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Kusaka K, Yokoyama T, Yamada T, Yano N, Tanaka I, Mizuguchi M. Neutron diffraction experiment with the Y116S variant of transthyretin using iBIX at J-PARC: application of a new integration method. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:1050-1056. [PMID: 33135676 DOI: 10.1107/s2059798320012498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 09/11/2020] [Indexed: 11/10/2022]
Abstract
Transthyretin (TTR) is one of more than 30 amyloidogenic proteins, and the amyloid fibrils found in patients afflicted with ATTR amyloidosis are composed of this protein. Wild-type TTR amyloids accumulate in the heart in senile systemic amyloidosis (SSA). ATTR amyloidosis occurs at a much younger age than SSA, and the affected individuals carry a TTR mutant. The naturally occurring amyloidogenic Y116S TTR variant forms more amyloid fibrils than wild-type TTR. Thus, the Y116S mutation reduces the stability of the TTR structure. A neutron diffraction experiment on Y116S TTR was performed to elucidate the mechanism of the changes in structural stability between Y116S variant and wild-type TTR through structural comparison. Large crystals of the Y116S variant were grown under optimal crystallization conditions, and a single 2.4 mm3 crystal was ultimately obtained. This crystal was subjected to time-of-flight (TOF) neutron diffraction using the IBARAKI biological crystal diffractometer (iBIX) at the Japan Proton Accelerator Research Complex, Tokai, Japan (J-PARC). A full data set for neutron structure analysis was obtained in 14 days at an operational accelerator power of 500 kW. A new integration method was developed and showed improved data statistics; the new method was applied to the reduction of the TOF diffraction data from the Y116S variant. Data reduction was completed and the integrated intensities of the Bragg reflections were obtained at 1.9 Å resolution for structure refinement. Moreover, X-ray diffraction data at 1.4 Å resolution were obtained for joint neutron-X-ray refinement.
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Affiliation(s)
- Katsuhiro Kusaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Takeshi Yokoyama
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama, Toyama 930-0194, Japan
| | - Taro Yamada
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Naomine Yano
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Ichiro Tanaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Mineyuki Mizuguchi
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama, Toyama 930-0194, 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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High-resolution neutron crystallography visualizes an OH-bound resting state of a copper-containing nitrite reductase. Proc Natl Acad Sci U S A 2020; 117:4071-4077. [PMID: 32041886 PMCID: PMC7049163 DOI: 10.1073/pnas.1918125117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
X-ray crystallography often fails to determine the positions of hydrogen atoms, which play crucial roles in enzymatic reactions. Despite many X-ray crystallographic studies, the reaction mechanism of copper-containing nitrite reductases (CuNIRs), which reduce nitrite using two protons, has been controversial. The high-resolution neutron structure of a CuNIR reveals the protonation states of catalytic residues and key water molecules, thus providing insights into the catalytic mechanism. The catalytic Cu is shown to be coordinated by a hydroxide ion and not water. Furthermore, the hydrogen-deuterium exchange ratio suggests that intramolecular electron transfer is involved in a hydrogen-bond jump. These observations are consistent with previous computational chemistry; therefore, our study forms a bridge between the structural biology and quantum chemistry of CuNIRs. Copper-containing nitrite reductases (CuNIRs) transform nitrite to gaseous nitric oxide, which is a key process in the global nitrogen cycle. The catalytic mechanism has been extensively studied to ultimately achieve rational control of this important geobiochemical reaction. However, accumulated structural biology data show discrepancies with spectroscopic and computational studies; hence, the reaction mechanism is still controversial. In particular, the details of the proton transfer involved in it are largely unknown. This situation arises from the failure of determining positions of hydrogen atoms and protons, which play essential roles at the catalytic site of CuNIRs, even with atomic resolution X-ray crystallography. Here, we determined the 1.50 Å resolution neutron structure of a CuNIR from Geobacillus thermodenitrificans (trimer molecular mass of ∼106 kDa) in its resting state at low pH. Our neutron structure reveals the protonation states of catalytic residues (deprotonated aspartate and protonated histidine), thus providing insights into the catalytic mechanism. We found that a hydroxide ion can exist as a ligand to the catalytic Cu atom in the resting state even at a low pH. This OH-bound Cu site is unexpected from previously given X-ray structures but consistent with a reaction intermediate suggested by computational chemistry. Furthermore, the hydrogen-deuterium exchange ratio in our neutron structure suggests that the intramolecular electron transfer pathway has a hydrogen-bond jump, which is proposed by quantum chemistry. Our study can seamlessly link the structural biology to the computational chemistry of CuNIRs, boosting our understanding of the enzymes at the atomic and electronic levels.
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Yamada T, Yano N, Hosoya T, Kusaka K. Single-crystal time-of-flight neutron Laue methods: application to manganese catalase from Thermus thermophilus HB27. J Appl Crystallogr 2019. [DOI: 10.1107/s1600576719010239] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The IBARAKI biological crystal diffractometer (iBIX) was used in single-crystal time-of-flight neutron diffraction experiments on manganese catalase from Thermus thermophilus. The unit-cell dimensions were 133 × 133 × 133 Å, which is close to the designed maximum limitation of iBIX (135 × 135 × 135 Å). The optimum integration box sizes were set and the degree of integration box overlap was calculated for each Laue spot. Using the overlap ratio as the criterion, the selection of the diffraction intensity data was performed to give a minimum R
p.i.m.. Subsequently, diffraction intensity data from Laue spots with overlap ratios ≤0.1 were selected and a complete reflection data set with d
min = 2.35 Å was obtained. Joint X-ray and neutron structure refinements were also successfully performed. It was difficult to determine the structures and protonation states of all the oxygen atoms in the manganese cluster owing to the disordered structure. No hydrogen atom was observed on the ordered μ-bridging oxygen atom O1003. Instead, this oxygen atom probably forms a hydrogen bond with Thr39. In addition, the refinements clearly showed the protonation states of the amino acid residues and hydrogen bonds, as observed in Tyr192, Glu167 and Glu280. This first neutron crystal structure of manganese catalase shows that iBIX can provide acceptable diffraction data for neutron single-crystal analyses of at least 2.4 Å resolution within the original targeted unit-cell dimensions of 135 × 135 × 135 Å.
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Sullivan B, Archibald R, Langan PS, Dobbek H, Bommer M, McFeeters RL, Coates L, Wang X, Gallmeier F, Carpenter JM, Lynch V, Langan P. Improving the accuracy and resolution of neutron crystallographic data by three-dimensional profile fitting of Bragg peaks in reciprocal space. Acta Crystallogr D Struct Biol 2018; 74:1085-1095. [PMID: 30387767 PMCID: PMC6213576 DOI: 10.1107/s2059798318013347] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 09/18/2018] [Indexed: 11/29/2022] Open
Abstract
Neutron crystallography is a powerful technique for directly visualizing the locations of H atoms in biological macromolecules. This information has provided key new insights into enzyme mechanisms, ligand binding and hydration. However, despite the importance of this information, the application of neutron crystallography in biology has been limited by the relatively low flux of available neutron beams and the large incoherent neutron scattering from hydrogen, both of which contribute to weak diffraction data with relatively low signal-to-background ratios. A method has been developed to fit weak data based on three-dimensional profile fitting of Bragg peaks in reciprocal space by an Ikeda-Carpenter function with a bivariate Gaussian. When applied to data collected from three different proteins, three-dimensional profile fitting yields intensities with higher correlation coefficients (CC1/2) at high resolutions, decreased Rfree factors, extended resolutions and improved nuclear density maps. Importantly, additional features are revealed in nuclear density maps that may provide additional scientific information. These results suggest that three-dimensional profile fitting will help to extend the capabilities of neutron macromolecular crystallography.
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Affiliation(s)
- Brendan Sullivan
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Rick Archibald
- Computer Science and Mathematics Division, Computing and Computational Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Patricia S. Langan
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Holger Dobbek
- Institut für Biologie, Humboldt-Universität zu Berlin, Philippstrasse 13, Leonor Michaelis Haus, 10115 Berlin, Germany
| | - Martin Bommer
- Institut für Biologie, Humboldt-Universität zu Berlin, Philippstrasse 13, Leonor Michaelis Haus, 10115 Berlin, Germany
| | - Robert L. McFeeters
- Department of Chemistry, University of Alabama in Huntsville, 301 Sparkman Drive, Huntsville, AL 35899, USA
| | - Leighton Coates
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Xiaoping Wang
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Franz Gallmeier
- Neutron Technologies Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - John M. Carpenter
- Neutron Technologies Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Vickie Lynch
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Paul Langan
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
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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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Abstract
The factors affecting the accuracy of structural refinements from image-plate neutron Laue diffractometers are analysed. From this analysis, an improved data-processing method is developed which optimizes the intensity corrections for exposure scaling, wavelength distribution, absorption and extinction corrections, and the wavelength/spatial/time dependence of the image-plate detector efficiencies. Of equal importance is an analysis of the sources of uncertainty in the final corrected intensities, without which bias of the merged intensities occurs, due to the dominance of measurements with small statistical errors though potentially large systematic errors. A new aspect of the impact of detector crosstalk on the counting statistics of area detectors is reported and shown to be significant for the case of neutron Laue diffraction. These methods have been implemented in software which processes data from the KOALA instrument at ANSTO and the now decommissioned VIVALDI instrument at ILL (Grenoble, France). A comparison with earlier data-analysis methods shows a significant improvement in accuracy of the refined structures.
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Abstract
An overview is presented of an integrated software package for the processing of Laue data from reactor and other continuous neutron sources. LaueG appears to the user as a graphical user interface with interactive graphic modes that depend on the task being performed: simple image display, cell indexing and refinement, peak integration, wavelength normalization and intensity corrections, or identification of statistical outliers. Other capabilities under development, though still usable, include satellite spots and modulated structures, twinned crystal analysis, and ab initio indexing of unit cells. The emphasis is on accurate intensities for structure refinement using an integrated graphical approach.
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Materials and Life Science Experimental Facility (MLF) at the Japan Proton Accelerator Research Complex II: Neutron Scattering Instruments. QUANTUM BEAM SCIENCE 2017. [DOI: 10.3390/qubs1030009] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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