1
|
Fukushima K, Taniguchi Y, Matsushita M, Sugiyama M, Kaneko K. Determination of the point resolution of high-resolution transmission electron microscope using the through-focus technique. Micron 2024; 182:103639. [PMID: 38688141 DOI: 10.1016/j.micron.2024.103639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 04/07/2024] [Accepted: 04/14/2024] [Indexed: 05/02/2024]
Abstract
From the viewpoint of evaluating the instrumental performance of high-resolution electron microscopy (HREM), the Scherzer condition was investigated using information theory. As a result, the optimum defocus amount Δf can be expressed based on [Formula: see text] , and the formula [Formula: see text] is obtained. Furthermore, a procedure for measuring point resolution using the through-focus technique is developed, and a new method for determining the spherical aberration coefficient using the variance of Δf is introduced in the procedure.
Collapse
Affiliation(s)
| | - Yoshifumi Taniguchi
- Core Technology & Solutions Business Group, Hitachi High-Tech Corporation, Ibaragi 312-8504, Japan
| | | | - Masaaki Sugiyama
- Research Center for Ultra-High Voltage Electron Microscopy, Osaka Univ., Osaka 567-0047, Japan
| | - Kenji Kaneko
- Department of Materials, Graduate School of Engineering, Kyushu Univ., Fukuoka 819-0395, Japan.
| |
Collapse
|
2
|
Kubo T, Sunami K, Koyama T, Kitami M, Fujiwara Y, Kondo S, Yonemori K, Noguchi E, Morizane C, Goto Y, Maejima A, Iwasa S, Hamaguchi T, Kawai A, Namikawa K, Arakawa A, Sugiyama M, Ohno M, Yoshida T, Hiraoka N, Yoshida A, Yoshida M, Nishino T, Furukawa E, Narushima D, Nagai M, Kato M, Ichikawa H, Fujiwara Y, Kohno T, Yamamoto N. The impact of rare cancer and early-line treatments on the benefit of comprehensive genome profiling-based precision oncology. ESMO Open 2024; 9:102981. [PMID: 38613908 PMCID: PMC11033064 DOI: 10.1016/j.esmoop.2024.102981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 03/04/2024] [Accepted: 03/04/2024] [Indexed: 04/15/2024] Open
Abstract
BACKGROUND Comprehensive genome profiling (CGP) serves as a guide for suitable genomically matched therapies for patients with cancer. However, little is known about the impact of the timing and types of cancer on the therapeutic benefit of CGP. MATERIALS AND METHODS A single hospital-based pan-cancer prospective study (TOP-GEAR; UMIN000011141) was conducted to examine the benefit of CGP with respect to the timing and types of cancer. Patients with advanced solid tumors (>30 types) who either progressed with or without standard treatments were genotyped using a single CGP test. The subjects were followed up for a median duration of 590 days to examine therapeutic response, using progression-free survival (PFS), PFS ratio, and factors associated with therapeutic response. RESULTS Among the 507 patients, 62 (12.2%) received matched therapies with an overall response rate (ORR) of 32.3%. The PFS ratios (≥1.3) were observed in 46.3% (19/41) of the evaluated patients. The proportion of subjects receiving such therapies in the rare cancer cohort was lower than that in the non-rare cancer cohort (9.6% and 17.4%, respectively; P = 0.010). However, ORR of the rare cancer patients was higher than that in the non-rare cancer cohort (43.8% and 20.0%, respectively; P = 0.046). Moreover, ORR of matched therapies in the first or second line after receiving the CGP test was higher than that in the third or later lines (62.5% and 21.7%, respectively; P = 0.003). Rare cancer and early-line treatment were significantly and independently associated with ORR of matched therapies in multivariable analysis (P = 0.017 and 0.004, respectively). CONCLUSION Patients with rare cancer preferentially benefited from tumor mutation profiling by increasing the chances of therapeutic response to matched therapies. Early-line treatments after profiling increase the therapeutic benefit, irrespective of tumor types.
Collapse
Affiliation(s)
- T Kubo
- Department of Laboratory Medicine, National Cancer Center Hospital, Tokyo; Department of Clinical Genomics, National Cancer Center Research Institute, Tokyo
| | - K Sunami
- Department of Laboratory Medicine, National Cancer Center Hospital, Tokyo; Division of Genome Biology, National Cancer Center Research Institute, Tokyo
| | - T Koyama
- Department of Experimental Therapeutics, National Cancer Center Hospital, Tokyo
| | - M Kitami
- Department of Laboratory Medicine, National Cancer Center Hospital, Tokyo
| | - Y Fujiwara
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo; Department of Thoracic Oncology, Aichi Cancer Center Hospital, Aichi
| | - S Kondo
- Department of Experimental Therapeutics, National Cancer Center Hospital, Tokyo; Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo
| | - K Yonemori
- Department of Experimental Therapeutics, National Cancer Center Hospital, Tokyo; Department of Medical Oncology, National Cancer Center Hospital, Tokyo
| | - E Noguchi
- Department of Medical Oncology, National Cancer Center Hospital, Tokyo
| | - C Morizane
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo
| | - Y Goto
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo
| | - A Maejima
- Department of Medical Oncology, National Cancer Center Hospital, Tokyo; Department of Urology, National Cancer Center Hospital, Tokyo
| | - S Iwasa
- Department of Experimental Therapeutics, National Cancer Center Hospital, Tokyo; Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo
| | - T Hamaguchi
- Department of Medical Oncology, Saitama Medical University International Medical Center, Saitama
| | - A Kawai
- Department of Musculoskeletal Oncology and Rehabilitation, National Cancer Center Hospital, Tokyo
| | - K Namikawa
- Department of Dermatologic Oncology, National Cancer Center Hospital, Tokyo
| | - A Arakawa
- Department of Pediatric Oncology, National Cancer Center Hospital, Tokyo
| | - M Sugiyama
- Department of Pediatric Oncology, National Cancer Center Hospital, Tokyo
| | - M Ohno
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, Tokyo
| | - T Yoshida
- Department of Genetic Services and Medicine, National Cancer Center Hospital, Tokyo
| | - N Hiraoka
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo
| | - A Yoshida
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo
| | - M Yoshida
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo
| | - T Nishino
- Department of Laboratory Medicine, National Cancer Center Hospital, Tokyo
| | - E Furukawa
- Division of Bioinformatics, National Cancer Center Research Institute, Tokyo
| | - D Narushima
- Division of Bioinformatics, National Cancer Center Research Institute, Tokyo
| | - M Nagai
- Division of Bioinformatics, National Cancer Center Research Institute, Tokyo
| | - M Kato
- Division of Bioinformatics, National Cancer Center Research Institute, Tokyo
| | - H Ichikawa
- Department of Clinical Genomics, National Cancer Center Research Institute, Tokyo; Division of Translational Genomics, National Cancer Center Exploratory Oncology Research & Clinical Trial Center, Tokyo, Japan
| | - Y Fujiwara
- Department of Medical Oncology, National Cancer Center Hospital, Tokyo
| | - T Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo; Division of Translational Genomics, National Cancer Center Exploratory Oncology Research & Clinical Trial Center, Tokyo, Japan
| | - N Yamamoto
- Department of Experimental Therapeutics, National Cancer Center Hospital, Tokyo.
| |
Collapse
|
3
|
Yuzu K, Imamura H, Nozaki T, Fujii Y, Badawy SMM, Morishima K, Okuda A, Inoue R, Sugiyama M, Chatani E. Mechanistic Modeling of Amyloid Oligomer and Protofibril Formation in Bovine Insulin. J Mol Biol 2024; 436:168461. [PMID: 38301805 DOI: 10.1016/j.jmb.2024.168461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/22/2024] [Accepted: 01/26/2024] [Indexed: 02/03/2024]
Abstract
Early phase of amyloid formation, where prefibrillar aggregates such as oligomers and protofibrils are often observed, is crucial for understanding pathogenesis. However, the detailed mechanisms of their formation have been difficult to elucidate because they tend to form transiently and heterogeneously. Here, we found that bovine insulin protofibril formation proceeds in a monodisperse manner, which allowed us to characterize the detailed early aggregation process by light scattering in combination with thioflavin T fluorescence and Fourier transform infrared spectroscopy. The protofibril formation was specific to bovine insulin, whereas no significant aggregation was observed in human insulin. The kinetic analysis combining static and dynamic light scattering data revealed that the protofibril formation process in bovine insulin can be divided into two steps based on fractal dimension. When modeling the experimental data based on Smoluchowski aggregation kinetics, an aggregation scheme consisting of initial fractal aggregation forming spherical oligomers and their subsequent end-to-end association forming protofibrils was clarified. Furthermore, the analysis of temperature and salt concentration dependencies showed that the end-to-end association is the rate-limiting step, involving dehydration. The established model for protofibril formation, wherein oligomers are incorporated as a precursor, provides insight into the molecular mechanism by which protein molecules assemble during the early stage of amyloid formation.
Collapse
Affiliation(s)
- Keisuke Yuzu
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe, Hyogo 657-8501, Japan
| | - Hiroshi Imamura
- Department of Bio-Science, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga 526-0829, Japan
| | - Takuro Nozaki
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe, Hyogo 657-8501, Japan
| | - Yuki Fujii
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe, Hyogo 657-8501, Japan
| | - Shaymaa Mohamed Mohamed Badawy
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe, Hyogo 657-8501, Japan; Department of Agricultural Biochemistry, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Ken Morishima
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Osaka 590-0494, Japan
| | - Aya Okuda
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Osaka 590-0494, Japan
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Osaka 590-0494, Japan
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Osaka 590-0494, Japan
| | - Eri Chatani
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe, Hyogo 657-8501, Japan.
| |
Collapse
|
4
|
Nishimura M, Fujii T, Tanaka H, Maehara K, Morishima K, Shimizu M, Kobayashi Y, Nozawa K, Takizawa Y, Sugiyama M, Ohkawa Y, Kurumizaka H. Genome-wide mapping and cryo-EM structural analyses of the overlapping tri-nucleosome composed of hexasome-hexasome-octasome moieties. Commun Biol 2024; 7:61. [PMID: 38191828 PMCID: PMC10774305 DOI: 10.1038/s42003-023-05694-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 12/11/2023] [Indexed: 01/10/2024] Open
Abstract
The nucleosome is a fundamental unit of chromatin in which about 150 base pairs of DNA are wrapped around a histone octamer. The overlapping di-nucleosome has been proposed as a product of chromatin remodeling around the transcription start site, and previously found as a chromatin unit, in which about 250 base pairs of DNA continuously bind to the histone core composed of a hexamer and an octamer. In the present study, our genome-wide analysis of human cells suggests another higher nucleosome stacking structure, the overlapping tri-nucleosome, which wraps about 300-350 base-pairs of DNA in the region downstream of certain transcription start sites of actively transcribed genes. We determine the cryo-electron microscopy (cryo-EM) structure of the overlapping tri-nucleosome, in which three subnucleosome moieties, hexasome, hexasome, and octasome, are associated by short connecting DNA segments. Small angle X-ray scattering and coarse-grained molecular dynamics simulation analyses reveal that the cryo-EM structure of the overlapping tri-nucleosome may reflect its structure in solution. Our findings suggest that nucleosome stacking structures composed of hexasome and octasome moieties may be formed by nucleosome remodeling factors around transcription start sites for gene regulation.
Collapse
Affiliation(s)
- Masahiro Nishimura
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, 111 TW, Alexander Drive, Research Triangle Park, NC, 27707, USA
| | - Takeru Fujii
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi, Fukuoka, 812-0054, Japan
| | - Hiroki Tanaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
- Department of Structural Virology, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo, 162-8655, Japan
| | - Kazumitsu Maehara
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi, Fukuoka, 812-0054, Japan
| | - Ken Morishima
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Masahiro Shimizu
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Yuki Kobayashi
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Kayo Nozawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan
| | - Yoshimasa Takizawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi, Fukuoka, 812-0054, Japan.
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.
| |
Collapse
|
5
|
Ishida H, Matsumoto A, Tanaka H, Okuda A, Morishima K, Wade PA, Kurumizaka H, Sugiyama M, Kono H. Structural and Dynamic Changes of Nucleosome upon GATA3 Binding. J Mol Biol 2023; 435:168308. [PMID: 37805066 PMCID: PMC10843466 DOI: 10.1016/j.jmb.2023.168308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/30/2023] [Accepted: 10/03/2023] [Indexed: 10/09/2023]
Abstract
Pioneer factors, which can directly bind to nucleosomes, have been considered to change chromatin conformations. However, the binding impact on the nucleosome is little known. Here, we show how the pioneer factor GATA3 binds to nucleosomal DNA and affects the conformation and dynamics of nucleosomes by using a combination of SAXS, molecular modeling, and molecular dynamics simulations. Our structural models, consistent with the SAXS data, indicate that only one of the two DNA binding domains, N- and C-fingers, of GATA3 binds to an end of the DNA in solution. Our MD simulations further showed that the other unbound end of the DNA increases the fluctuation and enhances the DNA dissociation from the histone core when the N-finger binds to a DNA end, a site near the entry or exit of the nucleosome. However, this was not true for the binding of the C-finger that binds to a location about 15 base pairs distant from the DNA end. In this case, DNA dissociation occurred on the bound end. Taken together, we suggest that the N-finger and C-finger bindings of GATA3 commonly enhance DNA dissociation at one of the two DNA ends (the bound end for the C-finger binding and the unbound end for the N-finger binding), leading to triggering a conformational change in the chromatin.
Collapse
Affiliation(s)
- Hisashi Ishida
- Institute for Quantum Life Science, Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba city, Chiba 263-8555, Japan
| | - Atsushi Matsumoto
- Institute for Quantum Life Science, Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba city, Chiba 263-8555, Japan
| | - Hiroki Tanaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan; Present address: Department of Structural Virology, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Aya Okuda
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Ken Morishima
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Paul A Wade
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC 27709, USA
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Hidetoshi Kono
- Institute for Quantum Life Science, Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba city, Chiba 263-8555, Japan; Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan.
| |
Collapse
|
6
|
Chatake T, Yanagisawa Y, Murakami R, Ohsugi T, Sumi H, Takata T, Okuda A, Morishima K, Inoue R, Sugiyama M. Characterization of K-binding factor involved in water-soluble complex of menaquinone-7 produced by Bacillus subtilis natto. J Biochem 2023; 174:383-389. [PMID: 37419501 DOI: 10.1093/jb/mvad051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 06/15/2023] [Accepted: 07/02/2023] [Indexed: 07/09/2023] Open
Abstract
Vitamin Ks are expected to contribute bone and cardiovascular health. Especially, menaquinone-7 has a higher bioavailability and a longer half-life than other vitamin Ks in the human body. However, their low water-solubility limits their application. On the other hand, Bacillus subtilis natto produces a water-soluble complex, which comprises menaquinone-7 and peptides. The peptide named K-binding factor (KBF) has been reported as the main component of the complex. In the present, the structural characteristics of KBF were studied. Mass spectrometry showed significant peaks at m/z = 1050, while the previous PAGE suggested that molecular weight of KBF was ~ 3k. Amino acid analysis revealed that the 1k peptides were the various combinations of nine amino acids, among which Asx, Glx, Val, Leu and Met were found to be the most abundant. The peptides could serve as detergent properties. The 1k peptides could be isolated by reverse-phase high performance liquid chromatography. The bundle of three 1k detergent-like peptides would participate to the micelle structure containing menqauinone-7 inside. In conclusion, a basic unit of KBF would be the ~ 1k peptides, and the three basic unit assemble to the ~ 3k bundle, then the bundle form a water-soluble micelle including menqauinone-7 inside.
Collapse
Affiliation(s)
- Toshiyuki Chatake
- Insititute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Asashironishi-2, Osaka 590-0484, Japan
| | - Yasuhide Yanagisawa
- Faculty of Pharmaceutical Sciences, Chiba Institute of Science, Cho-shi, Shiomi-cho 15-8, Chiba 288-0025, Japan
| | - Risa Murakami
- Faculty of Pharmaceutical Sciences, Chiba Institute of Science, Cho-shi, Shiomi-cho 15-8, Chiba 288-0025, Japan
| | - Tadanori Ohsugi
- Department of Life Science, Kurashiki University of Science and the Arts, Kurashiki, Tsurajima-cho, Nishinoura, Okayama 712-8001, Japan
| | - Hiroyuki Sumi
- Department of Life Science, Kurashiki University of Science and the Arts, Kurashiki, Tsurajima-cho, Nishinoura, Okayama 712-8001, Japan
| | - Takumi Takata
- Insititute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Asashironishi-2, Osaka 590-0484, Japan
| | - Aya Okuda
- Insititute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Asashironishi-2, Osaka 590-0484, Japan
| | - Ken Morishima
- Insititute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Asashironishi-2, Osaka 590-0484, Japan
| | - Rintaro Inoue
- Insititute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Asashironishi-2, Osaka 590-0484, Japan
| | - Masaaki Sugiyama
- Insititute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Asashironishi-2, Osaka 590-0484, Japan
| |
Collapse
|
7
|
Sugiyama M, Chau HW, Abe T, Kato Y, Jamei E, Veeroja P, Mori K, Sugiyama T. Third Places for Older Adults' Social Engagement: A Scoping Review and Research Agenda. Gerontologist 2023; 63:1149-1161. [PMID: 36512515 DOI: 10.1093/geront/gnac180] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Indexed: 08/25/2023] Open
Abstract
BACKGROUND AND OBJECTIVES Neighborhood places that facilitate older residents to meet and interact (third places) receive an increasing research interest as studies have consistently shown the benefits of social engagement for older adults' health. This scoping review synthesized the findings of studies examining the role of third places in older adults' social engagement. RESEARCH DESIGN AND METHODS Searching 5 databases (CINAHL, Medline, PsycInfo, Scopus, and Web of Science) in October 2021, this study identified quantitative and qualitative studies that examined the relationships between third places and social engagement (interaction and network) among older adults. RESULTS A total of 32 studies (12 quantitative and 20 qualitative studies) met the eligibility criteria. These studies examined 4 types of third place, namely, community facilities, local businesses, open/green spaces, and transition spaces. More than two thirds of the studies reviewed found that access to community facilities, local businesses, and open/green spaces were related to older adults' social interaction. For the relationships between third places and social networks, the importance of accessible local businesses and the quality of open/green spaces was supported by fewer studies. DISCUSSION AND IMPLICATIONS The findings of quantitative and qualitative studies suggest that local places that are convenient to visit and comfortable to stay in for older adults are likely to enhance their social interaction and network. However, more specific evidence is needed to inform the planning and design of third places. The review discusses future research topics that address the gaps identified in the current literature.
Collapse
Affiliation(s)
- Masaaki Sugiyama
- Graduate School of Human Life Science, Osaka Metropolitan University, Osaka, Japan
| | - Hing-Wah Chau
- Institute for Sustainable Industries and Liveable Cities, Victoria University, Melbourne, Australia
| | - Takumi Abe
- Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
- Centre for Urban Transitions, Swinburne University of Technology, Melbourne, Australia
| | - Yusuke Kato
- College of Human Life and Environment, Kinjo Gakuin University, Nagoya, Japan
| | - Elmira Jamei
- Institute for Sustainable Industries and Liveable Cities, Victoria University, Melbourne, Australia
| | - Piret Veeroja
- Centre for Urban Transitions, Swinburne University of Technology, Melbourne, Australia
| | - Kazuhiko Mori
- Graduate School of Human Life Science, Osaka Metropolitan University, Osaka, Japan
| | - Takemi Sugiyama
- Centre for Urban Transitions, Swinburne University of Technology, Melbourne, Australia
- Baker Heart and Diabetes Institute, Melbourne, Australia
| |
Collapse
|
8
|
Morishima K, Inoue R, Sugiyama M. Derivation of the small-angle scattering profile of a target biomacromolecule from a profile deteriorated by aggregates. AUC-SAS. J Appl Crystallogr 2023; 56:624-632. [PMID: 37284265 PMCID: PMC10241049 DOI: 10.1107/s1600576723002406] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 03/12/2023] [Indexed: 06/08/2023] Open
Abstract
Aggregates cause a fatal problem in the structural analysis of a biomacro-mol-ecule in solution using small-angle X-ray or neutron scattering (SAS): they deteriorate the scattering profile of the target molecule and lead to an incorrect structure. Recently, an integrated method of analytical ultracentrifugation (AUC) and SAS, abbreviated AUC-SAS, was developed as a new approach to overcome this problem. However, the original version of AUC-SAS does not offer a correct scattering profile of the target molecule when the weight fraction of aggregates is higher than ca 10%. In this study, the obstacle point in the original AUC-SAS approach is identified. The improved AUC-SAS method is then applicable to a solution with a relatively larger weight fraction of aggregates (≤20%).
Collapse
Affiliation(s)
- Ken Morishima
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| |
Collapse
|
9
|
Okuda A, Shimizu M, Inoue R, Urade R, Sugiyama M. Efficient Multiple Domain Ligation for Proteins Using Asparaginyl Endopeptidase by Selection of Appropriate Ligation Sites Based on Steric Hindrance. Angew Chem Int Ed Engl 2023; 62:e202214412. [PMID: 36347766 DOI: 10.1002/anie.202214412] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Indexed: 11/10/2022]
Abstract
Three domain fragments of a multi-domain protein, ER-60, were ligated in two short linker regions using asparaginyl endopeptidase not involving denaturation. To identify appropriate ligation sites, by selecting several potential ligation sites with fewer mutations around two short linker regions, their ligation efficiencies and the functions of the ligated ER-60s were examined experimentally. To evaluate the dependence of ligation efficiencies on the ligation sites computationally, steric hinderances around the sites for the ligation were calculated through molecular dynamics simulations. Utilizing the steric hindrance, a site-dependent ligation potential index was introduced as reproducing the experimental ligation efficiency. Referring to this index, the reconstruction of ER-60 was succeeded by the ligation of the three domains for the first time. In addition, the new ligation potential index well-worked for application to other domain ligations. Therefore, the index may serve as a more time-effective tool for multi-site ligations.
Collapse
Affiliation(s)
- Aya Okuda
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - Masahiro Shimizu
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - Reiko Urade
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| |
Collapse
|
10
|
Yamamoto N, Inoue R, Makino Y, Sekiguchi H, Shibayama N, Naito A, Sugiyama M, Chatani E. Tracking the Structural Development of Amyloid Precursors in the Insulin B Chain and the Inhibition Effect by Fibrinogen. J Phys Chem B 2022; 126:10797-10812. [PMID: 36534755 DOI: 10.1021/acs.jpcb.2c05136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Amyloid fibrils are abnormal protein aggregates associated with several amyloidoses and neurodegenerative diseases. Prefibrillar intermediates, which emerge before amyloid fibril formation, play an important role in structure formation. Therefore, to prevent fibril formation, the mechanisms underpinning the structural development of prefibrillar intermediates must be elucidated. An insulin-derived peptide, the insulin B chain, is known for its stable accumulation of prefibrillar intermediates. In this study, the structural development of B chain prefibrillar intermediates and their inhibition by fibrinogen (Fg) were monitored by transmission electron microscopy (TEM) and small-angle X-ray scattering (SAXS) combined with solid-state nuclear magnetic resonance spectroscopy (NMR) and size exclusion chromatography. TEM images obtained in a time-lapse manner demonstrated that prefibrillar intermediates were wavy rod-like structures emerging from initial non-rod-like aggregates, and their bundling was responsible for protofilament formation. Time-resolved SAXS revealed that the prefibrillar intermediates became thicker and longer as a function of time. Solid-state NMR measurement suggested a β-sheet formation around Ala14 residue was crucial for the structural conversion from prefibrillar intermediates to amyloid fibril. These observations suggested that prefibrillar intermediates serve as reaction fields for amyloid nucleation and its structural propagation. Time-resolved SAXS also demonstrated that Fg prevented elongation of the prefibrillar intermediates by forming specific complexes together, which implied that regulation of the length of prefibrillar intermediates upon Fg binding was the factor suppressing the prefibrillar intermediate elongation. The fibril formation mechanism and the inhibition strategy found in this study will be helpful in seeking appropriate methods against amyloid-related diseases.
Collapse
Affiliation(s)
- Naoki Yamamoto
- Division of Biophysics, Physiology, School of Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi329-0498, Japan
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2 Asashiro-Nishi, Kumatori, Sennan-gun, Osaka590-0494, Japan
| | - Yoshiteru Makino
- Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hotogaya-ku, Yokohama240-8501, Japan
| | - Hiroshi Sekiguchi
- Japan Synchrotron Radiation Research Institute, 1-1-1, Koto, Sayo-cho, Sayo-gun, Hyogo679-5148, Japan
| | - Naoya Shibayama
- Division of Biophysics, Physiology, School of Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi329-0498, Japan
| | - Akira Naito
- Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hotogaya-ku, Yokohama240-8501, Japan
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2 Asashiro-Nishi, Kumatori, Sennan-gun, Osaka590-0494, Japan
| | - Eri Chatani
- Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe657-8501, Japan
| |
Collapse
|
11
|
Okuda A, Shimizu M, Inoue R, Urade R, Sugiyama M. Efficient Multiple Domain Ligation for Proteins using Asparaginyl Endopeptidase by Selection of Appropriate Ligation Sites Based on Steric Hindrance. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202214412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Aya Okuda
- Kyoto University: Kyoto Daigaku Institute for Integrated Radiation and Nuclear Science JAPAN
| | - Masahiro Shimizu
- Kyoto University: Kyoto Daigaku Institute for Integrated Radiation and Nuclear Science JAPAN
| | - Rintaro Inoue
- Kyoto University: Kyoto Daigaku Institute for Integrated Radiation and Nuclear Science JAPAN
| | - Reiko Urade
- Kyoto University: Kyoto Daigaku Institute for Integrated Radiation and Nuclear Science JAPAN
| | - Masaaki Sugiyama
- Kyoto University: Kyoto Daigaku Institute for integrated Radiation and Nuclear Science 2-1010, asashiro-nishi,Kumatori 590-0494 Sennnan JAPAN
| |
Collapse
|
12
|
Yoshikawa Y, Yuzu K, Yamamoto N, Morishima K, Inoue R, Sugiyama M, Iwasaki T, So M, Goto Y, Tamura A, Chatani E. Pathway Dependence of the Formation and Development of Prefibrillar Aggregates in Insulin B Chain. Molecules 2022; 27:molecules27133964. [PMID: 35807211 PMCID: PMC9268647 DOI: 10.3390/molecules27133964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/18/2022] [Accepted: 06/19/2022] [Indexed: 11/16/2022] Open
Abstract
Amyloid fibrils have been an important subject as they are involved in the development of many amyloidoses and neurodegenerative diseases. The formation of amyloid fibrils is typically initiated by nucleation, whereas its exact mechanisms are largely unknown. With this situation, we have previously identified prefibrillar aggregates in the formation of insulin B chain amyloid fibrils, which have provided an insight into the mechanisms of protein assembly involved in nucleation. Here, we have investigated the formation of insulin B chain amyloid fibrils under different pH conditions to better understand amyloid nucleation mediated by prefibrillar aggregates. The B chain showed strong propensity to form amyloid fibrils over a wide pH range, and prefibrillar aggregates were formed under all examined conditions. In particular, different structures of amyloid fibrils were found at pH 5.2 and pH 8.7, making it possible to compare different pathways. Detailed investigations at pH 5.2 in comparison with those at pH 8.7 have suggested that the evolution of protofibril-like aggregates is a common mechanism. In addition, different processes of evolution of the prefibrillar aggregates have also been identified, suggesting that the nucleation processes diversify depending on the polymorphism of amyloid fibrils.
Collapse
Affiliation(s)
- Yuki Yoshikawa
- Graduate School of Science, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Hyogo, Japan; (Y.Y.); (K.Y.); (T.I.); (A.T.)
| | - Keisuke Yuzu
- Graduate School of Science, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Hyogo, Japan; (Y.Y.); (K.Y.); (T.I.); (A.T.)
| | - Naoki Yamamoto
- Division of Biophysics, Physiology, School of Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke 329-0498, Tochigi, Japan;
| | - Ken Morishima
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2 Asashiro-Nishi, Kumatori, Sennan-gun 590-0494, Osaka, Japan; (K.M.); (R.I.); (M.S.)
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2 Asashiro-Nishi, Kumatori, Sennan-gun 590-0494, Osaka, Japan; (K.M.); (R.I.); (M.S.)
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2 Asashiro-Nishi, Kumatori, Sennan-gun 590-0494, Osaka, Japan; (K.M.); (R.I.); (M.S.)
| | - Tetsushi Iwasaki
- Graduate School of Science, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Hyogo, Japan; (Y.Y.); (K.Y.); (T.I.); (A.T.)
- Biosignal Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Hyogo, Japan
| | - Masatomo So
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Osaka, Japan;
| | - Yuji Goto
- Global Center for Medical Engineering and Informatics, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Osaka, Japan;
| | - Atsuo Tamura
- Graduate School of Science, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Hyogo, Japan; (Y.Y.); (K.Y.); (T.I.); (A.T.)
| | - Eri Chatani
- Graduate School of Science, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Hyogo, Japan; (Y.Y.); (K.Y.); (T.I.); (A.T.)
- Correspondence:
| |
Collapse
|
13
|
Shimizu M, Okuda A, Morishima K, Inoue R, Sato N, Yunoki Y, Urade R, Sugiyama M. Extracting time series matching a small-angle X-ray scattering profile from trajectories of molecular dynamics simulations. Sci Rep 2022; 12:9970. [PMID: 35705644 PMCID: PMC9200744 DOI: 10.1038/s41598-022-13982-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 05/31/2022] [Indexed: 11/30/2022] Open
Abstract
Solving structural ensembles of flexible biomolecules is a challenging research area. Here, we propose a method to obtain possible structural ensembles of a biomolecule based on small-angle X-ray scattering (SAXS) and molecular dynamics simulations. Our idea is to clip a time series that matches a SAXS profile from a simulation trajectory. To examine its practicability, we applied our idea to a multi-domain protein ER-60 and successfully extracted time series longer than 1 micro second from trajectories of coarse-grained molecular dynamics simulations. In the extracted time series, the domain conformation was distributed continuously and smoothly in a conformational space. Preferred domain conformations were also observed. Diversity among scattering curves calculated from each ER-60 structure was interpreted to reflect an open-close motion of the protein. Although our approach did not provide a unique solution for the structural ensemble of the biomolecule, each extracted time series can be an element of the real behavior of ER-60. Considering its low computational cost, our approach will play a key role to identify biomolecular dynamics by integrating SAXS, simulations, and other experiments.
Collapse
Affiliation(s)
- Masahiro Shimizu
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan.
| | - Aya Okuda
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Ken Morishima
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Nobuhiro Sato
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Yasuhiro Yunoki
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Reiko Urade
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan.
| |
Collapse
|
14
|
Tominaga T, Nakagawa H, Sahara M, Oda T, Inoue R, Sugiyama M. Data Collection for Dilute Protein Solutions via a Neutron Backscattering Spectrometer. Life (Basel) 2022; 12:life12050675. [PMID: 35629343 PMCID: PMC9145923 DOI: 10.3390/life12050675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/12/2022] [Accepted: 04/29/2022] [Indexed: 11/16/2022] Open
Abstract
Understanding protein functions requires not only static but also dynamic structural information. Incoherent quasi-elastic neutron scattering (QENS), which utilizes the highly incoherent scattering ability of hydrogen, is a powerful technique for revealing the dynamics of proteins in deuterium oxide (D2O) buffer solutions. The background scattering of sample cells suitable for aqueous protein solution samples, conducted with a neutron backscattering spectrometer, was evaluated. It was found that the scattering intensity of an aluminum sample cell coated with boehmite using D2O was lower than that of a sample cell coated with regular water (H2O). The D2O-Boehmite coated cell was used for the QENS measurement of a 0.8 wt.% aqueous solution of an intrinsically disordered protein in an intrinsically disordered region of a helicase-associated endonuclease for a fork-structured type of DNA. The cell was inert against aqueous samples at 283–363 K. In addition, meticulous attention to cells with small individual weight differences and the positional reproducibility of the sample cell relative to the spectrometer neutron beam position enabled the accurate subtraction of the scattering profiles of the D2O buffer and the sample container. Consequently, high-quality information on protein dynamics could be extracted from dilute protein solutions.
Collapse
Affiliation(s)
- Taiki Tominaga
- Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society (CROSS), 162-1 Shirakata, Ibaraki 319-1106, Japan;
- Correspondence:
| | - Hiroshi Nakagawa
- Materials Sciences Research Center, Japan Atomic Energy Agency, Ibaraki 319-1195, Japan;
- J-PARC Center, Japan Atomic Energy Agency, Ibaraki 319-1195, Japan
| | - Masae Sahara
- Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society (CROSS), 162-1 Shirakata, Ibaraki 319-1106, Japan;
| | - Takashi Oda
- Department of Life Science, Rikkyo University, Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan;
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan; (R.I.); (M.S.)
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan; (R.I.); (M.S.)
| |
Collapse
|
15
|
Yunoki Y, Matsumoto A, Morishima K, Martel A, Porcar L, Sato N, Yogo R, Tominaga T, Inoue R, Yagi-Utsumi M, Okuda A, Shimizu M, Urade R, Terauchi K, Kono H, Yagi H, Kato K, Sugiyama M. Overall structure of fully assembled cyanobacterial KaiABC circadian clock complex by an integrated experimental-computational approach. Commun Biol 2022; 5:184. [PMID: 35273347 PMCID: PMC8913699 DOI: 10.1038/s42003-022-03143-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 02/08/2022] [Indexed: 12/24/2022] Open
Abstract
In the cyanobacterial circadian clock system, KaiA, KaiB and KaiC periodically assemble into a large complex. Here we determined the overall structure of their fully assembled complex by integrating experimental and computational approaches. Small-angle X-ray and inverse contrast matching small-angle neutron scatterings coupled with size-exclusion chromatography provided constraints to highlight the spatial arrangements of the N-terminal domains of KaiA, which were not resolved in the previous structural analyses. Computationally built 20 million structural models of the complex were screened out utilizing the constrains and then subjected to molecular dynamics simulations to examine their stabilities. The final model suggests that, despite large fluctuation of the KaiA N-terminal domains, their preferential positionings mask the hydrophobic surface of the KaiA C-terminal domains, hindering additional KaiA-KaiC interactions. Thus, our integrative approach provides a useful tool to resolve large complex structures harboring dynamically fluctuating domains. The revealed full KaiA12B6C6 complex is assembled including the dynamic and asynchronous KaiA N-terminal domains that have been missing in cryo-EM structures.
Collapse
Affiliation(s)
- Yasuhiro Yunoki
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, 444-8787, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuhoku, Nagoya, 467-8603, Japan.,Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Atsushi Matsumoto
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology (QST), Umemidai, Kizu, Kyoto, 619-0215, Japan
| | - Ken Morishima
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Anne Martel
- Institut Laue-Langevin, 71, avenue des martyrs, 38042, Grenoble, France
| | - Lionel Porcar
- Institut Laue-Langevin, 71, avenue des martyrs, 38042, Grenoble, France
| | - Nobuhiro Sato
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Rina Yogo
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, 444-8787, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuhoku, Nagoya, 467-8603, Japan.,Biomedical Research Centre, School of Biomedical Engineering, The University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Taiki Tominaga
- Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society (CROSS), Tokai, Ibaraki, 319-1106, Japan
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Maho Yagi-Utsumi
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, 444-8787, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuhoku, Nagoya, 467-8603, Japan
| | - Aya Okuda
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Masahiro Shimizu
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Reiko Urade
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Kazuki Terauchi
- Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga, 525-8577, Japan
| | - Hidetoshi Kono
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology (QST), Umemidai, Kizu, Kyoto, 619-0215, Japan.
| | - Hirokazu Yagi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuhoku, Nagoya, 467-8603, Japan.
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, 444-8787, Japan. .,Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuhoku, Nagoya, 467-8603, Japan.
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka, 590-0494, Japan.
| |
Collapse
|
16
|
Sugiyama T, Carver A, Sugiyama M, Lorenzon A, Davison TE. Views of Greenery and Psychological Well-Being in Residential Aged Care Facilities: Longitudinal Associations. HERD 2021; 15:219-232. [PMID: 34809476 DOI: 10.1177/19375867211059757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVES This study examined associations of objectively measured views of greenery in residential aged care facilities (RACFs) with changes in multiple psychological well-being measures among residents who were newly admitted to RACFs. METHODS Data were collected from 52 residents (mean age: 84, 73% women) of 13 RACFs, located in Melbourne, Australia. The outcomes were changes in depression, stress, anxiety, and quality of life (QoL) between baseline and 8-week follow-up. The exposure measures were the amount and presence of greenery visible from participant's bedroom and common areas (lounge, dining). Greenery was categorized as being either within or beyond the RACF perimeter. RESULTS Regression analyses found that greenery visible from participant's bedroom was not associated with any outcomes. The amount of greenery visible from common areas within the RACF perimeter was adversely related to stress, unexpectedly: Each additional 1 m2 of greenery was associated with a greater increase in stress (b = 0.05; 95% CI [0.07, 0.94]). However, greenery visible from common areas beyond the perimeter contributed favorably to stress and QoL. The presence of such greenery was associated with a lower increase in stress (b = -3.99; 95% CI [-7.75, -0.23]; reference: no greenery), and a 1 m2 increment was associated with a greater increase in QoL (b = 0.07; 95% CI [0.02, 0.11]). CONCLUSION Views of greenery outside of the RACF from lounge and dining areas may be protective against residents' stress increase and improve their QoL. Locating residents in areas with such outdoor views may prevent their psychological condition from worsening.
Collapse
Affiliation(s)
- Takemi Sugiyama
- Centre for Urban Transitions, Swinburne University of Technology, Melbourne, Australia.,Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, Australia.,Baker Heart and Diabetes Institute, Melbourne, Australia
| | - Alison Carver
- Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, Australia
| | - Masaaki Sugiyama
- Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, Australia.,Graduate School of Human Life Science, Osaka City University, Japan
| | - Alanna Lorenzon
- Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, Australia
| | - Tanya E Davison
- Health and Ageing Research Group, Swinburne University of Technology, Melbourne, Australia
| |
Collapse
|
17
|
Nakagawa H, Saio T, Nagao M, Inoue R, Sugiyama M, Ajito S, Tominaga T, Kawakita Y. Conformational dynamics of a multidomain protein by neutron scattering and computational analysis. Biophys J 2021; 120:3341-3354. [PMID: 34242590 PMCID: PMC8391080 DOI: 10.1016/j.bpj.2021.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 06/07/2021] [Accepted: 07/01/2021] [Indexed: 11/25/2022] Open
Abstract
The flexible conformations of a multidomain protein are responsible for its biological functions. Although MurD, a 47-kDa protein that consists of three domains, sequentially changes its domain conformation from an open form to a closed form through a semiclosed form in its enzymatic reaction, the domain dynamics in each conformation remains unclear. In this study, we verify the conformational dynamics of MurD in the corresponding three states (apo and ATP- and inhibitor-bound states) with a combination of small-angle x-ray and neutron scattering (SAXS and SANS), dynamic light scattering (DLS), neutron backscattering (NBS), neutron spin echo (NSE) spectroscopy, and molecular dynamics (MD) simulations. Applying principal component analysis of the MD trajectories, twisting and open-closed domain modes are identified as the major collective coordinates. The deviations of the experimental SAXS profiles from the theoretical calculations based on the known crystal structures become smaller in the ATP-bound state than in the apo state, and a further decrease is evident upon inhibitor binding. These results suggest that domain motions of the protein are suppressed step by step of each ligand binding. The DLS and NBS data yield collective and self-translational diffusion constants, respectively, and we used them to extract collective domain motions in nanometer and nanosecond scales from the NSE data. In the apo state, MurD shows both twisting and open-closed domain modes, whereas an ATP binding suppresses twisting domain motions, and a further reduction of open-closed mode is seen in the inhibitor-binding state. These observations are consistent with the structure modifications measured by the small-angle scattering as well as the MD simulations. Such changes in the domain dynamics associated with the sequential enzymatic reactions should be related to the affinity and reaction efficiency with a ligand that binds specifically to each reaction state.
Collapse
Affiliation(s)
- Hiroshi Nakagawa
- Materials Sciences Research Center, Japan Atomic Energy Agency, Tokai, Ibaraki, Japan; 2 J-PARC Center, Japan Atomic Energy Agency, Tokai, Ibaraki, Japan.
| | - Tomohide Saio
- Division of Molecular Life Science, Institute of Advanced Medical Sciences, Tokushima University, Tokushima, Japan
| | - Michihiro Nagao
- NIST Centre for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland; Department of Materials Science and Engineering, University of Maryland, College Park, Maryland; Department of Physics and Astronomy, University of Delaware, Newark, Delaware
| | - Rintaro Inoue
- Institute for Integrative Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, Japan
| | - Masaaki Sugiyama
- Institute for Integrative Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, Japan
| | - Satoshi Ajito
- Materials Sciences Research Center, Japan Atomic Energy Agency, Tokai, Ibaraki, Japan
| | - Taiki Tominaga
- Neutron Science and Technology Center, CROSS, Tokai, Ibaraki, Japan
| | | |
Collapse
|
18
|
Shimizu M, Okuda A, Morishima K, Sato N, Inoue R, Urade R, Sugiyama M. Dynamics of multi-domain protein ER-60 revealed by small-angle X-ray scattering data and molecular dynamics simulations. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321089169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
19
|
Sato N, Yogo R, Yanaka S, Martel A, Porcar L, Morishima K, Inoue R, Tominaga T, Arimori T, Takagi J, Sugiyama M, Kato K. Structural analysis of antibody complexes by inverse contrast-matching small-angle neutron scattering combined with size-exclusion chromatography (SEC-iCM-SANS). Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321085305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
20
|
Inoue R, Sakamaki Y, Takata T, Morishima K, Wood K, Sato N, Okuda A, Shimizu M, Urade R, Fujii N, Sugiyama M. Subunit dynamics in alpha-crystallin through deuteration-assisted small-angle neutron scattering. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321089170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
|
21
|
Okuda A, Inoue R, Morishima K, Yunoki Y, Shimizu M, Sato N, Urade R, Sugiyama M. Establishment of basic techniques related to protein sample preparation for neutron scattering. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321089182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
22
|
Morishima K, Inoue R, Shimizu M, Okuda A, Sato N, Urade R, Sugiyama M. AUC–SAS: integrated analysis of biomacromolecular structure with analytical ultracentrifugation (AUC) and small-angle scattering (SAS). Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321089194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
23
|
Sugiyama T, Sugiyama M, Mavoa S, Barnett A, Kamruzzaman M, Turrell G. Neighborhood environmental attributes and walking mobility decline: A longitudinal ecological study of mid-to-older aged Australian adults. PLoS One 2021; 16:e0252017. [PMID: 34081707 PMCID: PMC8174704 DOI: 10.1371/journal.pone.0252017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 05/09/2021] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVES Cross-sectional studies have found some built environmental attributes to be associated with residents' lower levels of mobility (functional capacity to walk outside the home). However, less is known about what environmental attributes are related to mobility decline. This longitudinal study examined area-level associations of specific environmental attributes with mid-to-older aged adults' changes in walking mobility. METHODS Data collected from 4,088 adults (aged 46-71 years at baseline) who participated in a cohort study in Brisbane, Australia were used. The outcome was the change in self-reported mobility score (SF-36) from 2013 to 2016, which were aggregated at the neighborhood (N = 156) and suburb (N = 99) levels, due to the known lack of sensitivity in SF-36 subscales to individual changes. Linear regression analysis examined associations of mobility change with seven environmental attributes measured at baseline (residential density, intersection density, land use mix, density of walking/bike paths, park density, bus stop density, density of social incivilities), adjusting for confounding variables. RESULTS Participants on average reported 4% of mobility decline during the 3-year study period. It was found that greater land use diversity was consistently associated with less decline in walking mobility, while greater density of social incivilities was associated with more decline in walking mobility. The latter finding was significant only at the neighborhood level. No consistent associations were observed for residential density, intersection density, density of walking/bike paths, park density, and bus stop density. DISCUSSION Our findings suggest that mid-to-older aged adults who live in areas with lower land use diversity and more social incivilities may be at risk of developing mobility limitations. Recommended policies to slow residents' mobility decline and to achieve aging in place include improving these environmental attributes where needed and advising older adults to relocate to safer, mixed-use neighborhoods.
Collapse
Affiliation(s)
- Takemi Sugiyama
- Centre for Urban Transitions, Swinburne University of Technology, Hawthorn, VIC, Australia
- Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, VIC, Australia
- Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- * E-mail:
| | - Masaaki Sugiyama
- Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, VIC, Australia
- Graduate School of Human Life Science, Osaka City University, Osaka, Japan
| | - Suzanne Mavoa
- Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, VIC, Australia
- Melbourne School of Population & Global Health, University of Melbourne, Melbourne, VIC, Australia
| | - Anthony Barnett
- Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, VIC, Australia
| | - Md. Kamruzzaman
- Monash Urban Planning and Design, Monash University, Caulfield East, VIC, Australia
| | - Gavin Turrell
- Centre for Research and Action in Public Health, Health Research Institute, University of Canberra, ACT, Australia
| |
Collapse
|
24
|
Okuda A, Inoue R, Morishima K, Saio T, Yunoki Y, Yagi-Utsumi M, Yagi H, Shimizu M, Sato N, Urade R, Kato K, Sugiyama M. Deuteration Aiming for Neutron Scattering. Biophys Physicobiol 2021; 18:16-27. [PMID: 33954079 PMCID: PMC8049778 DOI: 10.2142/biophysico.bppb-v18.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/03/2021] [Indexed: 01/17/2023] Open
Abstract
The distinguished feature of neutron as a scattering probe is an isotope effect, especially the large difference in neutron scattering length between hydrogen and deuterium. The difference renders the different visibility between hydrogenated and deuterated proteins. Therefore, the combination of deuterated protein and neutron scattering enables the selective visualization of a target domain in the complex or a target protein in the multi-component system. Despite of this fascinating character, there exist several problems for the general use of this method: difficulty and high cost for protein deuteration, and control and determination of deuteration ratio of the sample. To resolve them, the protocol of protein deuteration techniques is presented in this report. It is strongly expected that this protocol will offer more opportunity for conducting the neutron scattering studies with deuterated proteins.
Collapse
Affiliation(s)
- Aya Okuda
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Sennan-gun, Osaka 590-0494 Japan
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Sennan-gun, Osaka 590-0494 Japan
| | - Ken Morishima
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Sennan-gun, Osaka 590-0494 Japan
| | - Tomohide Saio
- Institute of Advanced Medical Sciences, Tokushima University, Tokushima 770-8503, Japan
| | - Yasuhiro Yunoki
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi 467-8603, Japan
| | - Maho Yagi-Utsumi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi 467-8603, Japan.,Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan.,Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Hirokazu Yagi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi 467-8603, Japan
| | - Masahiro Shimizu
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Sennan-gun, Osaka 590-0494 Japan
| | - Nobuhiro Sato
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Sennan-gun, Osaka 590-0494 Japan
| | - Reiko Urade
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Sennan-gun, Osaka 590-0494 Japan
| | - Koichi Kato
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi 467-8603, Japan.,Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan.,Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Sennan-gun, Osaka 590-0494 Japan
| |
Collapse
|
25
|
Suto H, Kamei K, Kato H, Misawa T, Unno M, Nitta H, Satoi S, Kawabata Y, Ohtsuka M, Rikiyama T, Sudo T, Matsumoto I, Hirao T, Okano K, Suzuki Y, Sata N, Isaji S, Sugiyama M, Takeyama Y. Diabetic control and nutritional status up to 1 year after total pancreatectomy: a nationwide multicentre prospective study. Br J Surg 2021; 108:e237-e238. [PMID: 33821972 DOI: 10.1093/bjs/znab097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 01/20/2021] [Accepted: 02/18/2021] [Indexed: 01/09/2023]
Affiliation(s)
- H Suto
- Department of Gastroenterological Surgery, Kagawa University, Kagawa, Japan
| | - K Kamei
- Department of Surgery, Kindai University, Osaka, Japan
| | - H Kato
- Department of Hepatobiliary Pancreatic and Transplant Surgery, Mie University Graduate School of Medicine, Mie, Japan
| | - T Misawa
- Department of Surgery, The Jikei University Kashiwa Hospital, Chiba, Japan
| | - M Unno
- Department of Surgery, Tohoku University, Miyagi, Japan
| | - H Nitta
- Department of Surgery, Iwate Medical University, Iwate, Japan
| | - S Satoi
- Department of Surgery, Kansai Medical University, Osaka, Japan
| | - Y Kawabata
- Department of Digestive and General Surgery, Faculty of Medicine, Shimane University, Shimane, Japan
| | - M Ohtsuka
- Department of General Surgery, Chiba University, Chiba, Japan
| | - T Rikiyama
- Department of Surgery, Saitama Medical Centre, Jichi Medical University, Saitama, Japan
| | - T Sudo
- Department of Surgery, Kure Medical Centre and Chugoku Cancer Centre, Hiroshima, Japan
| | - I Matsumoto
- Department of Surgery, Kindai University, Osaka, Japan
| | - T Hirao
- Department of Public Health, Kagawa University, Kagawa, Japan
| | - K Okano
- Department of Gastroenterological Surgery, Kagawa University, Kagawa, Japan
| | - Y Suzuki
- Department of Gastroenterological Surgery, Kagawa University, Kagawa, Japan
| | - N Sata
- Department of Surgery, Jichi Medical University, Tochigi, Japan
| | - S Isaji
- Director of Mie University Hospital, Mie, Japan
| | - M Sugiyama
- Director of Tokyo Rosai Hospital, Tokyo, Japan
| | - Y Takeyama
- Department of Surgery, Kindai University, Osaka, Japan
| |
Collapse
|
26
|
Sato N, Yogo R, Yanaka S, Martel A, Porcar L, Morishima K, Inoue R, Tominaga T, Arimori T, Takagi J, Sugiyama M, Kato K. A feasibility study of inverse contrast-matching small-angle neutron scattering method combined with size exclusion chromatography using antibody interactions as model systems. J Biochem 2021; 169:701-708. [PMID: 33585933 DOI: 10.1093/jb/mvab012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 01/24/2021] [Indexed: 01/06/2023] Open
Abstract
Small-angle neutron scattering (SANS) and small- angle X-ray scattering (SAXS) are powerful techniques for the structural characterization of biomolecular complexes. In particular, SANS enables a selective observation of specific components in complexes by selective deuteration with contrast-matching techniques. In most cases, however, biomolecular interaction systems with heterogeneous oligomers often contain unfavorable aggregates and unbound species, hampering data interpretation. To overcome these problems, SAXS has been recently combined with size exclusion chromatography (SEC), which enables the isolation of the target complex in a multi-component system. By contrast, SEC-SANS is only at a preliminary stage. Hence, we herein perform a feasibility study of this method based on our newly developed inverse contrast-matching (iCM) SANS technique using antibody interactions as model systems. Immunoglobulin G (IgG) or its Fc fragment was mixed with 75% deuterated Fc-binding proteins, i.e. a mutated form of IgG-degrading enzyme of Streptococcus pyogenes and a soluble form of Fcγ receptor IIIb, and subjected to SEC-SANS as well as SEC-SAXS as reference. We successfully observe SANS from the non-deuterated IgG or Fc formed in complex with these binding partners, which were unobservable in terms of SANS in D2O, hence demonstrating the potential utility of the SEC-iCM-SANS approach.
Collapse
Affiliation(s)
- Nobuhiro Sato
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashiro-nishi, Kumatori, Osaka 590-0494, Japan
| | - Rina Yogo
- Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan.,Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Saeko Yanaka
- Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan.,Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Anne Martel
- Institut Laue-Langevin, 71 avenue des Martyrs, 38042, Grenoble, France
| | - Lionel Porcar
- Institut Laue-Langevin, 71 avenue des Martyrs, 38042, Grenoble, France
| | - Ken Morishima
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashiro-nishi, Kumatori, Osaka 590-0494, Japan
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashiro-nishi, Kumatori, Osaka 590-0494, Japan
| | - Taiki Tominaga
- Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society (CROSS), Tokai, Ibaraki 319-1106, Japan
| | - Takao Arimori
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Junichi Takagi
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashiro-nishi, Kumatori, Osaka 590-0494, Japan
| | - Koichi Kato
- Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan.,Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| |
Collapse
|
27
|
Inoue R, Sakamaki Y, Takata T, Wood K, Morishima K, Sato N, Okuda A, Shimizu M, Urade R, Fujii N, Sugiyama M. Elucidation of the mechanism of subunit exchange in αB crystallin oligomers. Sci Rep 2021; 11:2555. [PMID: 33510404 PMCID: PMC7843597 DOI: 10.1038/s41598-021-82250-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 01/18/2021] [Indexed: 11/15/2022] Open
Abstract
AlphaB crystallin (αB-crystallin) is a key protein for maintaining the long-term transparency of the eye lens. In the eye lens, αB-crystallin is a "dynamical" oligomer regulated by subunit exchange between the oligomers. To elucidate the unsettled mechanism of subunit exchange in αB-crystallin oligomers, the study was carried out at two different protein concentrations, 28.5 mg/mL (dense sample) and 0.45 mg/mL (dilute sample), through inverse contrast matching small-angle neutron scattering. Interestingly, the exchange rate of the dense sample was the same as that of the dilute sample. From analytical ultracentrifuge measurements, the coexistence of small molecular weight components and oligomers was detected, regardless of the protein concentration. The model proposed that subunit exchange could proceed through the assistance of monomers and other small oligomers; the key mechanism is attaching/detaching monomers and other small oligomers to/from oligomers. Moreover, this model successfully reproduced the experimental results for both dense and dilute solutions. It is concluded that the monomer and other small oligomers attaching/detaching mainly regulates the subunit exchange in αB-crystallin oligomer.
Collapse
Affiliation(s)
- Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan.
| | - Yusuke Sakamaki
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Takumi Takata
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Kathleen Wood
- Australian Nuclear Science and Technology Organization, Lucas Heights, NSW, Australia
| | - Ken Morishima
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Nobuhiro Sato
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Aya Okuda
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Masahiro Shimizu
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Reiko Urade
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Noriko Fujii
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan.
| |
Collapse
|
28
|
Okuda A, Matsusaki M, Masuda T, Morishima K, Sato N, Inoue R, Sugiyama M, Urade R. A novel soybean protein disulphide isomerase family protein possesses dithiol oxidation activity: identification and characterization of GmPDIL6. J Biochem 2020; 168:393-405. [PMID: 32458972 DOI: 10.1093/jb/mvaa058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 05/02/2020] [Indexed: 01/04/2023] Open
Abstract
Secretory and membrane proteins synthesized in the endoplasmic reticulum (ER) are folded with intramolecular disulphide bonds, viz. oxidative folding, catalysed by the protein disulphide isomerase (PDI) family proteins. Here, we identified a novel soybean PDI family protein, GmPDIL6. GmPDIL6 has a single thioredoxin-domain with a putative N-terminal signal peptide and an active centre (CKHC). Recombinant GmPDIL6 forms various oligomers binding iron. Oligomers with or without iron binding and monomers exhibited a dithiol oxidase activity level comparable to those of other soybean PDI family proteins. However, they displayed no disulphide reductase and extremely low oxidative refolding activity. Interestingly, GmPDIL6 was mainly expressed in the cotyledon during synthesis of seed storage proteins and GmPDIL6 mRNA was up-regulated under ER stress. GmPDIL6 may play a role in the formation of disulphide bonds in nascent proteins for oxidative folding in the ER.
Collapse
Affiliation(s)
- Aya Okuda
- Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Motonori Matsusaki
- Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Taro Masuda
- Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Ken Morishima
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - Nobuhiro Sato
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - Reiko Urade
- Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| |
Collapse
|
29
|
Fujita M, Kusumoto S, Sugiyama M, Fujisawa T, Mizokami M, Hata A. Cost-effectiveness analysis for preventing hepatitis B virus reactivation-related death in Japan. Eur J Public Health 2020. [DOI: 10.1093/eurpub/ckaa166.566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
There is no worldwide standard recommendation for preventing hepatitis B virus (HBV) reactivation for patients with resolved infection treated with an anti-CD20 antibody for B-cell non-Hodgkin lymphoma. This study aims to compare the cost-effectiveness between two commonly used strategies to prevent HBV reactivation-related death.
Methods
The two strategies compared were prophylactic antiviral therapy (Pro NAT) and HBV DNA monitoring followed by on-demand antiviral therapy (HBV DNA monitoring) using entecavir (Entecavir, a generic drug for Baraclude). Effectiveness was defined as the prevention of death due to HBV reactivation and costs were calculated under the health insurance system of Japan as of April 2018 using Markov model. A cost-minimization analysis, one of the cost-effectiveness analyses, was applied, since the effectiveness was the same between the two strategies according to a meta-analysis. To consider the effect of uncertainty for each parameter, probabilistic sensitivity analysis (PSA) was performed. In the scenario analysis, costs were calculated using lamivudine (Zefix) or tenofovir alafenamide (Vemlidy) instead of entecavir. All analyses were done using TreeAge Pro 2019 (TreeAge Software, Inc., MA, USA).
Results
Estimated costs per patient during the 30 months after initiation of chemotherapy for lymphoma were 1,513 USD with Pro NAT and 1,265 USD with HBV DNA monitoring. A PSA revealed that HBV DNA monitoring was more consistently cost-effective compared with Pro NAT when some parameters were set randomly according to probability distributions. In our scenario analysis, costs of Pro NAT and HBV DNA monitoring were calculated as 2,762 and 1,401 USD using lamivudine, 4,857 and 1,629 USD using tenofovir alafenamide.
Conclusions
Our cost-effectiveness analysis shows that an HBV DNA monitoring strategy using entecavir should be recommended for preventing HBV reactivation-related death in Japan.
Key messages
Cost-effectiveness analysis demonstrated that HBV DNA monitoring was more cost-effective compared to Pro NAT; this result was consistent with PSA. HBV DNA monitoring strategy should be recommended to prevent HBV reactivation-related death for the patients with resolved HBV infection in Japan.
Collapse
Affiliation(s)
- M Fujita
- Department of Health Research, Chiba Foundation for Health Promotion and Disease Prevention, Chiba, Japan
- Genome Medical Sciences Project, National Center for Global Health and Medicine, Chiba, Japan
| | - S Kusumoto
- Department of Hematology and Oncology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - M Sugiyama
- Genome Medical Sciences Project, National Center for Global Health and Medicine, Chiba, Japan
| | - T Fujisawa
- Department of Health Research, Chiba Foundation for Health Promotion and Disease Prevention, Chiba, Japan
| | - M Mizokami
- Genome Medical Sciences Project, National Center for Global Health and Medicine, Chiba, Japan
| | - A Hata
- Department of Health Research, Chiba Foundation for Health Promotion and Disease Prevention, Chiba, Japan
| |
Collapse
|
30
|
Hajek M, Sugiyama M, Kolb G, Tucker DM, Pinak M. CHARACTERISATION OF RADIOPHOTOLUMINESCENCE DOSIMETRY SYSTEM FOR INDIVIDUAL MONITORING. Radiat Prot Dosimetry 2020; 190:66-70. [PMID: 32542374 DOI: 10.1093/rpd/ncaa077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/05/2020] [Accepted: 05/13/2020] [Indexed: 06/11/2023]
Abstract
Performance evaluation is typically assessed as part of the approval procedure to verify that a dosimetry system fulfils specified national or international type-test requirements under representative exposure conditions that are expected to mimic workplace fields from the radiological activities being monitored. The International Atomic Energy Agency Radiation Safety Technical Services Laboratory has recently implemented an integrated radiophotoluminescence (RPL) personal dosimetry system developed by Chiyoda Technol Corporation. This paper reports on the successful verification of dosimetric performance properties of the RPL dosimetry system to IEC 62387:2020, in which the badges were exposed to a range of radiation energies and angles of incidence as well as other influence parameters. Characteristics under test included the coefficient of variation, non-linearity of response due to dose dependence as well as the energy and angular response to photon and beta radiation.
Collapse
Affiliation(s)
- M Hajek
- Division of Radiation, Transport and Waste Safety, International Atomic Energy Agency, Vienna International Centre, PO Box 100, 1400 Vienna, Austria
| | - M Sugiyama
- Division of Radiation, Transport and Waste Safety, International Atomic Energy Agency, Vienna International Centre, PO Box 100, 1400 Vienna, Austria
- Oarai Research Center, Chiyoda Technol Corporation, 3681 Narita-cho, Oarai-machi, Higashi-Ibaraki-gun, Ibaraki-ken 311-1313, Japan
| | - G Kolb
- Division of Radiation, Transport and Waste Safety, International Atomic Energy Agency, Vienna International Centre, PO Box 100, 1400 Vienna, Austria
| | - D M Tucker
- Division of Radiation, Transport and Waste Safety, International Atomic Energy Agency, Vienna International Centre, PO Box 100, 1400 Vienna, Austria
| | - M Pinak
- Division of Radiation, Transport and Waste Safety, International Atomic Energy Agency, Vienna International Centre, PO Box 100, 1400 Vienna, Austria
| |
Collapse
|
31
|
Oba Y, Motokawa R, Hino M, Adachi N, Todaka Y, Inoue R, Sugiyama M. Nanostructural Characterization of Oleyl Acid Phosphate in Poly-α-olefin Using Small-angle X-ray Scattering. CHEM LETT 2020. [DOI: 10.1246/cl.200204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yojiro Oba
- Materials Sciences Research Center, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai, Ibaraki 319-1195, Japan
| | - Ryuhei Motokawa
- Materials Sciences Research Center, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai, Ibaraki 319-1195, Japan
| | - Masahiro Hino
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2 Asashiro-Nishi, Kumatori, Osaka 590-0494, Japan
| | - Nozomu Adachi
- Department of Mechanical Engineering, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - Yoshikazu Todaka
- Department of Mechanical Engineering, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2 Asashiro-Nishi, Kumatori, Osaka 590-0494, Japan
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2 Asashiro-Nishi, Kumatori, Osaka 590-0494, Japan
| |
Collapse
|
32
|
Fujii N, Takata T, Kim I, Morishima K, Inoue R, Magami K, Matsubara T, Sugiyama M, Koide T. Asp isomerization increases aggregation of α-crystallin and decreases its chaperone activity in human lens of various ages. Biochim Biophys Acta Proteins Proteom 2020; 1868:140446. [PMID: 32442520 DOI: 10.1016/j.bbapap.2020.140446] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 05/12/2020] [Accepted: 05/14/2020] [Indexed: 10/24/2022]
Abstract
α-Crystallin, comprising 40-50 subunits of αA- and αB-subunits, is a long-lived major soluble chaperone protein in lens. During aging, α-crystallin forms aggregates of high molecular weight (HMW) protein and eventually becomes water-insoluble (WI). Isomerization of Asp in α-crystallin has been proposed as a trigger of protein aggregation, ultimately leading to cataract formation. Here, we have investigated the relationship between protein aggregation and Asp isomerization of αA-crystallin by a series of analyses of the soluble α-crystallin, HMW and WI fractions from human lens samples of different ages (10-76 years). Analytical ultracentrifugation showed that the HMW fraction had a peak sedimentation coefficient of 40 S and a wide distribution of values (10-450 S) for lens of all ages, whereas the α-crystallin had a much smaller peak sedimentation coefficient (10-20 S) and was less heterogeneous, regardless of lens age. Measurement of the ratio of isomers (Lα-, Lβ-, Dα-, Dβ-) at Asp58, Asp91/92 and Asp151 in αA-crystallin by liquid chromatography-mass spectrometry showed that the proportion of isomers at all three sites increased in order of aggregation level (α-crystallin < HMW < WI fractions). Among the abnormal isomers of Asp58 and Asp151, Dβ-isomers were predominant with a very few exceptions. Notably, the chaperone activity of HMW protein was minimal for lens of all ages, whereas that of α-crystallin decreased with increasing lens age. Thus, abnormal aggregation caused by Asp isomerization might contribute to the loss of chaperone activity of α-crystallin in aged human lens.
Collapse
Affiliation(s)
- Noriko Fujii
- Institute for Integrated Radiation and Nuclear Science, Kyoto University Kumatori-cho, Sennan-gun, Osaka 590-0494, Japan.
| | - Takumi Takata
- Institute for Integrated Radiation and Nuclear Science, Kyoto University Kumatori-cho, Sennan-gun, Osaka 590-0494, Japan
| | - Ingu Kim
- Institute for Integrated Radiation and Nuclear Science, Kyoto University Kumatori-cho, Sennan-gun, Osaka 590-0494, Japan
| | - Ken Morishima
- Institute for Integrated Radiation and Nuclear Science, Kyoto University Kumatori-cho, Sennan-gun, Osaka 590-0494, Japan
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University Kumatori-cho, Sennan-gun, Osaka 590-0494, Japan
| | - Kousuke Magami
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | | | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University Kumatori-cho, Sennan-gun, Osaka 590-0494, Japan
| | - Tamaki Koide
- Rexxam Co., Ltd., Nishi-ku, Nagoya, Aichi 541-0054, Japan
| |
Collapse
|
33
|
Khan FS, Sugiyama M, Fujii K, Tver'yanovich YS, Nakano Y. Electrochemical reduction of CO 2 using Germanium-Sulfide-Indium amorphous glass structures. Heliyon 2020; 6:e03513. [PMID: 32346624 PMCID: PMC7182728 DOI: 10.1016/j.heliyon.2020.e03513] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 08/20/2019] [Accepted: 02/26/2020] [Indexed: 11/25/2022] Open
Abstract
The research in electrochemical reduction of CO2 is shifting towards the discovery of new and novel materials. This study shows a new class of material, that of Ge-S-In chalcogenide glass, to be active for reduction of CO2 in aqueous solutions. Experiments were conducted with bulk and particle form of the material, yielding different product for each structural form. Faradaic efficiency of upto 15% was observed in bulk form for CO production while formic acid with up to 26.1 % faradaic efficiency was measured in powder form. Chalcogenide studies have focused primarily on the photoelectrochemical reduction however these results provide a strong merit for introducing metal in chalcogenide glass structures for electrochemical reduction of CO2. The activity for CO2 reduction and the change in product selectivity reflects that further efforts to improve the glass structures can be undertaken in order to increase the faradaic efficiency and selectivity of the products.
Collapse
Affiliation(s)
- F S Khan
- Department of Advanced Interdisciplinary Studies, School of Engineering, University of Tokyo, Japan
| | - M Sugiyama
- Department of Advanced Interdisciplinary Studies, School of Engineering, University of Tokyo, Japan
| | - K Fujii
- RIKEN Center for Advanced Photonics, Wako, Japan
| | | | - Y Nakano
- Department of Electrical Engineering, School of Engineering, University of Tokyo, Japan
| |
Collapse
|
34
|
Nishi H, Hosomi N, Ohta K, Aoki S, Nakamori M, Nezu T, Shigeishi H, Shintani T, Obayashi T, Ishikawa K, Kinoshita N, Shiga Y, Sugiyama M, Ohge H, Maruyama H, Kawaguchi H, Kurihara H. Serum immunoglobulin G antibody titer to Fusobacterium nucleatum is associated with unfavorable outcome after stroke. Clin Exp Immunol 2020; 200:302-309. [PMID: 32155293 DOI: 10.1111/cei.13430] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 03/05/2020] [Accepted: 03/05/2020] [Indexed: 12/21/2022] Open
Abstract
Stroke can be a cause of death, while in non-fatal cases it is a common cause of various disabilities resulting from associated brain damage. However, whether a specific periodontal pathogen is associated with increased risk of unfavorable outcome after stroke remains unknown. We examined risk factors for unfavorable outcome following stroke occurrence, including serum antibody titers to periodontal pathogens. The enrolled cohort included 534 patients who had experienced an acute stroke, who were divided into favorable (n = 337) and unfavorable (n = 197) outcome groups according to modified ranking scale (mRS) score determined at 3 months after onset (favorable = score 0 or 1; unfavorable = score 2-6). The associations of risk factors with unfavorable outcome, including serum titers of IgG antibodies to 16 periodontal pathogens, were examined. Logistic regression analysis showed that the initial National Institutes of Health stroke scale score [odds ratio (OR) = 1·24, 95% confidence interval (CI) = 1·18-1·31, P < 0·001] and C-reactive protein (OR = 1·29, 95% CI = 1·10-1·51, P = 0·002) were independently associated with unfavorable outcome after stroke. Following adjustment with those, detection of the antibody for Fusobacterium nucleatum ATCC 10953 in serum remained an independent predictor of unfavorable outcome (OR = 3·12, 95% CI = 1·55-6·29, P = 0·002). Determination of the antibody titer to F. nucleatum ATCC 10953 in serum may be useful as a predictor of unfavorable outcome after stroke.
Collapse
Affiliation(s)
- H Nishi
- Department of General Dentistry, Hiroshima University Hospital, Hiroshima, Japan
| | - N Hosomi
- Department of Neurology, Chikamori Hospital, Kochi, Japan.,Department of Disease Model, Research Institute of Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - K Ohta
- Department of Public Oral Health, Program of Oral Health Sciences, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - S Aoki
- Department of Clinical Neuroscience and Therapeutics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - M Nakamori
- Department of Neurology, Suiseikai Kajikawa Hospital, Hiroshima, Japan
| | - T Nezu
- Department of Clinical Neuroscience and Therapeutics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - H Shigeishi
- Department of Public Oral Health, Program of Oral Health Sciences, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - T Shintani
- Center of Oral Examination, Hiroshima University Hospital, Hiroshima, Japan
| | - T Obayashi
- Department of General Dentistry, Hiroshima University Hospital, Hiroshima, Japan
| | - K Ishikawa
- Department of Clinical Neuroscience and Therapeutics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.,Department of Neurology, Suiseikai Kajikawa Hospital, Hiroshima, Japan
| | - N Kinoshita
- Department of Clinical Neuroscience and Therapeutics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Y Shiga
- Department of Clinical Neuroscience and Therapeutics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - M Sugiyama
- Department of Public Oral Health, Program of Oral Health Sciences, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - H Ohge
- Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima, Japan
| | - H Maruyama
- Department of Clinical Neuroscience and Therapeutics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - H Kawaguchi
- Department of General Dentistry, Hiroshima University Hospital, Hiroshima, Japan
| | - H Kurihara
- Department of Periodontal Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| |
Collapse
|
35
|
Matsumoto A, Sugiyama M, Li Z, Martel A, Porcar L, Inoue R, Kato D, Osakabe A, Kurumizaka H, Kono H. Structural Studies of Overlapping Dinucleosomes in Solution. Biophys J 2019; 118:2209-2219. [PMID: 31952809 PMCID: PMC7202943 DOI: 10.1016/j.bpj.2019.12.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/17/2019] [Accepted: 12/10/2019] [Indexed: 10/27/2022] Open
Abstract
An overlapping dinucleosome (OLDN) is a structure composed of one hexasome and one octasome and appears to be formed through nucleosome collision promoted by nucleosome remodeling factor(s). In this study, the solution structure of the OLDN was investigated through the integration of small-angle x-ray and neutron scattering (SAXS and SANS, respectively), computer modeling, and molecular dynamics simulations. Starting from the crystal structure, we generated a conformational ensemble based on normal mode analysis and searched for the conformations that reproduced the SAXS and SANS scattering curves well. We found that inclusion of histone tails, which are not observed in the crystal structure, greatly improved model quality. The obtained structural models suggest that OLDNs adopt a variety of conformations stabilized by histone tails situated at the interface between the hexasome and octasome, simultaneously binding to both the hexasomal and octasomal DNA. In addition, our models define a possible direction for the conformational changes or dynamics, which may provide important information that furthers our understanding of the role of chromatin dynamics in gene regulation.
Collapse
Affiliation(s)
- Atsushi Matsumoto
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, Kizugawa, Japan
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Japan.
| | - Zhenhai Li
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, Kizugawa, Japan
| | | | | | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Japan
| | - Daiki Kato
- Graduate School of Advanced Science & Engineering, Waseda University, Tokyo, Japan
| | - Akihisa Osakabe
- Graduate School of Advanced Science & Engineering, Waseda University, Tokyo, Japan
| | - Hitoshi Kurumizaka
- Graduate School of Advanced Science & Engineering, Waseda University, Tokyo, Japan; Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.
| | - Hidetoshi Kono
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, Kizugawa, Japan.
| |
Collapse
|
36
|
Iddamalgoda A, Hayashi S, Goto E, Sugiyama M, Oguri K. Current Asian trends in egg production and consumption: a demand analysis of selected countries. WORLD POULTRY SCI J 2019. [DOI: 10.1079/wps20010005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - S. Hayashi
- Faculty of Agriculture, Gifu University, 1–1 Yanagido
| | | | - M. Sugiyama
- Gifu City Women's College, Gifu University, Gifu, Japan
| | - K. Oguri
- Faculty of Regional Studies, Gifu University, Gifu, Japan
| |
Collapse
|
37
|
Hirai M, Ajito S, Sugiyama M, Iwase H, Takata SI, Shimizu N, Igarashi N, Martel A, Porcar L. Direct Evidence for the Effect of Glycerol on Protein Hydration and Thermal Structural Transition. Biophys J 2019; 115:313-327. [PMID: 30021107 DOI: 10.1016/j.bpj.2018.06.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 05/30/2018] [Accepted: 06/04/2018] [Indexed: 01/07/2023] Open
Abstract
The mechanisms of protein stabilization by uncharged solutes, such as polyols and sugars, have been intensively studied with respect to the chemical thermodynamics of molecular crowding. In particular, many experimental and theoretical studies have been conducted to explain the mechanism of the protective action on protein structures by glycerol through the relationship between hydration and glycerol solvation on protein surfaces. We used wide-angle x-ray scattering (WAXS), small-angle neutron scattering, and theoretical scattering function simulation to quantitatively characterize the hydration and/or solvation shell of myoglobin in aqueous solutions of up to 75% v/v glycerol. At glycerol concentrations below ∼40% v/v, the preservation of the hydration shell was dominant, which was reasonably explained by the preferential exclusion of glycerol from the protein surface (preferential hydration). In contrast, at concentrations above 50% v/v, the partial penetration or replacement of glycerol into or with hydration-shell water (neutral solvation by glycerol) was gradually promoted. WAXS results quantitatively demonstrated the neutral solvation, in which the replacement of hydrated water by glycerol was proportional to the volume fraction of glycerol in the solvent multiplied by an exchange rate (β ≤ 1). These phenomena were confirmed by small-angle neutron scattering measurements. The observed WAXS data covered the entire hierarchical structure of myoglobin, ranging from tertiary to secondary structures. We separately analyzed the effect of glycerol on the thermal stability of myoglobin at each hierarchical structural level. The thermal transition midpoint temperature at each hierarchical structural level was raised depending on the glycerol concentration, with enhanced transition cooperativeness between different hierarchical structural levels. The onset temperature of the helix-to-cross β-sheet transition (the initial process of amyloid formation) was evidently elevated. However, oligomerization connected to fibril formation was suppressed, even at a low glycerol concentration.
Collapse
Affiliation(s)
- Mitsuhiro Hirai
- Graduate School of Science and Technology, Gunma University, Maebashi, Gunma, Japan.
| | - Satoshi Ajito
- Graduate School of Science and Technology, Gunma University, Maebashi, Gunma, Japan
| | - Masaaki Sugiyama
- Kyoto University Research Reactor Institute, Kumatori, Osaka, Japan
| | - Hiroki Iwase
- Comprehensive Research Organization for Science and Society, Tokai, Japan
| | | | - Nobutaka Shimizu
- Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba, Ibaraki, Japan
| | - Noriyuki Igarashi
- Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba, Ibaraki, Japan
| | | | | |
Collapse
|
38
|
Inoue R, Nakagawa T, Morishima K, Sato N, Okuda A, Urade R, Yogo R, Yanaka S, Yagi-Utsumi M, Kato K, Omoto K, Ito K, Sugiyama M. Newly developed Laboratory-based Size exclusion chromatography Small-angle x-ray scattering System (La-SSS). Sci Rep 2019; 9:12610. [PMID: 31471544 PMCID: PMC6717197 DOI: 10.1038/s41598-019-48911-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 08/15/2019] [Indexed: 02/07/2023] Open
Abstract
To understand a biological system, it is important to observe structures of biomolecules in the solution where the system is functionalized. Small-Angle X-ray Scattering coupled with Size Exclusion Chromatography (SEC-SAXS) is one of techniques to selectively observe the target molecules in the multi-component system. However, this technique is believed to be available only with a synchrotron-based SAXS instrument due to requirement of high beam intensity and, therefore, the limitation of the beam time was obstacle to satisfy demands from many bio-researchers. We newly developed Laboratory-based Size exclusion chromatography SAXS System (La-SSS) by utilizing a latest laboratory-based SAXS instrument and finely optimization of the balance between flow rate, cell volume, irradiation time and so on. La-SSS succeeded not only decoupling of target protein(s) from non-specific aggregates but also measurement of each concerned component in a multi-component system. In addition, an option: "stopping mode", which is designed for improving statistics of SAXS profile, realized a high S/N data acquisition for the most interesting protein in a multi-component system. Furthermore, by utilizing a column having small bed volume, the small-scale SEC-SAXS study makes available. Through optimization of instrumental parameters and environments, La-SSS is highly applicable for experimental requirements from various biological samples. It is strongly expected that a La-SSS concept must be a normal option for laboratory-based SAXS in the near future.
Collapse
Affiliation(s)
- Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan.
| | - Tatsuo Nakagawa
- Unisoku Co. Ltd., 3-4-2 Kasugano, Hirakata City, Osaka, 573-0131, Japan
| | - Ken Morishima
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Nobuhiro Sato
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Aya Okuda
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Reiko Urade
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Rina Yogo
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi, 467-8603, Japan
| | - Saeko Yanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi, 467-8603, Japan
| | - Maho Yagi-Utsumi
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi, 467-8603, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi, 467-8603, Japan
| | - Kazuki Omoto
- Rigaku Corp. 12-9-3 Matsubara, Akishima City, Tokyo, 196-8666, Japan
| | - Kazuki Ito
- Rigaku Corp. 12-9-3 Matsubara, Akishima City, Tokyo, 196-8666, Japan
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan.
| |
Collapse
|
39
|
Sugiyama M, Fukaya T, Moon JY, Ishida K, Matsushita A, Kim SY, Yeo SH. Analysis and enhancement of the ethanol resistance of Pichia kudriavzevii N77-4, a strain newly isolated from the Korean traditional fermentation starter Nuruk, for improved fermentation performance. ACTA ACUST UNITED AC 2019. [DOI: 10.1088/1742-6596/1282/1/012062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
40
|
Yanaka S, Yogo R, Inoue R, Sugiyama M, Itoh SG, Okumura H, Miyanoiri Y, Yagi H, Satoh T, Yamaguchi T, Kato K. Dynamic Views of the Fc Region of Immunoglobulin G Provided by Experimental and Computational Observations. Antibodies (Basel) 2019; 8:antib8030039. [PMID: 31544845 PMCID: PMC6784063 DOI: 10.3390/antib8030039] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 06/08/2019] [Accepted: 06/12/2019] [Indexed: 01/08/2023] Open
Abstract
The Fc portion of immunoglobulin G (IgG) is a horseshoe-shaped homodimer, which interacts with various effector proteins, including Fcγ receptors (FcγRs). These interactions are critically dependent on the pair of N-glycans packed between the two CH2 domains. Fucosylation of these N-glycans negatively affects human IgG1-FcγRIIIa interaction. The IgG1-Fc crystal structures mostly exhibit asymmetric quaternary conformations with divergent orientations of CH2 with respect to CH3. We aimed to provide dynamic views of IgG1-Fc by performing long-timescale molecular dynamics (MD) simulations, which were experimentally validated by small-angle X-ray scattering and nuclear magnetic resonance spectroscopy. Our simulation results indicated that the dynamic conformational ensembles of Fc encompass most of the previously reported crystal structures determined in both free and complex forms, although the major Fc conformers in solution exhibited almost symmetric, stouter quaternary structures, unlike the crystal structures. Furthermore, the MD simulations suggested that the N-glycans restrict the motional freedom of CH2 and endow quaternary-structure plasticity through multiple intramolecular interaction networks. Moreover, the fucosylation of these N-glycans restricts the conformational freedom of the proximal tyrosine residue of functional importance, thereby precluding its interaction with FcγRIIIa. The dynamic views of Fc will provide opportunities to control the IgG interactions for developing therapeutic antibodies.
Collapse
Affiliation(s)
- Saeko Yanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
- Department of Functional Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8787, Japan
| | - Rina Yogo
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashiro-Nishi, Kumatori, Osaka 590-0494, Japan
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashiro-Nishi, Kumatori, Osaka 590-0494, Japan
| | - Satoru G Itoh
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Department of Structural Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Hisashi Okumura
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Department of Structural Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Yohei Miyanoiri
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hirokazu Yagi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Tadashi Satoh
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Takumi Yamaguchi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi 923-1292, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan.
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan.
- Department of Functional Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8787, Japan.
| |
Collapse
|
41
|
Yamamoto N, Akai T, Inoue R, Sugiyama M, Tamura A, Chatani E. Structural Insights into the Inhibition of Amyloid Fibril Formation by Fibrinogen via Interaction with Prefibrillar Intermediates. Biochemistry 2019; 58:2769-2781. [DOI: 10.1021/acs.biochem.9b00439] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Naoki Yamamoto
- Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Taiki Akai
- Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2, Asashiro-Nishi, Kumatori-cho, Sennan-gun, Osaka 590-0494, Japan
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2, Asashiro-Nishi, Kumatori-cho, Sennan-gun, Osaka 590-0494, Japan
| | - Atsuo Tamura
- Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Eri Chatani
- Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| |
Collapse
|
42
|
Fukasawa H, Hashimoto H, Hiramoto K, Sugiyama M, Taniguchi K, Yoshioka K. Morphological characterization of small hepatocytes after bile duct ligation in chicken. Poult Sci 2019; 98:717-721. [DOI: 10.3382/ps/pey455] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 09/05/2018] [Indexed: 01/01/2023] Open
|
43
|
Fujita M, Sugiyama M, Sato Y, Nagashima K, Takahashi S, Mizokami M, Hata A. Hepatitis B virus reactivation in patients with rheumatoid arthritis: Analysis of the National Database of Japan. J Viral Hepat 2018; 25:1312-1320. [PMID: 29770539 DOI: 10.1111/jvh.12933] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/03/2018] [Indexed: 02/06/2023]
Abstract
This study aimed to determine the incidence and risk factors for hepatitis B virus (HBV) reactivation in patients with rheumatoid arthritis (RA) undergoing immunosuppressive therapy. The National Database of Japan, in which insurance claim data have been comprehensively accumulated, was utilized. The subjects were 76 641 RA patients who were plausibly initiated on immunosuppressive therapy from April 2013 to March 2014. Laboratory tests of the hepatitis B surface antigen, anti-hepatitis B virus surface antibody, and anti-hepatitis B virus core antibody were performed in 28.23%, 12.52% and 14.63% of patients, respectively, when the therapy was initiated. We found that HBV reactivation and fulminant hepatitis occurred in both the patients with and without HBV DNA monitoring, indicating insufficient monitoring in Japan during the study. The cumulative incidence of HBV reactivation over 24 months was 1.57% (95% confidence interval [CI] = 1.28%-1.92%) in the monitoring group, which consisted of those with resolved HBV infection. Glucocorticoid administration was a potent risk factor for HBV reactivation (hazard ratio [HR] = 1.70, 95% CI = 1.26-2.29, P = .001 in all subjects, and HR = 1.82, 95% CI = 1.18-2.81, P = .007 in the nonmonitoring group), although it was not statistically significant in the monitoring group (HR = 1.49, 95% CI = 0.99-2.26 and P = .057). No significant risk difference was observed between single administration of methotrexate and biological drugs.
Collapse
Affiliation(s)
- M Fujita
- Department of Public Health, Chiba University Graduate School of Medicine, Chiba City, Japan
| | - M Sugiyama
- Genome Medical Sciences Project, National Center for Global Health and Medicine, Ichikawa City, Japan
| | - Y Sato
- Department of Global Clinical Research, Chiba University Graduate School of Medicine, Chiba City, Japan
| | - K Nagashima
- Department of Global Clinical Research, Chiba University Graduate School of Medicine, Chiba City, Japan
| | - S Takahashi
- Clinical Research Center, Chiba University Hospital, Chiba City, Japan
| | - M Mizokami
- Genome Medical Sciences Project, National Center for Global Health and Medicine, Ichikawa City, Japan
| | - A Hata
- Department of Public Health, Chiba University Graduate School of Medicine, Chiba City, Japan
| |
Collapse
|
44
|
Murayama H, Sugiyama M, Inagaki H, Ura C, Miyamae F, Edahiro A, Okamura T, Awata S. SOCIOECONOMIC DISADVANTAGE IN EARLY LIFE PREDICTS POOR PHYSICAL PERFORMANCE IN LATE LIFE AMONG OLDER JAPANESE. Innov Aging 2018. [DOI: 10.1093/geroni/igy023.2471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- H Murayama
- Institute of Gerontology, The University of Tokyo
| | - M Sugiyama
- Tokyo Metropolitan Institute of Gerontology
| | - H Inagaki
- Tokyo Metropolitan Institute of Gerontology
| | - C Ura
- Tokyo Metropolitan Institute of Gerontology
| | - F Miyamae
- Tokyo Metropolitan Institute of Gerontology
| | - A Edahiro
- Tokyo Metropolitan Institute of Gerontology
| | - T Okamura
- Tokyo Metropolitan Institute of Gerontology
| | - S Awata
- Tokyo Metropolitan Institute of Gerontology
| |
Collapse
|
45
|
Hoshino K, Sugiyama M, Date T, Maruwaka S, Arakaki S, Shibata D, Maeshiro T, Hokama A, Sakugawa H, Kanto T, Fujita J, Mizokami M. Phylogenetic and phylodynamic analyses of hepatitis C virus subtype 1a in Okinawa, Japan. J Viral Hepat 2018; 25:976-985. [PMID: 29577516 DOI: 10.1111/jvh.12898] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 02/02/2018] [Indexed: 12/28/2022]
Abstract
Okinawa Island, located in Southern Japan, has a higher prevalence rate of hepatitis C virus subtype 1a (HCV-1a) infection than that in mainland Japan. Okinawa has a history of US military occupation after World War II. To elucidate the transmission history of HCV-1a in Okinawa, 26 whole-genome sequences were obtained from 29 patients during 2011-2016. Phylogenetic trees were reconstructed to identify the origin and characteristics of HCV-1a in Okinawa with epidemiological information. A phylogenetic tree based on whole-genome sequencing revealed that all of the samples were located below the US branches. Additionally, we identified one cluster comprised of 17 strains (Okinawa, n = 16; United States, n = 1). The majority of the patients in this cluster were people who inject drugs (PWID), indicating the presence of a people who inject drugs (PWID) cluster. Subsequently, Bayesian analyses were employed to reveal viral population dynamics. Intriguingly, a phylodynamic analysis uncovered a substantial increase in effective population size of HCV-1a from 1965 to 1980 and a slight increase in mid-2000, which were associated with an increase in illicit drug use in Okinawa. The estimated divergence time of the PWID cluster was 1967.6 (1964.2-1971.1). These findings suggest that HCV-1a was introduced into Okinawa from the United States in the late 1960s, coincident with the Vietnam War. Subsequently, HCV-1a might have spread among the Japanese population with the spread of injecting drug use. Our study provides an understanding of HCV transmission dynamics in Okinawa, as well as the key role of PWID in HCV transmission.
Collapse
Affiliation(s)
- K Hoshino
- Genome Medical Science Project, National Center for Global Health and Medicine, Chiba, Japan.,Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - M Sugiyama
- Genome Medical Science Project, National Center for Global Health and Medicine, Chiba, Japan
| | - T Date
- Genome Medical Science Project, National Center for Global Health and Medicine, Chiba, Japan
| | - S Maruwaka
- Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - S Arakaki
- Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - D Shibata
- Digestive Division, Heart Life Hospital, Okinawa, Japan
| | - T Maeshiro
- Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - A Hokama
- Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - H Sakugawa
- Digestive Division, Heart Life Hospital, Okinawa, Japan
| | - T Kanto
- Department of Liver Diseases, National Center for Global Health and Medicine, Chiba, Japan
| | - J Fujita
- Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - M Mizokami
- Genome Medical Science Project, National Center for Global Health and Medicine, Chiba, Japan
| |
Collapse
|
46
|
Kino T, Ishigami T, Doi H, Chen L, Nakashima R, Sugiyama M, Arakawa K, Minegishi S, Sugano T, Ishikawa T, Tamura K. P6262A novel optimal medical therapy for preventing secondary cardiovascular events in subjects with coronary artery diseases in Japan. Eur Heart J 2018. [DOI: 10.1093/eurheartj/ehy566.p6262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- T Kino
- Yokohama City University, Graduate school of Medicine Department of Medical Science and Cardio-Renal Medicine., Yokohama, Japan
| | - T Ishigami
- Yokohama City University, Graduate school of Medicine Department of Medical Science and Cardio-Renal Medicine., Yokohama, Japan
| | - H Doi
- Yokohama City University, Graduate school of Medicine Department of Medical Science and Cardio-Renal Medicine., Yokohama, Japan
| | - L Chen
- Yokohama City University, Graduate school of Medicine Department of Medical Science and Cardio-Renal Medicine., Yokohama, Japan
| | - R Nakashima
- Yokohama City University, Graduate school of Medicine Department of Medical Science and Cardio-Renal Medicine., Yokohama, Japan
| | - M Sugiyama
- Yokohama City University, Graduate school of Medicine Department of Medical Science and Cardio-Renal Medicine., Yokohama, Japan
| | - K Arakawa
- Yokohama City University, Graduate school of Medicine Department of Medical Science and Cardio-Renal Medicine., Yokohama, Japan
| | - S Minegishi
- Kanagawa Cardiovascular and Respiratory Center, Department of Cardiology, Yokohama, Japan
| | - T Sugano
- Yokohama City University, Graduate school of Medicine Department of Medical Science and Cardio-Renal Medicine., Yokohama, Japan
| | - T Ishikawa
- Yokohama City University, Graduate school of Medicine Department of Medical Science and Cardio-Renal Medicine., Yokohama, Japan
| | - K Tamura
- Yokohama City University, Graduate school of Medicine Department of Medical Science and Cardio-Renal Medicine., Yokohama, Japan
| |
Collapse
|
47
|
Hirai M, Ajito S, Sugiyama M, Iwase H, Takata SI, Shimizu N, Igarashi N, Martel A, Porcar L. Direct Evidence for the Effect of Glycerol on Protein Hydration and Thermal Structural Transition. Biophys J 2018; 115:748. [PMID: 30077335 DOI: 10.1016/j.bpj.2018.07.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
|
48
|
Chatake T, Yanagisawa Y, Inoue R, Sugiyama M, Matsuo T, Fujiwara S, Ohsugi T, Sumi H. Purification and structural characterization of water‐soluble menaquinone‐7 produced by
Bacillus subtilis natto. J Food Biochem 2018. [DOI: 10.1111/jfbc.12630] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
| | | | - Rintaro Inoue
- Research Reactor Institute, Kyoto University Osaka Japan
| | | | - Tatsuhito Matsuo
- Quantum Beam Science Research DirectorateNational Institutes for Quantum and Radiological Science and Technology Tokai Japan
| | - Satoru Fujiwara
- Quantum Beam Science Research DirectorateNational Institutes for Quantum and Radiological Science and Technology Tokai Japan
| | - Tadanori Ohsugi
- Department of Life ScienceKurashiki University of Science and the Arts Kurashiki Japan
| | - Hiroyuki Sumi
- Department of Life ScienceKurashiki University of Science and the Arts Kurashiki Japan
| |
Collapse
|
49
|
Kawahara T, Hanzawa N, Sugiyama M. Effect of Lactobacillus strains on thymus and chemokine expression in keratinocytes and development of atopic dermatitis-like symptoms. Benef Microbes 2018; 9:643-652. [PMID: 29798706 DOI: 10.3920/bm2017.0162] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Lactobacillus strains, a major group of lactic acid bacteria, are representative food microorganisms that have many potential beneficial effects via their interactions with immune and intestinal epithelial cells. However, little is known about the effect of Lactobacillus strains on atopic dermatitis via keratinocytes, which comprise the physical barrier of the skin. In this study, we report that Lactobacillus strains have a significant suppressive effect on tumour necrosis factor (TNF)-α-induced expression and production of thymus and activation-regulated chemokine (TARC), a T helper 2 cell chemokine responsible for atopic dermatitis, in human keratinocytes. An RNA interference study showed that the effect of Lactobacillus reuteri strain Japan Collection of Microorganisms (JCM) 1112, the most suppressive strain, depended on the presence of Toll-like receptor 2 and the induction of A20 (also known as TNF-α-induced protein 3) and cylindromatosis in HaCaT cells. Topical application of a water-soluble extract of homogenised JCM 1112 cells significantly suppressed the development of house dust mite-induced atopic skin lesions and TARC expression at the lesion sites in NC/Nga mice. Our study provides new insights into the use of Lactobacillus strains as suppressive agents against keratinocyte-involved atopic inflammation of the skin.
Collapse
Affiliation(s)
- T Kawahara
- 1 Faculty of Agriculture, Shinshu University, 8304 Minamiminowa, Kamiina, Nagano 399-4598, Japan.,2 Department of Interdisciplinary Genome Sciences and Cell Metabolism, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research (IBS-ICCER) Shinshu University, 8304 Minamiminowa, Kamiina, Nagano 399-4598, Japan
| | - N Hanzawa
- 1 Faculty of Agriculture, Shinshu University, 8304 Minamiminowa, Kamiina, Nagano 399-4598, Japan
| | - M Sugiyama
- 1 Faculty of Agriculture, Shinshu University, 8304 Minamiminowa, Kamiina, Nagano 399-4598, Japan
| |
Collapse
|
50
|
Saeki A, Sugiyama M, Hasebe A, Suzuki T, Shibata K. Activation of NLRP3 inflammasome in macrophages by mycoplasmal lipoproteins and lipopeptides. Mol Oral Microbiol 2018; 33:300-311. [PMID: 29682880 DOI: 10.1111/omi.12225] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2018] [Indexed: 12/29/2022]
Abstract
The NLRP3 inflammasome, an intracellular sensor consisting of the nucleotide-binding oligomerization domain-like receptor family, pyrin domain containing 3 (NLRP3), the adaptor protein apoptosis-associated speck-like protein containing a caspase-recruitment domain (ASC), and procaspase-1, plays critical roles in host defense against microbial pathogens by inducing production of interleukin-1β (IL-1β) and IL-18. Mycoplasma salivarium and Mycoplasma pneumoniae cells activated murine bone marrow-derived macrophages (BMMs) to induce production of IL-1α, IL-1β, and IL-18. The IL-1β production-inducing activities of these mycoplasmas toward BMMs from Toll-like receptor 2 (TLR2)-deficient mice were significantly attenuated compared with those from C57BL/6 mice (B6BMMs). This result suggests the possibility that their lipoproteins as TLR2 agonists are involved in the activity. Lipoproteins of M. salivarium and M. pneumoniae (MsLP and MpLP), and the M. salivarium-derived lipopeptide FSL-1 induced IL-1β production by B6BMMs, but not by BMMs from caspase-1-, NLRP3- or ASC-deficient mice. The activities of MsLP and MpLP were not downregulated by the proteinase K treatment, suggesting that the active sites are their N-terminal lipopeptide moieties. B6BMMs internalized the mycoplasmal N-terminal lipopeptide FSL-1 at least 30 min after incubation, FSL-1-containing endosomes started to fuse with the lysosomes around 2 hours, and then FSL-1 translocated into the cytosol from LAMP-1+ endosomes. The artificial delivery of FSL-1 into the cytosol of B6BMMs drastically enhanced the IL-1β production-inducing activity. FSL-1 as well as the representative NLRP3 inflammasome activator nigericin induced the NLRP3/ASC speck, but FSL-1 located in a compartment different from the NLRP3/ASC speck.
Collapse
Affiliation(s)
- A Saeki
- Department of Oral Molecular Microbiology, Faculty of Dental Medicine and Graduate School of Dental Medicine, Hokkaido University, Sapporo, Japan
| | - M Sugiyama
- Department of Oral Molecular Microbiology, Faculty of Dental Medicine and Graduate School of Dental Medicine, Hokkaido University, Sapporo, Japan
| | - A Hasebe
- Department of Oral Molecular Microbiology, Faculty of Dental Medicine and Graduate School of Dental Medicine, Hokkaido University, Sapporo, Japan
| | - T Suzuki
- Department of Bacterial Pathogenesis, Infection and Host Response Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - K Shibata
- Department of Oral Molecular Microbiology, Faculty of Dental Medicine and Graduate School of Dental Medicine, Hokkaido University, Sapporo, Japan
| |
Collapse
|