - Volker S. Urban
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN
- Center for Structural Molecular Biology, Oak Ridge National Laboratory, Oak Ridge, TN
| | - Brian H. Davison
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN
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Okazaki N, Adachi M, Tamada T, Kurihara K, Ooga T, Kamiya N, Kuramitsu S, Kuroki R. Crystallization and preliminary neutron diffraction studies of ADP-ribose pyrophosphatase-I from Thermus thermophilus HB8. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:49-52. [PMID: 22232170 PMCID: PMC3253833 DOI: 10.1107/s1744309111044551] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Accepted: 10/25/2011] [Indexed: 11/10/2022]
Abstract
ADP-ribose pyrophosphatase-I from Thermus thermophilus HB8 (TtADPRase-I) prevents the intracellular accumulation of ADP-ribose by hydrolyzing it to AMP and ribose 5'-phosphate. To understand the catalytic mechanism of TtADPRase-I, it is necessary to investigate the role of glutamates and metal ions as well as the coordination of water molecules located at the active site. A macroseeding method was developed in order to obtain a large TtADPRase-I crystal which was suitable for a neutron diffraction study to provide structural information. Neutron and X-ray diffraction experiments were performed at room temperature using the same crystal. The crystal diffracted to 2.1 and 1.5 Å resolution in the neutron and X-ray diffraction experiments, respectively. The crystal belonged to the primitive space group P3(2)21, with unit-cell parameters a = b = 50.7, c = 119 Å.
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Affiliation(s)
- Nobuo Okazaki
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 4 Shirakata-Shirane, Tokai, Ibaraki 319-1195, Japan
| | - Motoyasu Adachi
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 4 Shirakata-Shirane, Tokai, Ibaraki 319-1195, Japan
| | - Taro Tamada
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 4 Shirakata-Shirane, Tokai, Ibaraki 319-1195, Japan
| | - Kazuo Kurihara
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 4 Shirakata-Shirane, Tokai, Ibaraki 319-1195, Japan
| | - Takushi Ooga
- Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 563-0043, Japan
| | - Nobuo Kamiya
- Department of Chemistry, Graduate School of Science, and the OCU Advanced Research Institute for Natural Science and Technology, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
| | - Seiki Kuramitsu
- Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 563-0043, Japan
| | - Ryota Kuroki
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 4 Shirakata-Shirane, Tokai, Ibaraki 319-1195, Japan
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Munshi P, Chung SL, Blakeley MP, Weiss KL, Myles DAA, Meilleur F. Rapid visualization of hydrogen positions in protein neutron crystallographic structures. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2011; 68:35-41. [PMID: 22194331 DOI: 10.1107/s0907444911048402] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Accepted: 11/15/2011] [Indexed: 11/10/2022]
Abstract
Neutron crystallography is a powerful technique for experimental visualization of the positions of light atoms, including hydrogen and its isotope deuterium. In recent years, structural biologists have shown increasing interest in the technique as it uniquely complements X-ray crystallographic data by revealing the positions of D atoms in macromolecules. With this regained interest, access to macromolecular neutron crystallography beamlines is becoming a limiting step. In this report, it is shown that a rapid data-collection strategy can be a valuable alternative to longer data-collection times in appropriate cases. Comparison of perdeuterated rubredoxin structures refined against neutron data sets collected over hours and up to 5 d shows that rapid neutron data collection in just 14 h is sufficient to provide the positions of 269 D atoms without ambiguity.
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Affiliation(s)
- Parthapratim Munshi
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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25
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Tanaka I, Kusaka K, Hosoya T, Ohhara T, Kurihara K, Niimura N. [Beginning of use of a new biological neutron diffractometer (iBIX) in J-PARC]. YAKUGAKU ZASSHI 2010; 130:665-70. [PMID: 20460861 DOI: 10.1248/yakushi.130.665] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
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 A. 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 A 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.
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Affiliation(s)
- Ichiro Tanaka
- College of Engineering, Ibaraki University, Ibaraki, Japan.
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26
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Kakinouchi K, Nakamura T, Tamada T, Adachi H, Sugiyama S, Maruyama M, Takahashi Y, Takano K, Murakami S, Inoue T, Kuroki R, Mori Y, Matsumura H. Growth of large protein crystals by a large-scale hanging-drop method. J Appl Crystallogr 2010. [DOI: 10.1107/s0021889810015967] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
A method for growing large protein crystals is described. In this method, a cut pipette tip is used to hang large-scale droplets (maximum volume 200 µl) consisting of protein and precipitating agents. A crystal grows at the vapor–liquid interface; thereafter the grown crystal can be retrieved by droplet–droplet contact both for repeated macroseeding and for mounting crystals in a capillary. Crystallization experiments with peroxiredoxin ofAeropyrum pernixK1 (thioredoxin peroxidase, ApTPx) and hen egg white lysozyme demonstrated that this large-scale hanging-drop method could produce a large-volume crystal very effectively. A neutron diffraction experiment confirmed that an ApTPx crystal (6.2 mm3) obtained by this method diffracted to beyond 3.5 Å resolution.
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KUROKI R, TAMADA T, KURIHARA K, OHHARA T, ADACHI M. Collaborative Use of Neutron and X-ray for Determination of Drug Target Proteins. YAKUGAKU ZASSHI 2010; 130:657-64. [DOI: 10.1248/yakushi.130.657] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Tadokoro M, Ohhara T, Ohhata Y, Suda T, Miyasato Y, Yamada T, Kikuchi T, Tanaka I, Kurihara K, Oguni M, Nakasuji K, Yamamuro O, Ryota K. Anomalous Water Molecules and Mechanistic Effects of Water Nanotube Clusters Confined to Molecular Porous Crystals. J Phys Chem B 2010; 114:2091-9. [PMID: 20102158 DOI: 10.1021/jp9069465] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Makoto Tadokoro
- Department of Chemistry, Faculty of Science, Tokyo University of Science, Kagurazaka 1-3, Shinjuku-ku, Tokyo 162-8601, Japan; Neutron Science Research Center, Japan Atomic Energy Research Institute, 2-4 Shirane Shirakata, Tokai, Naka-gun, Ibaraki 319-1195, Japan; Neutron Science Laboratory, Institute for Solid State Physics, University of Tokyo, 106-1 Shirakata, Tokai, Naka-gun, Ibaraki 319-1106, Japan; Department of Biomolecular Functional Engineering, College of Engineering, Ibaraki University, 4-12-1
| | - Takashi Ohhara
- Department of Chemistry, Faculty of Science, Tokyo University of Science, Kagurazaka 1-3, Shinjuku-ku, Tokyo 162-8601, Japan; Neutron Science Research Center, Japan Atomic Energy Research Institute, 2-4 Shirane Shirakata, Tokai, Naka-gun, Ibaraki 319-1195, Japan; Neutron Science Laboratory, Institute for Solid State Physics, University of Tokyo, 106-1 Shirakata, Tokai, Naka-gun, Ibaraki 319-1106, Japan; Department of Biomolecular Functional Engineering, College of Engineering, Ibaraki University, 4-12-1
| | - Yuhki Ohhata
- Department of Chemistry, Faculty of Science, Tokyo University of Science, Kagurazaka 1-3, Shinjuku-ku, Tokyo 162-8601, Japan; Neutron Science Research Center, Japan Atomic Energy Research Institute, 2-4 Shirane Shirakata, Tokai, Naka-gun, Ibaraki 319-1195, Japan; Neutron Science Laboratory, Institute for Solid State Physics, University of Tokyo, 106-1 Shirakata, Tokai, Naka-gun, Ibaraki 319-1106, Japan; Department of Biomolecular Functional Engineering, College of Engineering, Ibaraki University, 4-12-1
| | - Takaaki Suda
- Department of Chemistry, Faculty of Science, Tokyo University of Science, Kagurazaka 1-3, Shinjuku-ku, Tokyo 162-8601, Japan; Neutron Science Research Center, Japan Atomic Energy Research Institute, 2-4 Shirane Shirakata, Tokai, Naka-gun, Ibaraki 319-1195, Japan; Neutron Science Laboratory, Institute for Solid State Physics, University of Tokyo, 106-1 Shirakata, Tokai, Naka-gun, Ibaraki 319-1106, Japan; Department of Biomolecular Functional Engineering, College of Engineering, Ibaraki University, 4-12-1
| | - Yuji Miyasato
- Department of Chemistry, Faculty of Science, Tokyo University of Science, Kagurazaka 1-3, Shinjuku-ku, Tokyo 162-8601, Japan; Neutron Science Research Center, Japan Atomic Energy Research Institute, 2-4 Shirane Shirakata, Tokai, Naka-gun, Ibaraki 319-1195, Japan; Neutron Science Laboratory, Institute for Solid State Physics, University of Tokyo, 106-1 Shirakata, Tokai, Naka-gun, Ibaraki 319-1106, Japan; Department of Biomolecular Functional Engineering, College of Engineering, Ibaraki University, 4-12-1
| | - Takeshi Yamada
- Department of Chemistry, Faculty of Science, Tokyo University of Science, Kagurazaka 1-3, Shinjuku-ku, Tokyo 162-8601, Japan; Neutron Science Research Center, Japan Atomic Energy Research Institute, 2-4 Shirane Shirakata, Tokai, Naka-gun, Ibaraki 319-1195, Japan; Neutron Science Laboratory, Institute for Solid State Physics, University of Tokyo, 106-1 Shirakata, Tokai, Naka-gun, Ibaraki 319-1106, Japan; Department of Biomolecular Functional Engineering, College of Engineering, Ibaraki University, 4-12-1
| | - Tatsuya Kikuchi
- Department of Chemistry, Faculty of Science, Tokyo University of Science, Kagurazaka 1-3, Shinjuku-ku, Tokyo 162-8601, Japan; Neutron Science Research Center, Japan Atomic Energy Research Institute, 2-4 Shirane Shirakata, Tokai, Naka-gun, Ibaraki 319-1195, Japan; Neutron Science Laboratory, Institute for Solid State Physics, University of Tokyo, 106-1 Shirakata, Tokai, Naka-gun, Ibaraki 319-1106, Japan; Department of Biomolecular Functional Engineering, College of Engineering, Ibaraki University, 4-12-1
| | - Ichiro Tanaka
- Department of Chemistry, Faculty of Science, Tokyo University of Science, Kagurazaka 1-3, Shinjuku-ku, Tokyo 162-8601, Japan; Neutron Science Research Center, Japan Atomic Energy Research Institute, 2-4 Shirane Shirakata, Tokai, Naka-gun, Ibaraki 319-1195, Japan; Neutron Science Laboratory, Institute for Solid State Physics, University of Tokyo, 106-1 Shirakata, Tokai, Naka-gun, Ibaraki 319-1106, Japan; Department of Biomolecular Functional Engineering, College of Engineering, Ibaraki University, 4-12-1
| | - Kazuo Kurihara
- Department of Chemistry, Faculty of Science, Tokyo University of Science, Kagurazaka 1-3, Shinjuku-ku, Tokyo 162-8601, Japan; Neutron Science Research Center, Japan Atomic Energy Research Institute, 2-4 Shirane Shirakata, Tokai, Naka-gun, Ibaraki 319-1195, Japan; Neutron Science Laboratory, Institute for Solid State Physics, University of Tokyo, 106-1 Shirakata, Tokai, Naka-gun, Ibaraki 319-1106, Japan; Department of Biomolecular Functional Engineering, College of Engineering, Ibaraki University, 4-12-1
| | - Masaharu Oguni
- Department of Chemistry, Faculty of Science, Tokyo University of Science, Kagurazaka 1-3, Shinjuku-ku, Tokyo 162-8601, Japan; Neutron Science Research Center, Japan Atomic Energy Research Institute, 2-4 Shirane Shirakata, Tokai, Naka-gun, Ibaraki 319-1195, Japan; Neutron Science Laboratory, Institute for Solid State Physics, University of Tokyo, 106-1 Shirakata, Tokai, Naka-gun, Ibaraki 319-1106, Japan; Department of Biomolecular Functional Engineering, College of Engineering, Ibaraki University, 4-12-1
| | - Kazuhiro Nakasuji
- Department of Chemistry, Faculty of Science, Tokyo University of Science, Kagurazaka 1-3, Shinjuku-ku, Tokyo 162-8601, Japan; Neutron Science Research Center, Japan Atomic Energy Research Institute, 2-4 Shirane Shirakata, Tokai, Naka-gun, Ibaraki 319-1195, Japan; Neutron Science Laboratory, Institute for Solid State Physics, University of Tokyo, 106-1 Shirakata, Tokai, Naka-gun, Ibaraki 319-1106, Japan; Department of Biomolecular Functional Engineering, College of Engineering, Ibaraki University, 4-12-1
| | - Osamu Yamamuro
- Department of Chemistry, Faculty of Science, Tokyo University of Science, Kagurazaka 1-3, Shinjuku-ku, Tokyo 162-8601, Japan; Neutron Science Research Center, Japan Atomic Energy Research Institute, 2-4 Shirane Shirakata, Tokai, Naka-gun, Ibaraki 319-1195, Japan; Neutron Science Laboratory, Institute for Solid State Physics, University of Tokyo, 106-1 Shirakata, Tokai, Naka-gun, Ibaraki 319-1106, Japan; Department of Biomolecular Functional Engineering, College of Engineering, Ibaraki University, 4-12-1
| | - Kuroki Ryota
- Department of Chemistry, Faculty of Science, Tokyo University of Science, Kagurazaka 1-3, Shinjuku-ku, Tokyo 162-8601, Japan; Neutron Science Research Center, Japan Atomic Energy Research Institute, 2-4 Shirane Shirakata, Tokai, Naka-gun, Ibaraki 319-1195, Japan; Neutron Science Laboratory, Institute for Solid State Physics, University of Tokyo, 106-1 Shirakata, Tokai, Naka-gun, Ibaraki 319-1106, Japan; Department of Biomolecular Functional Engineering, College of Engineering, Ibaraki University, 4-12-1
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Tamada T, Kinoshita T, Kurihara K, Adachi M, Ohhara T, Imai K, Kuroki R, Tada T. Combined high-resolution neutron and X-ray analysis of inhibited elastase confirms the active-site oxyanion hole but rules against a low-barrier hydrogen bond. J Am Chem Soc 2009; 131:11033-40. [PMID: 19603802 DOI: 10.1021/ja9028846] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To help resolve long-standing questions regarding the catalytic activity of the serine proteases, the structure of porcine pancreatic elastase has been analyzed by high-resolution neutron and X-ray crystallography. To mimic the tetrahedral transition intermediate, a peptidic inhibitor was used. A single large crystal was used to collect room-temperature neutron data to 1.65 A resolution and X-ray data to 1.20 A resolution. Another crystal provided a low-temperature X-ray data set to 0.94 A resolution. The neutron data are to higher resolution than previously reported for a serine protease and the X-ray data are comparable with other studies. The neutron and X-ray data show that the hydrogen bond between His57 and Asp102 (chymotrypsin numbering) is 2.60 A in length and that the hydrogen-bonding hydrogen is 0.80-0.96 A from the histidine nitrogen. This is not consistent with a low-barrier hydrogen which is predicted to have the hydrogen midway between the donor and acceptor atom. The observed interaction between His57 and Asp102 is essentially a short but conventional hydrogen bond, sometimes described as a short ionic hydrogen bond. The neutron analysis also shows that the oxygen of the oxopropyl group of the inhibitor is present as an oxygen anion rather than a hydroxyl group, supporting the role of the "oxyanion hole" in stabilizing the tetrahedral intermediate in catalysis.
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Affiliation(s)
- Taro Tamada
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-Shirane, Tokai, Ibaraki 319-1195, Japan
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Niimura N, Chatake T, Ostermann A, Kurihara K, Tanaka I. High resolution neutron protein crystallography. Hydrogen and hydration in proteins. ACTA ACUST UNITED AC 2009. [DOI: 10.1524/zkri.218.2.96.20666] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Abstract
Neutron diffraction provides an experimental method of directly locating hydrogen atoms in proteins, and the development of the neutron imaging plate (NIP) became a breakthrough event in neutron protein crystallography. The general features of the NIP are reviewed. A high resolution neutron diffractometer dedicated to biological macromolecules (BIX-3) with the NIP has been constructed at Japan Atomic Energy Research Institute and this has enabled 1.5 Å resolution structural analyses of several proteins to be carried out. The specifications of BIX-3 and LADI (a quasi-Laue type diffractometer installed in the Institut Laue-Langevin) are compared. The crystal structures of myoglobin, wild type rubredoxin and a mutant of rubredoxin have been carried out using BIX-3. From these studies, several topics, such as the location of hydrogen bonds and certain acidic hydrogen atoms, the identification of methyl hydrogen atoms, details of H/D exchange and dynamical behavior of hydration structures have been investigated, and important information has been extracted from the structural results. Finally, a systematic procedure to grow large single crystals of proteins or nucleic acids is described.
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McGrady GS, Sirsch P, Chatterton NP, Ostermann A, Gatti C, Altmannshofer S, Herz V, Eickerling G, Scherer W. Nature of the Bonding in Metal-Silane σ-Complexes. Inorg Chem 2009; 48:1588-98. [DOI: 10.1021/ic8019777] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- G. Sean McGrady
- Department of Chemistry, University of New Brunswick, P.O. Box 4400, Fredericton, N.B. E3B 5A3, Canada, Department of Health and Human Sciences, London Metropolitan University, 166-220 Holloway Road, London N7 8D8, U.K., Forschungsneutronenquelle Heinz Maier-Leibnitz (FRM-II), Technische Universität München, D-85747 Garching, Germany, CNR-ISTM, Istituto di Scienze e Tecnologie Molecolari, via C. Golgi 19, 20133 Milano, Italy, and Lehrstuhl für Chemische Physik und Materialwissenschaften, Universität
| | - Peter Sirsch
- Department of Chemistry, University of New Brunswick, P.O. Box 4400, Fredericton, N.B. E3B 5A3, Canada, Department of Health and Human Sciences, London Metropolitan University, 166-220 Holloway Road, London N7 8D8, U.K., Forschungsneutronenquelle Heinz Maier-Leibnitz (FRM-II), Technische Universität München, D-85747 Garching, Germany, CNR-ISTM, Istituto di Scienze e Tecnologie Molecolari, via C. Golgi 19, 20133 Milano, Italy, and Lehrstuhl für Chemische Physik und Materialwissenschaften, Universität
| | - Nicholas P. Chatterton
- Department of Chemistry, University of New Brunswick, P.O. Box 4400, Fredericton, N.B. E3B 5A3, Canada, Department of Health and Human Sciences, London Metropolitan University, 166-220 Holloway Road, London N7 8D8, U.K., Forschungsneutronenquelle Heinz Maier-Leibnitz (FRM-II), Technische Universität München, D-85747 Garching, Germany, CNR-ISTM, Istituto di Scienze e Tecnologie Molecolari, via C. Golgi 19, 20133 Milano, Italy, and Lehrstuhl für Chemische Physik und Materialwissenschaften, Universität
| | - Andreas Ostermann
- Department of Chemistry, University of New Brunswick, P.O. Box 4400, Fredericton, N.B. E3B 5A3, Canada, Department of Health and Human Sciences, London Metropolitan University, 166-220 Holloway Road, London N7 8D8, U.K., Forschungsneutronenquelle Heinz Maier-Leibnitz (FRM-II), Technische Universität München, D-85747 Garching, Germany, CNR-ISTM, Istituto di Scienze e Tecnologie Molecolari, via C. Golgi 19, 20133 Milano, Italy, and Lehrstuhl für Chemische Physik und Materialwissenschaften, Universität
| | - Carlo Gatti
- Department of Chemistry, University of New Brunswick, P.O. Box 4400, Fredericton, N.B. E3B 5A3, Canada, Department of Health and Human Sciences, London Metropolitan University, 166-220 Holloway Road, London N7 8D8, U.K., Forschungsneutronenquelle Heinz Maier-Leibnitz (FRM-II), Technische Universität München, D-85747 Garching, Germany, CNR-ISTM, Istituto di Scienze e Tecnologie Molecolari, via C. Golgi 19, 20133 Milano, Italy, and Lehrstuhl für Chemische Physik und Materialwissenschaften, Universität
| | - Sandra Altmannshofer
- Department of Chemistry, University of New Brunswick, P.O. Box 4400, Fredericton, N.B. E3B 5A3, Canada, Department of Health and Human Sciences, London Metropolitan University, 166-220 Holloway Road, London N7 8D8, U.K., Forschungsneutronenquelle Heinz Maier-Leibnitz (FRM-II), Technische Universität München, D-85747 Garching, Germany, CNR-ISTM, Istituto di Scienze e Tecnologie Molecolari, via C. Golgi 19, 20133 Milano, Italy, and Lehrstuhl für Chemische Physik und Materialwissenschaften, Universität
| | - Verena Herz
- Department of Chemistry, University of New Brunswick, P.O. Box 4400, Fredericton, N.B. E3B 5A3, Canada, Department of Health and Human Sciences, London Metropolitan University, 166-220 Holloway Road, London N7 8D8, U.K., Forschungsneutronenquelle Heinz Maier-Leibnitz (FRM-II), Technische Universität München, D-85747 Garching, Germany, CNR-ISTM, Istituto di Scienze e Tecnologie Molecolari, via C. Golgi 19, 20133 Milano, Italy, and Lehrstuhl für Chemische Physik und Materialwissenschaften, Universität
| | - Georg Eickerling
- Department of Chemistry, University of New Brunswick, P.O. Box 4400, Fredericton, N.B. E3B 5A3, Canada, Department of Health and Human Sciences, London Metropolitan University, 166-220 Holloway Road, London N7 8D8, U.K., Forschungsneutronenquelle Heinz Maier-Leibnitz (FRM-II), Technische Universität München, D-85747 Garching, Germany, CNR-ISTM, Istituto di Scienze e Tecnologie Molecolari, via C. Golgi 19, 20133 Milano, Italy, and Lehrstuhl für Chemische Physik und Materialwissenschaften, Universität
| | - Wolfgang Scherer
- Department of Chemistry, University of New Brunswick, P.O. Box 4400, Fredericton, N.B. E3B 5A3, Canada, Department of Health and Human Sciences, London Metropolitan University, 166-220 Holloway Road, London N7 8D8, U.K., Forschungsneutronenquelle Heinz Maier-Leibnitz (FRM-II), Technische Universität München, D-85747 Garching, Germany, CNR-ISTM, Istituto di Scienze e Tecnologie Molecolari, via C. Golgi 19, 20133 Milano, Italy, and Lehrstuhl für Chemische Physik und Materialwissenschaften, Universität
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Huang H, Stewart T, Gutmann M, Ohhara T, Niimura N, Li YX, Wen JF, Bau R, Wong HNC. To Flip or Not To Flip? Assessing the Inversion Barrier of the Tetraphenylene Framework with Enantiopure 2,15-Dideuteriotetraphenylene and 2,7-Dimethyltetraphenylene. J Org Chem 2008; 74:359-69. [DOI: 10.1021/jo802061p] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hui Huang
- Shanghai-Hong Kong Joint Laboratory in Chemical Synthesis, Shanghai Institute of Organic Chemistry, The Chinese Academy of Sciences, 354 Feng Lin Road, Shanghai 200032, China, Department of Chemistry, University of Southern California, Los Angeles, California 90089, ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot, OX11, 0QX, U.K., Japan Atomic Energy Agency, 2-4 Shirakata-Shirane, Tokai, Ibaraki 319-1195, Japan, Institute of Applied Beam Science, Ibaraki University, Naka-Narusawa, 4-12,
| | - Timothy Stewart
- Shanghai-Hong Kong Joint Laboratory in Chemical Synthesis, Shanghai Institute of Organic Chemistry, The Chinese Academy of Sciences, 354 Feng Lin Road, Shanghai 200032, China, Department of Chemistry, University of Southern California, Los Angeles, California 90089, ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot, OX11, 0QX, U.K., Japan Atomic Energy Agency, 2-4 Shirakata-Shirane, Tokai, Ibaraki 319-1195, Japan, Institute of Applied Beam Science, Ibaraki University, Naka-Narusawa, 4-12,
| | - Matthias Gutmann
- Shanghai-Hong Kong Joint Laboratory in Chemical Synthesis, Shanghai Institute of Organic Chemistry, The Chinese Academy of Sciences, 354 Feng Lin Road, Shanghai 200032, China, Department of Chemistry, University of Southern California, Los Angeles, California 90089, ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot, OX11, 0QX, U.K., Japan Atomic Energy Agency, 2-4 Shirakata-Shirane, Tokai, Ibaraki 319-1195, Japan, Institute of Applied Beam Science, Ibaraki University, Naka-Narusawa, 4-12,
| | - Takashi Ohhara
- Shanghai-Hong Kong Joint Laboratory in Chemical Synthesis, Shanghai Institute of Organic Chemistry, The Chinese Academy of Sciences, 354 Feng Lin Road, Shanghai 200032, China, Department of Chemistry, University of Southern California, Los Angeles, California 90089, ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot, OX11, 0QX, U.K., Japan Atomic Energy Agency, 2-4 Shirakata-Shirane, Tokai, Ibaraki 319-1195, Japan, Institute of Applied Beam Science, Ibaraki University, Naka-Narusawa, 4-12,
| | - Nobuo Niimura
- Shanghai-Hong Kong Joint Laboratory in Chemical Synthesis, Shanghai Institute of Organic Chemistry, The Chinese Academy of Sciences, 354 Feng Lin Road, Shanghai 200032, China, Department of Chemistry, University of Southern California, Los Angeles, California 90089, ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot, OX11, 0QX, U.K., Japan Atomic Energy Agency, 2-4 Shirakata-Shirane, Tokai, Ibaraki 319-1195, Japan, Institute of Applied Beam Science, Ibaraki University, Naka-Narusawa, 4-12,
| | - Yu-Xue Li
- Shanghai-Hong Kong Joint Laboratory in Chemical Synthesis, Shanghai Institute of Organic Chemistry, The Chinese Academy of Sciences, 354 Feng Lin Road, Shanghai 200032, China, Department of Chemistry, University of Southern California, Los Angeles, California 90089, ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot, OX11, 0QX, U.K., Japan Atomic Energy Agency, 2-4 Shirakata-Shirane, Tokai, Ibaraki 319-1195, Japan, Institute of Applied Beam Science, Ibaraki University, Naka-Narusawa, 4-12,
| | - Jian-Feng Wen
- Shanghai-Hong Kong Joint Laboratory in Chemical Synthesis, Shanghai Institute of Organic Chemistry, The Chinese Academy of Sciences, 354 Feng Lin Road, Shanghai 200032, China, Department of Chemistry, University of Southern California, Los Angeles, California 90089, ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot, OX11, 0QX, U.K., Japan Atomic Energy Agency, 2-4 Shirakata-Shirane, Tokai, Ibaraki 319-1195, Japan, Institute of Applied Beam Science, Ibaraki University, Naka-Narusawa, 4-12,
| | - Robert Bau
- Shanghai-Hong Kong Joint Laboratory in Chemical Synthesis, Shanghai Institute of Organic Chemistry, The Chinese Academy of Sciences, 354 Feng Lin Road, Shanghai 200032, China, Department of Chemistry, University of Southern California, Los Angeles, California 90089, ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot, OX11, 0QX, U.K., Japan Atomic Energy Agency, 2-4 Shirakata-Shirane, Tokai, Ibaraki 319-1195, Japan, Institute of Applied Beam Science, Ibaraki University, Naka-Narusawa, 4-12,
| | - Henry N. C. Wong
- Shanghai-Hong Kong Joint Laboratory in Chemical Synthesis, Shanghai Institute of Organic Chemistry, The Chinese Academy of Sciences, 354 Feng Lin Road, Shanghai 200032, China, Department of Chemistry, University of Southern California, Los Angeles, California 90089, ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot, OX11, 0QX, U.K., Japan Atomic Energy Agency, 2-4 Shirakata-Shirane, Tokai, Ibaraki 319-1195, Japan, Institute of Applied Beam Science, Ibaraki University, Naka-Narusawa, 4-12,
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Ishikawa T, Chatake T, Morimoto Y, Maeda M, Kurihara K, Tanaka I, Niimura N. An abnormal pK(a) value of internal histidine of the insulin molecule revealed by neutron crystallographic analysis. Biochem Biophys Res Commun 2008; 376:32-5. [PMID: 18725203 DOI: 10.1016/j.bbrc.2008.08.071] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2008] [Accepted: 08/11/2008] [Indexed: 12/01/2022]
Abstract
Insulin is stored in pancreatic beta-cell as hexameric form with Zn2+ ions, while the hormonally active form is monomer. The hexamer requires the coordination of Zn2+ ions to the HisB10. In order to reveal the mechanism of the hexamerization of insulin, we investigated the Zn2+ free insulin at pD6.6 and pD9 by neutron crystallographic analyses. HisB10 is doubly protonated not only at pD6.6 but also at pD9, indicating an abnormal pK(a) of this histidine. It is suggested that HisB10 acts on a strong cation capture and contributes to the high stability of the hexameric form in pancreas.
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Affiliation(s)
- Takuya Ishikawa
- Kyoto University Research Reactor, Asashironishi 2, Kumatori, Osaka 590-0494, Japan
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Blakeley MP, Langan P, Niimura N, Podjarny A. Neutron crystallography: opportunities, challenges, and limitations. Curr Opin Struct Biol 2008; 18:593-600. [PMID: 18656544 DOI: 10.1016/j.sbi.2008.06.009] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2008] [Accepted: 06/26/2008] [Indexed: 10/21/2022]
Abstract
Neutron crystallography has had an important, but relatively small role in structural biology over the years. In this review of recently determined neutron structures, a theme emerges of a field currently expanding beyond its traditional boundaries, to address larger and more complex problems, with smaller samples and shorter data collection times, and employing more sophisticated structure determination and refinement methods. The origin of this transformation can be found in a number of advances including first, the development of neutron image-plates and quasi-Laue methods at nuclear reactor neutron sources and the development of time-of-flight Laue methods and electronic detectors at spallation neutron sources; second, new facilities and methods for sample perdeuteration and crystallization; third, new approaches and computational tools for structure determination.
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Ishikawa T, Chatake T, Ohnishi Y, Tanaka I, Kurihara K, Kuroki R, Niimura N. A neutron crystallographic analysis of a cubic porcine insulin at pD 6.6. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2007.06.053] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Niimura N, Bau R. Neutron protein crystallography: beyond the folding structure of biological macromolecules. Acta Crystallogr A 2007; 64:12-22. [DOI: 10.1107/s0108767307043498] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2007] [Accepted: 09/05/2007] [Indexed: 11/10/2022] Open
Abstract
Neutron diffraction provides an experimental method of directly locating H atoms in proteins, a technique complementary to ultra-high-resolution X-ray diffraction. Three different types of neutron diffractometers for biological macromolecules have been constructed in Japan, France and the USA, and they have been used to determine the crystal structures of proteins up to resolution limits of 1.5–2.5 Å. Results relating to H-atom positions and hydration patterns in proteins have been obtained from these studies. Examples include the geometrical details of hydrogen bonds, the role of H atoms in enzymatic activity, CH3configuration, H/D exchange in proteins and oligonucleotides, and the dynamical behavior of hydration structures, all of which have been extracted from these structural results and reviewed. Other techniques, such as the growth of large single crystals and a database of hydrogen and hydration in proteins, are described.
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Tashiro K, Hanesaka M, Ohhara T, Ozeki T, Kitano T, Nishu T, Kurihara K, Tamada T, Kuroki R, Fujiwara S, Tanaka I, Niimura N. Structural Refinement and Extraction of Hydrogen Atomic Positions in Polyoxymethylene Crystal Based on the First Successful Measurements of 2-Dimensional High-Energy Synchrotron X-ray Diffraction and Wide-Angle Neutron Diffraction Patterns of Hydrogenated and Deuterated Species. Polym J 2007. [DOI: 10.1295/polymj.pj2007076] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Hosoya T, Uekusa H, Ohashi Y, Ohhara T, Kuroki R. A New Photoisomerization Process of the 4-Cyanobutyl Group in a Cobaloxime Complex Crystal Observed by Neutron Diffraction. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2006. [DOI: 10.1246/bcsj.79.692] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Affiliation(s)
- B Leif Hanson
- University of Toledo, MS 602, Toledo, OH 43606, USA.
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Kurihara K, Tanaka I, Chatake T, Adams MWW, Jenney FE, Moiseeva N, Bau R, Niimura N. Neutron crystallographic study on rubredoxin from Pyrococcus furiosus by BIX-3, a single-crystal diffractometer for biomacromolecules. Proc Natl Acad Sci U S A 2004; 101:11215-20. [PMID: 15272083 PMCID: PMC509186 DOI: 10.1073/pnas.0403807101] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2003] [Indexed: 11/18/2022] Open
Abstract
The structure of a partially deuterated rubredoxin from the hyperthermophilic archaeon Pyrococcus furiosus, an organism that grows optimally at 100 degrees C, was determined by using the neutron single-crystal diffractometer dedicated for biological macromolecules (BIX-3) at the JRR-3M reactor of the Japan Atomic Energy Research Institute. Data were collected at room temperature up to a resolution of 1.5 A, and the completeness factor of the data set was 81.9%. The model contains 306 H and 50 D atoms. A total of 37 hydration water molecules were identified, with 15 having all three atoms fully located and the remaining D2O molecules partially defined. The model has been refined to final agreement factors of R = 18.6% and Rfree = 21.7%. Several orientations of the O-D bonds of side chains, whose assignments from x-ray data were previously ambiguous, were clearly visible in the neutron structure. Although most backbone N-H bonds had undergone some degree of H/D exchange throughout the rubredoxin molecule, 5 H atom positions still had distinctly negative (H) peaks. The neutron Fourier maps clearly showed the details of an extensive set of H bonds involving the ND3+ terminus that may contribute to the unusual thermostability of this molecule.
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Affiliation(s)
- Kazuo Kurihara
- Neutron Science Research Center, Japan Atomic Energy Research Institute, Tokai, Ibaraki 319-1195, Japan
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Tashiro K, Tanaka I, Oohara T, Niimura N, Fujiwara S, Kamae T. Extraction of Hydrogen-Atom Positions in Polyethylene Crystal Lattice from Wide-Angle Neutron Diffraction Data Collected by a Two-Dimensional Imaging Plate System: Comparison with the X-ray and Electron Diffraction Results. Macromolecules 2004. [DOI: 10.1021/ma036003o] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kohji Tashiro
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan, Advanced Science Research Center, Japan Atomic Energy Institute, Tokai-mura, Ibaraki 319-1195, Japan, Institute of Materials Structure Science, High Energy Accelerator Research Organization, Oho 1-1, Tsukuba, Ibaraki 305-0801, Japan, and Department of Technology, Ibaraki University, Hitachi, Ibaraki 316-8511, Japan
| | - Ichiro Tanaka
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan, Advanced Science Research Center, Japan Atomic Energy Institute, Tokai-mura, Ibaraki 319-1195, Japan, Institute of Materials Structure Science, High Energy Accelerator Research Organization, Oho 1-1, Tsukuba, Ibaraki 305-0801, Japan, and Department of Technology, Ibaraki University, Hitachi, Ibaraki 316-8511, Japan
| | - Takashi Oohara
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan, Advanced Science Research Center, Japan Atomic Energy Institute, Tokai-mura, Ibaraki 319-1195, Japan, Institute of Materials Structure Science, High Energy Accelerator Research Organization, Oho 1-1, Tsukuba, Ibaraki 305-0801, Japan, and Department of Technology, Ibaraki University, Hitachi, Ibaraki 316-8511, Japan
| | - Nobuo Niimura
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan, Advanced Science Research Center, Japan Atomic Energy Institute, Tokai-mura, Ibaraki 319-1195, Japan, Institute of Materials Structure Science, High Energy Accelerator Research Organization, Oho 1-1, Tsukuba, Ibaraki 305-0801, Japan, and Department of Technology, Ibaraki University, Hitachi, Ibaraki 316-8511, Japan
| | - Satoru Fujiwara
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan, Advanced Science Research Center, Japan Atomic Energy Institute, Tokai-mura, Ibaraki 319-1195, Japan, Institute of Materials Structure Science, High Energy Accelerator Research Organization, Oho 1-1, Tsukuba, Ibaraki 305-0801, Japan, and Department of Technology, Ibaraki University, Hitachi, Ibaraki 316-8511, Japan
| | - Toshiya Kamae
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan, Advanced Science Research Center, Japan Atomic Energy Institute, Tokai-mura, Ibaraki 319-1195, Japan, Institute of Materials Structure Science, High Energy Accelerator Research Organization, Oho 1-1, Tsukuba, Ibaraki 305-0801, Japan, and Department of Technology, Ibaraki University, Hitachi, Ibaraki 316-8511, Japan
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Takahashi Y, Kumano T. Neutron crystal structure analysis of polyethylene-d4: The application of a neutron imaging plate. ACTA ACUST UNITED AC 2004. [DOI: 10.1002/polb.20245] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Engler N, Ostermann A, Niimura N, Parak FG. Hydrogen atoms in proteins: positions and dynamics. Proc Natl Acad Sci U S A 2003; 100:10243-8. [PMID: 12937341 PMCID: PMC193546 DOI: 10.1073/pnas.1834279100] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2002] [Indexed: 11/18/2022] Open
Abstract
Hydrogen atoms constitute about half of the atoms in proteins. Thus they contribute to the complex energy landscape of proteins [Frauenfelder, H., Sligar, S. G. & Wolynes, P. G. (1991) Science 254, 1598-1603]. Neutron crystal structure analysis was used to study the positions and mean-square displacements of hydrogen in myoglobin. A test of the reliability of calculated hydrogen atom coordinates by a comparison with our experimental results has been carried out. The result shows that >70% of the coordinates for hydrogen atoms that have a degree of freedom is predicted worse than 0.2 A. It is shown that the mean-square displacements of the hydrogen atoms obtained from the Debye-Waller factor can be divided into three classes. A comparison with the dynamic mean-square displacements calculated from the elastic intensities obtained from incoherent neutron scattering [Doster, W., Cusack, S. & Petry, W. (1989) Nature 337, 754-756] shows that mainly the side-chain hydrogen atoms contribute to dynamic displacements on a time scale faster than 100 ps.
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Affiliation(s)
- Niklas Engler
- Physik Department E17, Technische Universität Munich, James-Franck-Strasse, 85748 Garching, Germany
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Chatake T, Ostermann A, Kurihara K, Parak FG, Niimura N. Hydration in proteins observed by high-resolution neutron crystallography. Proteins 2003; 50:516-23. [PMID: 12557193 DOI: 10.1002/prot.10303] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
It is well known that water molecules surrounding a protein play important roles in maintaining its structural stability. Water molecules are known to participate in several physiological processes through the formation of hydrogen bonds. However, the hydration structures of most proteins are not known well at an atomic level at present because X-ray protein crystallography has difficulties to localize hydrogen atoms. In contrast, neutron crystallography has no problem in determining the position of hydrogens with high accuracy.1 In this article, the hydration structures of three proteins are described- myoglobin, wild-type rubredoxin, and a mutant rubredoxin-the structures of which were solved at 1.5- or 1.6-A resolution by neutron structure determination. These hydration patterns show fascinating features and the water molecules adopt a variety of shapes in the neutron Fourier maps, revealing details of intermolecular hydrogen bond formation and dynamics of hydration. Our results further show that there are strong relationships between these shapes and the water environments.
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Affiliation(s)
- Toshiyuki Chatake
- Advanced Science Research Center, Japan Atomic Energy Research Institute, Tokai-mura, Ibaraki-ken, Japan
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