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新井 達也 (アライ タツヤ)
| 先端生命科学研究院 | 助教 |
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■ 学位■ URL
researchmap URLホームページURL■ ID 各種
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- 90890145
研究キーワード研究分野■ 担当教育組織
研究活動情報
■ 受賞- 2017年10月, 5th International Life-Science Symposium, Excellent Presentation Award for Oral Session
"X-ray Crystallography of Ice-Binding Protein from an Antarctic Ascomycete Suggests Ice-like Bound Waters Contribute to its Ligand Recognition"
Tatsuya Arai - 2017年05月, 第62回低温生物工学会大会, ベストプレゼンテーション賞
『子嚢菌由来不凍タンパク質の氷結晶結合メカニズムの解明』
新井 達也
- Machine Learning-Enabled Quantification of Fucosylated Human Milk Oligosaccharides in Human Breast Milk by Benchtop 1H NMR Spectroscopy
Zhiyan Hu; Jiaxi Jiang; Jun Abe; Thanawat Thumrongtaradol; Miho Akasaka; Yuki Ohnishi; Seiji Osada; Tatsuya Arai; Hiroyuki Kumeta; Yasuhiro Kumaki; Kazuo Yamauchi; Yu Shimizu; Yuki Yokoi; Kiminori Nakamura; Tokiyoshi Ayabe; Koshi Nakamura; Takashi Kimura; Akiko Tamakoshi; Tomoyasu Aizawa
Journal of Agricultural and Food Chemistry, 2026年08月05日
研究論文（学術雑誌） - Benchtop NMR-based lactose quantification in human milk: correction of oligosaccharide interference and comparison with high-field NMR
Jiaxi Jiang; Zhiyan Hu; Jun Abe; Thanawat Thumrongtaradol; Miho Akasaka; Yuki Ohnishi; Seiji Osada; Tatsuya Arai; Hiroyuki Kumeta; Yasuhiro Kumaki; Kazuo Yamauchi; Yu Shimizu; Yuki Yokoi; Kiminori Nakamura; Tokiyoshi Ayabe; Koshi Nakamura; Takashi Kimura; Akiko Tamakoshi; Tomoyasu Aizawa
Microchemical Journal, 226, 118371, 118371, Elsevier BV, 2026年07月, ［査読有り］
研究論文（学術雑誌） - Hyperactive ice‐binding proteins stabilize cell membranes and improve resistance to dehydration stress in Caenorhabditis elegans
Daiki Shimose; Kotaro Ozaki; Ryohei Kuriyama; Yuka Ikemoto; Kazuhiro Mio; Yuji C. Sasaki; Tatsuya Arai; Sakae Tsuda; Yoichi Shinkai; Masahiro Kuramochi
FEBS Open Bio, 2026年05月21日
英語, 研究論文（学術雑誌）,
Ice‐binding proteins (IBPs) are known to modulate ice growth and promote freezing tolerance and have recently attracted attention due to their cell‐protective functions under freezing or low‐temperature conditions. In this study, we demonstrate that IBP expression improves resistance to dehydration stress in
. After 30 min of drying, transgenic worms expressing a high‐activity fungal IBP (TisIBP8) showed a modest but significant increase in survival compared with wild‐type worms. Furthermore, imaging revealed reduced muscle‐cell damage in the TisIBP8‐expressing worms while synchrotron radiation infrared microspectroscopy showed membrane structural changes during dehydration were attenuated by TisIBP8 expression. These findings suggest that IBPs exert protective effects by stabilizing cell membranes independent of ice binding, therefore broadening the potential applications of IBPs for biological preservation under nonfreezing stress conditions.
- Direct observation of thermally induced fluctuation in lipid membranes using TEM-based gold nanoparticle tracking
Kazuhiro Mio; Takaaki Shiina; Tatsunari Ohkubo; Tatsuya Arai; Daisuke Sasaki; Yuji C. Sasaki
Exploration of BioMat-X, 2026年03月04日
研究論文（学術雑誌） - Sub-microsecond molecular motion analysis of polymer resins via transmitted X-ray blinking
Masahiro Kuramochi; Kentaro Hoshisashi; Shunya Shimomura; Daisuke Sasaki; Tatsuya Arai; Kazuhiro Mio; Hiroshi Sekiguchi; Kentaro Uesugi; Yoshio Suzuki; Shotaro Akaho; Yuji C. Sasaki
Optics Express, 33, 24, 51657, 51657, Optica Publishing Group, 2025年11月26日
研究論文（学術雑誌）, We developed transmitted X-ray blinking (TXB), a time-resolved transmission imaging technique with 900-nanosecond resolution for probing sub-microsecond molecular dynamics. TXB was applied to semi-crystalline polyetheretherketone (PEEK) and amorphous polyetherimide (PEI), two polymer resins with nearly identical X-ray absorption properties and indistinguishable static transmission images. Single-pixel autocorrelation analysis (spACF) of the TXB data revealed statistically significant differences in dynamic behavior between the two materials, consistent with results from diffracted X-ray blinking (DXB). Although conventional two-dimensional decay constant maps provided limited visual separation, further analysis using machine learning enabled clearer dynamic contrast and >90% classification accuracy. Spectral decomposition also identified periodic fluctuations in the 300–400 kHz range. These results demonstrate that TXB enables material differentiation based on intrinsic dynamic properties, even in the absence of static contrast, and offers new avenues for visualizing subtle motions in soft and biological systems. - Fluctuation of Time-Resolved X-ray Diffraction Reveals the Rotational Dynamics of Nanoparticles in Polymer Materials
Tatsuya Arai; Masahiro Kuramochi; Kazuhiro Mio; Hiroshi Sekiguchi; Sakae Tsuda; Daisuke Sasaki; Tomoyasu Aizawa; Yuji C. Sasaki
Nano Letters, 2025年09月24日
研究論文（学術雑誌） - Recombinant production of isotope-labeled human α-defensin 5 via calmodulin fusion and insights into its expression enhancement
Shaonan Yan; Hao Gu; Mitsuki Shibagaki; Jeremia Oktavian Chrisnanto; Fumi Hirai; Hiroyuki Kumeta; Yasuhiro Kumaki; Yuki Yokoi; Kiminori Nakamura; Takashi Kikukawa; Tokiyoshi Ayabe; Tatsuya Arai; Tomoyasu Aizawa
Peptides, 191, 171425, 171425, Elsevier BV, 2025年09月, ［査読有り］
研究論文（学術雑誌） - Amphibian-Derived Cathelicidin-DM and Cathelicidin-BG: Recombinant Overexpression in Escherichia coli and Comparison of Their Structures and Antimicrobial Activities
Chinonso Anthony Ezema; Mitsuki Shibagaki; Takashi Kikukawa; Tatsuya Arai; Tomoyasu Aizawa
ACS Omega, 10, 21, 21875, 21888, American Chemical Society (ACS), 2025年05月22日, ［査読有り］
研究論文（学術雑誌） - Real-Time Observation of Polymer Fluctuations During Phase Transition Using Transmission Electron Microscope
Takaaki Shiina; Tatsunari Ohkubo; Keegan McGehee; Rena Inamasu; Tatsuya Arai; Daisuke Sasaki; Yuji C. Sasaki; Kazuhiro Mio
Polymers, 2025年01月23日, ［査読有り］
研究論文（学術雑誌） - Micro-second time-resolved X-ray single-molecule internal motions of SARS-CoV-2 spike variants
Daisuke Sasaki; Tatsuya Arai; Yue Yang; Masahiro Kuramochi; Wakako Furuyama; Asuka Nanbo; Hiroshi Sekiguchi; Nobuhiro Morone; Kazuhiro Mio; Yuji C. Sasaki
Biochemistry and Biophysics Reports, 38, 101712, 101712, Elsevier BV, 2024年07月, ［査読有り］
研究論文（学術雑誌） - Simultaneous Recording of Remote Domain Dynamics in Membrane Proteins Using the Double-Labeled DXB/DXT Technique
Kazuhiro Mio; Tatsunari Ohkubo; Daisuke Sasaki; Mayui Sugiura; Kayoko Kawaguchi; Kazutaka Araki; Keizaburo Taninaka; Masaki Sakaguchi; Shunsuke Nozawa; Tatsuya Arai; Yuji C. Sasaki
Membranes, 14, 4, 75, 75, MDPI AG, 2024年03月27日, ［査読有り］
研究論文（学術雑誌）, Protein dynamics play important roles in biological functions, which accompany allosteric structure changes. Diffracted X-ray blinking (DXB) uses monochromatic X-rays and nanocrystal probes. The intramolecular motion of target proteins is analyzed from the intensity changes in detector signals at the diffraction rings. In contrast, diffracted X-ray tracking (DXT) elucidates molecular dynamics by analyzing the trajectories of Laue spots. In this study, we have developed a dual-labeling technique for DXB and DXT, allowing the simultaneous observation of motions at different domains in proteins. We identified zinc oxide (ZnO) crystals as promising candidates for the second labeling probes due to their excellent diffraction patterns, high chemical stability, and favorable binding properties with proteins. The diffraction spots from the ZnO crystals are sufficiently separated from those of gold, enabling independent motion analysis at different domains. Dual-labeling DXB was employed for the motion analysis of the 5-HT2A receptor in living cells. Simultaneous motion recording of the N-terminus and the second extracellular loop demonstrated ligand-induced motion suppression at both domains. The dual-labeling DXT technique demonstrated a capsaicin-induced peak shift in the two-dimensional motion maps at the N-terminus of the TRPV1 protein, but the peak shift was not obvious in the C-terminus. The capsaicin-induced motion modulation was recovered by the addition of the competitive inhibitor AMG9810. - Real-time tilting and twisting motions of ligand-bound states of α7 nicotinic acetylcholine receptor
Yue Yang; Tatsuya Arai; Daisuke Sasaki; Masahiro Kuramochi; Hidetoshi Inagaki; Sumiko Ohashi; Hiroshi Sekiguchi; Kazuhiro Mio; Tai Kubo; Yuji C. Sasaki
European Biophysics Journal, 53, 1-2, 15, 25, Springer Science and Business Media LLC, 2024年01月17日, ［査読有り］
研究論文（学術雑誌）, Abstract
The α7 nicotinic acetylcholine receptor is a member of the nicotinic acetylcholine receptor family and is composed of five α7 subunits arranged symmetrically around a central pore. It is localized in the central nervous system and immune cells and could be a target for treating Alzheimer’s disease and schizophrenia. Acetylcholine is a ligand that opens the channel, although prolonged application rapidly decreases the response. Ivermectin was reported as one of the positive allosteric modulators, since the binding of Ivermectin to the channel enhances acetylcholine-evoked α7 currents. One research has suggested that tilting motions of the nicotinic acetylcholine receptor are responsible for channel opening and activation. To verify this hypothesis applies to α7 nicotinic acetylcholine receptor, we utilized a diffracted X-ray tracking method to monitor the stable twisting and tilting motion of nAChR α7 without a ligand, with acetylcholine, with Ivermectin, and with both of them. The results show that the α7 nicotinic acetylcholine receptor twists counterclockwise with the channel transiently opening, transitioning to a desensitized state in the presence of acetylcholine and clockwise without the channel opening in the presence of Ivermectin. We propose that the conformational transition of ACh-bound nAChR α7 may be due to the collective twisting of the five α7 subunits, resulting in the compression and movement, either downward or upward, of one or more subunits, thus manifesting tilting motions. These tilting motions possibly represent the transition from the resting state to channel opening and potentially to the desensitized state. - Visualization of the Dynamics of Photoinduced Crawling Motion of 4-(Methylamino)Azobenzene Crystals via Diffracted X-ray Tracking
Koichiro Saito; Kouhei Ichiyanagi; Ryo Fukaya; Rie Haruki; Shunsuke Nozawa; Daisuke Sasaki; Tatsuya Arai; Yuji C. SASAKI; Keegan McGehee; Makoto Saikawa; Minghao Gao; Zhichao Wei; Dennis Kwaria; Yasuo Norikane
International Journal of Molecular Sciences, 2023年12月14日, ［査読有り］
研究論文（学術雑誌） - The Blinking of Small-Angle X-ray Scattering Reveals the Degradation Process of Protein Crystals at Microsecond Timescale
Tatsuya Arai; Kazuhiro Mio; Hiroki Onoda; Leonard M. G. Chavas; Yasufumi Umena; Yuji C. Sasaki
International Journal of Molecular Sciences, 2023年11月23日, ［査読有り］, ［筆頭著者, 責任著者］
研究論文（学術雑誌） - The ice-binding site of antifreeze protein irreversibly binds to cell surface for its hypothermic protective function
Yue Yang; Akari Yamauchi; Sakae Tsuda; Masahiro Kuramochi; Kazuhiro Mio; Yuji C. Sasaki; Tatsuya Arai
Biochemical and Biophysical Research Communications, 2023年11月, ［査読有り］, ［責任著者］
研究論文（学術雑誌） - Direct observation of 890 ns dynamics of carbon black and polybutadiene in rubber materials using diffracted x-ray blinking
Masahiro Kuramochi; Henry J. Kirkwood; Jayanath C. P. Koliyadu; Romain Letrun; Raphael de Wijn; Chan Kim; Tomomi Masui; Kazuhiro Mio; Tatsuya Arai; Hiroshi Sekiguchi; Hiroyuki Kishimoto; Adrian P. Mancuso; Tokushi Sato; Yuji C. Sasaki
Applied Physics Letters, 123, 10, AIP Publishing, 2023年09月04日, ［査読有り］
研究論文（学術雑誌）, Dynamic behavior in soft matter physics, biology, and nanoscience frequently occurs on submicrosecond timescales. Diffracted x-ray blinking (DXB) is a unique method that can provide a broad range of spatial scale information and is becoming an attractive tool for use at high repetition rate x-ray facilities. In this study, we performed DXB experiments with 890 ns time resolution at the European X-ray Free-Electron Laser Facility to obtain dynamic information about rubber samples that are typically used in automobile tires. Time-resolved scattering was simultaneously recorded for two samples that mainly consisted of carbon black (CB) and polybutadiene (PB). These samples contained either graphitized or non-graphitized CB and displayed significantly different dynamics. A clear interaction between CB and PB was observed, indicating that the mobility of PB was changed by the introduction of CB. Restricted polymer motion was observed in the q-range of 0.78–1.58 Å−1 regions. Our results suggest that the particle network can be flexibly controlled without impairing the mechanical strength of the rubber. - Real-Time Observation of Capsaicin-Induced Intracellular Domain Dynamics of TRPV1 Using the Diffracted X-ray Tracking Method
Kazuhiro Mio; Tatsunari Ohkubo; Daisuke Sasaki; Tatsuya Arai; Mayui Sugiura; Shoko Fujimura; Shunsuke Nozawa; Hiroshi SEKIGUCHI; Masahiro Kuramochi; Yuji C. SASAKI
Membranes, 13, 8, 2023年07月, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）, The transient receptor potential vanilloid type 1 (TRPV1) is a multimodal receptor which responds to various stimuli, including capsaicin, protons, and heat. Recent advances in cryo-electron microscopy have revealed the structures of TRPV1. However, due to the large size of TRPV1 and its structural complexity, the detailed process of channel gating has not been well documented. In this study, we applied the diffracted X-ray tracking (DXT) technique to analyze the intracellular domain dynamics of the TRPV1 protein. DXT enables the capture of intramolecular motion through the analysis of trajectories of Laue spots generated from attached gold nanocrystals. Diffraction data were recorded at two different frame rates: 100 μs/frame and 12.5 ms/frame. The data from the 100 μs/frame recording were further divided into two groups based on the moving speed, using the lifetime filtering technique, and they were analyzed separately. Capsaicin increased the slope angle of the MSD curve of the C-terminus in 100 μs/frame recording, which accompanied a shifting of the rotational bias toward the counterclockwise direction, as viewed from the cytoplasmic side. This capsaicin-induced fluctuation was not observed in the 12.5 ms/frame recording, indicating that it is a high-frequency fluctuation. An intrinsiccounterclockwise twisting motion was observed in various speed components at the N-terminus, regardless of the capsaicin administration. Additionally, the competitive inhibitor AMG9810 induced a clockwise twisting motion, which is the opposite direction to capsaicin. These findings contribute to our understanding of the activation mechanisms of the TRPV1 channel. - The effect of ice-binding proteins on the cryopreservation of Caenorhabditis elegans
Masahiro Kuramochi; Tatsuya Arai; Kazuhiro Mio; Sakae Tsuda; Yuji C Sasaki
microPublication Biology, microPublication Biology, 2023年04月, ［査読有り］
研究論文（学術雑誌）,Ice-binding proteins (IBPs) are capable of binding ice crystals and inhibiting their growth. IBPs have also been reported to stabilize cell membranes under non-freezing conditions. The effects of IBPs help to reduce cold- and freezing-induced damage to cells and tissues in cryopreservation. Here, we examined whether certain IBPs, namely, fish NfeIBP6 and NfeIBP8 and fungal AnpIBP1a N55D (AnpIBP), improve the recovery rate of the nematode Caenorhabditis elegans after a deep cryopreservation at −80°C. The expression of fungus-derived AnpIBP in C. elegans significantly improved its recovery rate. This result provides useful information to establish a cryopreservation technique for long-term storage using IBP molecules.
- Observation of molecular motions in polymer thin films by laboratory grazing incidence diffracted X-ray blinking
Rena Inamasu; Hiroki Yamaguchi; Tatsuya Arai; Jaewon Chang; Masahiro Kuramochi; Kazuhiro Mio; Yuji C. Sasaki
Polymer Journal, Springer Science and Business Media LLC, 2023年02月13日, ［査読有り］
研究論文（学術雑誌）, Abstract
Research on polymer surfaces has shown that the mobilities of polymer chains, which affect the aggregation state and thus the physical properties of the material, differ between the surface and bulk. However, the mobilities of the surface polymers have not been fully characterized. Therefore, we propose a time-resolved method for evaluating surface mobility. This measurement scheme is called grazing incidence diffracted X-ray blinking (GI-DXB) and can be used to evaluate the molecular motions occurring at polymer surfaces by continuously measuring X-ray diffraction patterns near the total reflection angle over small time periods. In this study, the crystallized polymer poly{2-(perfluorooctyl)ethyl acrylate}(PC8FA) was measured. The decay constants, which are indexes of molecular motions, were calculated to be 3.98 × 10−3 s−1 for the fluoroalkyl groups in the side chains observed along the in-plane direction and 3.36 × 10−3 s−1 for the lamellar structure observed along the out-of-plane direction when 2000 diffraction profiles of 500 ms were recorded and the incident angle was 0.07°. In contrast, transmission DXB indicated decay constants of 2.63 × 10−3 s−1 for the side chains and 2.87 × 10−3 s−1 for the lamellar structures. These results suggested that the PC8FA surface is mobile, because a larger decay constant indicates a higher mobility. GI-DXB can be used to measure surface dynamics. The authors contend that GI-DXB is a highly versatile tool because it allows the evaluation of local motions with a laboratory X-ray system, and these motions cannot be detected by conventional surface analyses. This measurement scheme may facilitate the development of high-performance polymers and discovery of new physical properties. - Visualizing Intramolecular Dynamics of Membrane Proteins
Tatsunari Ohkubo; Takaaki Shiina; Kayoko Kawaguchi; Daisuke Sasaki; Rena Inamasu; Yue Yang; Zhuoqi Li; Keizaburo Taninaka; Masaki Sakaguchi; Shoko Fujimura; Hiroshi Sekiguchi; Masahiro Kuramochi; Tatsuya Arai; Sakae Tsuda; Yuji C. Sasaki; Kazuhiro Mio
International Journal of Molecular Sciences, 23, 23, 14539, 14539, MDPI AG, 2022年11月22日, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）, Membrane proteins play important roles in biological functions, with accompanying allosteric structure changes. Understanding intramolecular dynamics helps elucidate catalytic mechanisms and develop new drugs. In contrast to the various technologies for structural analysis, methods for analyzing intramolecular dynamics are limited. Single-molecule measurements using optical microscopy have been widely used for kinetic analysis. Recently, improvements in detectors and image analysis technology have made it possible to use single-molecule determination methods using X-rays and electron beams, such as diffracted X-ray tracking (DXT), X-ray free electron laser (XFEL) imaging, and cryo-electron microscopy (cryo-EM). High-speed atomic force microscopy (HS-AFM) is a scanning probe microscope that can capture the structural dynamics of biomolecules in real time at the single-molecule level. Time-resolved techniques also facilitate an understanding of real-time intramolecular processes during chemical reactions. In this review, recent advances in membrane protein dynamics visualization techniques were presented. - A mutation to a fish ice-binding protein synthesized in transgenic Caenorhabditis elegans modulates its cold tolerance.
Masahiro Kuramochi; Shumiao Zhu; Chiaki Takanashi; Yue Yang; Tatsuya Arai; Yoichi Shinkai; Motomichi Doi; Kazuhiro Mio; Sakae Tsuda; Yuji C Sasaki
Biochemical and biophysical research communications, 628, 98, 103, 2022年11月05日, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）, A cryoprotectant known as ice-binding protein (IBP) is thought to facilitate the cold survival of plants, insects, and fungi. Here, we prepared a genetically modified Caenorhabditis elegans strain to synthesize fish-derived IBPs in its body wall muscles and examined whether the antifreeze activity modification of this IBP by point mutation affects the cold tolerance of this worm. We chose a 65-residue IBP identified from notched-fin eelpout, for which the replacement of the 20th alanine residue (A20) modifies its antifreeze activity. These mutant proteins are denoted A20L, A20G, A20T, A20V, and A20I along with the wild-type (WT) protein. We evaluated the survival rate (%) of the transgenic C. elegans that synthesized each IBP mutant following 24 h of preservation at -5, +2, and +5 °C. Significantly, a dramatic improvement in the survival rate was detected for the worms synthesizing the activity-enhanced mutants (A20T and A20I), especially at +2 °C. In contrast, the rate was not improved by the expression of the defective mutants (A20L, A20G, WT and A20V). The survival rate (%) probably correlates with the antifreeze activity of the IBP. These data suggest that IBP protects the cell membrane by employing its ice-binding mechanism, which ultimately improves the cold tolerance of an IBP-containing animal. - Adsorption of ice-binding proteins onto whole ice crystal surfaces does not necessarily confer a high thermal hysteresis activity
Tatsuya Arai; Akari Yamauchi; Yue Yang; Shiv Mohan Singh; Yuji C. Sasaki; Sakae Tsuda
Scientific Reports, 12, 1, 15443, 15443, Springer Science and Business Media LLC, 2022年09月14日, ［査読有り］, ［筆頭著者］, ［国際誌］
英語, 研究論文（学術雑誌）, Abstract
Many psychrophilic microorganisms synthesize ice-binding proteins (IBPs) to survive the cold. The functions of IBPs are evaluated by the effect of the proteins on the nonequilibrium water freezing-point depression, which is called “thermal hysteresis (TH)”, and the inhibitory effect of the proteins on the growth of larger ice crystals, which is called “ice recrystallization inhibition (IRI)”. To obtain mechanical insight into the two activities, we developed a modified method of ice affinity purification and extracted two new IBP isoforms from Psychromyces glacialis, an Arctic glacier fungus. One isoform was found to be an approximately 25 kDa protein (PsgIBP_S), while the other is a 28 kDa larger protein (PsgIBP_L) that forms an intermolecular dimer. Their TH activities were less than 1 °C at millimolar concentrations, implying that both isoforms are moderately active but not hyperactive IBP species. It further appeared that both isoforms exhibit high IRI activity even at submicromolar concentrations. Furthermore, the isoforms can bind to the whole surface of a hemispherical single ice crystal, although such ice-binding was generally observed for hyperactive IBP species. These results suggest that the binding ability of IBPs to whole ice crystal surfaces is deficient for hyperactivity but is crucial for significant IRI activity. - Dynamic observations of various oligomers in amyloid β isoforms using laboratory diffracted X-ray blinking
Jaewon Chang; Tatsuya Arai; Masahiro Kuramochi; Rena Inamasu; Zhuoqi Lee; Tatsunari Ohkubo; Kazuhiro Mio; Yuji C. Sasaki
Biochemistry and Biophysics Reports, 31, 101298, 101298, Elsevier BV, 2022年09月, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）, Acceleration of societal ageing has increased the global incidence of geriatric diseases such as Alzheimer's disease (AD), and the demands for proper diagnosis and monitoring of those diseases are also increasing daily. We utilized diffracted X-ray blinking (DXB) for amyloid β (Aβ) isoforms, which are thought to be closely related to AD, to discriminate among the dynamics of individual particles in early and long-term oligomerisation and aggregation inhibiting environments. Among the various Aβ isoforms, the dynamics of Aβ (1-42), which is known to be the most toxic form, were the slowest (the dynamics were lower by 78% com-pared with short-term incubation), and the dynamics were restored (the dynamics increased by 105% compared with normal aggregation) in an environment that suppressed oligomerisation of Aβ (1-42). It has been confirmed that the use of DXB allows measurements of dynamics related to the functional states of the target molecules. - Dynamic motions of ice-binding proteins in living Caenorhabditis elegans using diffracted X-ray blinking and tracking
Masahiro Kuramochi; Yige Dong; Yue Yang; Tatsuya Arai; Rio Okada; Yoichi Shinkai; Motomichi Doi; Kouki Aoyama; Hiroshi Sekiguchi; Kazuhiro Mio; Sakae Tsuda; Yuji C. Sasaki
Biochemistry and Biophysics Reports, 29, 101224, 101224, Elsevier {BV}, 2022年03月, ［査読有り］
英語, 研究論文（学術雑誌） - Diffracted X-ray Tracking Method for Measuring Intramolecular Dynamics of Membrane Proteins
Shoko Fujimura; Kazuhiro Mio; Tatsunari Ohkubo; Tatsuya Arai; Masahiro Kuramochi; Hiroshi Sekiguchi; Yuji C. Sasaki
International Journal of Molecular Sciences, 23, 4, 2343, 2343, {MDPI} {AG}, 2022年02月20日, ［査読有り］
英語, 研究論文（学術雑誌）, - Characterization of microbial antifreeze protein with intermediate activity suggests that a bound-water network is essential for hyperactivity
N. M.-Mofiz Uddin Khan; Tatsuya Arai; Sakae Tsuda; Hidemasa Kondo
Scientific Reports, 11, 1, 5971, 5971, Springer Science and Business Media {LLC}, 2021年12月, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）, - Subzero Nonfreezing Hypothermia with Insect Antifreeze Protein Dramatically Improves Survival Rate of Mammalian Cells
Akari Yamauchi; Ai Miura; Hidemasa Kondo; Tatsuya Arai; Yuji C. Sasaki; Sakae Tsuda
International Journal of Molecular Sciences, 22, 23, 2021年11月24日, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）, Cells for therapeutic use are often preserved at +4 °C, and the storage period is generally limited to 2-3 days. Here, we report that the survival rate (%) of mammalian cells is improved to 10-20 days when they are preserved with a subzero supercooled solution containing the antifreeze protein (AFP), for which an ability to stabilize both supercooled water and cell membrane integrity has been postulated. We chose adherent rat insulinoma (RIN-5F) cells as the preservation target, which were immersed into -5 °C-, -2 °C-, or +4 °C-chilled "unfrozen" solution of Euro-Collins or University of Washington (UW) containing the AFP sample obtained from insect or fish. Our results show that the survival rate of the cells preserved with the solution containing insect AFP was always higher than that of the fish AFP solution. A combination of the -5 °C-supercooling and insect AFP gave the best preservation result, namely, UW solution containing insect AFP kept 53% of the cells alive, even after 20 days of preservation at -5 °C. The insect AFP locates highly organized ice-like waters on its molecular surface. Such waters may bind to semiclathrate waters constructing both embryonic ice crystals and a membrane-water interface in the supercooled solution, thereby protecting the cells from damage due to chilling. - Laboratory diffracted x-ray blinking to monitor picometer motions of protein molecules and application to crystalline materials
Tatsuya Arai; Rena Inamasu; Hiroki Yamaguchi; Daisuke Sasaki; Ayana Sato-Tomita; Hiroshi Sekiguchi; Kazuhiro Mio; Sakae Tsuda; Masahiro Kuramochi; Yuji C. Sasaki
Structural Dynamics, 8, 4, 044302, 044302, {AIP} Publishing, 2021年07月, ［査読有り］, ［筆頭著者, 責任著者］
研究論文（学術雑誌） - Discovery of Hyperactive Antifreeze Protein from Phylogenetically Distant Beetles Questions Its Evolutionary Origin
Tatsuya Arai; Akari Yamauchi; Ai Miura; Hidemasa Kondo; Yoshiyuki Nishimiya; Yuji C. SASAKI; Sakae Tsuda
International Journal of Molecular Sciences, 22, 7, 2021年03月31日, ［査読有り］, ［筆頭著者］, ［国際誌］
英語, 研究論文（学術雑誌）, Beetle hyperactive antifreeze protein (AFP) has a unique ability to maintain a supercooling state of its body fluids, however, less is known about its origination. Here, we found that a popular stag beetle Dorcus hopei binodulosus (Dhb) synthesizes at least 6 isoforms of hyperactive AFP (DhbAFP). Cold-acclimated Dhb larvae tolerated -5 °C chilled storage for 24 h and fully recovered after warming, suggesting that DhbAFP facilitates overwintering of this beetle. A DhbAFP isoform (~10 kDa) appeared to consist of 6-8 tandem repeats of a 12-residue consensus sequence (TCTxSxNCxxAx), which exhibited 3 °C of high freezing point depression and the ability of binding to an entire surface of a single ice crystal. Significantly, these properties as well as DNA sequences including the untranslated region, signal peptide region, and an AFP-encoding region of Dhb are highly similar to those identified for a known hyperactive AFP (TmAFP) from the beetle Tenebrio molitor (Tm). Progenitor of Dhb and Tm was branched off approximately 300 million years ago, so no known evolution mechanism hardly explains the retainment of the DNA sequence for such a lo-ng divergence period. Existence of unrevealed gene transfer mechanism will be hypothesized between these two phylogenetically distant beetles to acquire this type of hyperactive AFP. - An Ice-Binding Protein from an Antarctic Ascomycete Is Fine-Tuned to Bind to Specific Water Molecules Located in the Ice Prism Planes
Akari Yamauchi; Tatsuya Arai; Hidemasa Kondo; Yuji C. Sasaki; Sakae Tsuda
Biomolecules, 10, 5, 759, 759, MDPI AG, 2020年05月13日, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）, Many microbes that survive in cold environments are known to secrete ice-binding proteins (IBPs). The structure–function relationship of these proteins remains unclear. A microbial IBP denoted AnpIBP was recently isolated from a cold-adapted fungus, Antarctomyces psychrotrophicus. The present study identified an orbital illumination (prism ring) on a globular single ice crystal when soaked in a solution of fluorescent AnpIBP, suggesting that AnpIBP binds to specific water molecules located in the ice prism planes. In order to examine this unique ice-binding mechanism, we carried out X-ray structural analysis and mutational experiments. It appeared that AnpIBP is made of 6-ladder β-helices with a triangular cross section that accompanies an “ice-like” water network on the ice-binding site. The network, however, does not exist in a defective mutant. AnpIBP has a row of four unique hollows on the IBS, where the distance between the hollows (14.7 Å) is complementary to the oxygen atom spacing of the prism ring. These results suggest the structure of AnpIBP is fine-tuned to merge with the ice–water interface of an ice crystal through its polygonal water network and is then bound to a specific set of water molecules constructing the prism ring to effectively halt the growth of ice. - Fish-Derived Antifreeze Proteins and Antifreeze Glycoprotein Exhibit a Different Ice-Binding Property with Increasing Concentration
Sakae Tsuda; Akari Yamauchi; N. M.-Mofiz Uddin Khan; Tatsuya Arai; Sheikh Mahatabuddin; Ai Miura; Hidemasa Kondo
Biomolecules, 10, 3, 423, 423, {MDPI} {AG}, 2020年03月09日, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）, The concentration of a protein is highly related to its biochemical properties, and is a key determinant for its biotechnological applications. Antifreeze proteins (AFPs) and antifreeze glycoproteins (AFGPs) are structurally diverse macromolecules that are capable of binding to embryonic ice crystals below 0 °C, making them useful as protectants of ice-block formation. In this study, we examined the maximal solubility of native AFP I-III and AFGP with distilled water, and evaluated concentration dependence of their ice-binding property. Approximately 400 mg/mL (AFP I), 200 mg/mL (AFP II), 100 mg/mL (AFP III), and >1800 mg/mL (AFGP) of the maximal solubility were estimated, and among them AFGP's solubility is much higher compared with that of ordinary proteins, such as serum albumin (~500 mg/mL). The samples also exhibited unexpectedly high thermal hysteresis values (2-3 °C) at 50-200 mg/mL. Furthermore, the analysis of fluorescence-based ice plane affinity showed that AFP II binds to multiple ice planes in a concentration-dependent manner, for which an oligomerization mechanism was hypothesized. The difference of concentration dependence between AFPs and AFGPs may provide a new clue to help us understand the ice-binding function of these proteins. - Ice recrystallization is strongly inhibited when antifreeze proteins bind to multiple ice planes
Anika T. Rahman; Tatsuya Arai; Akari Yamauchi; Ai Miura; Hidemasa Kondo; Yasushi Ohyama; Sakae Tsuda
Scientific Reports, 9, 1, 2212, 2212, Springer Science and Business Media {LLC}, 2019年12月, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）, Ice recrystallization is a phenomenon observed as the increase in ice crystal size within an already frozen material. Antifreeze proteins (AFPs), a class of proteins capable of arresting ice crystal growth, are known to inhibit this phenomenon even at sub milli-molar concentrations. A tremendous range in the possible applications of AFPs is hence expected in both medical and industrial fields, while a key determinant of the ice recrystallization inhibition (IRI) is hardly understood. Here, IRI efficiency and ice plane affinity were examined for the wild-type AFPI-III, a defective AFPIII isoform, and a fungal AFP isoform. To simplify the IRI analysis using the formal representation of Ostwald-ripening (r3 = r03 + kt), we monitored specific ice grains exhibiting only uniform growth, for which maximum Feret diameter was measured. The cube of an ice grain's radius (r3) increased proportionately with time (t), and its slope gave the recrystallization rate (k). There was a significant difference in the IRI efficiency between the samples, and the fungal AFP possessing the activity with the smallest amount (0.27 μM) exhibited an affinity to multiple ice planes. These results suggest that the IRI efficiency is maximized when AFPs bind to a whole set of ice planes. - Calcium-Binding Generates the Semi-Clathrate Waters on a Type II Antifreeze Protein to Adsorb onto an Ice Crystal Surface
Tatsuya Arai; Yoshiyuki Nishimiya; Yasushi Ohyama; Hidemasa Kondo; Sakae Tsuda
Biomolecules, 9, 5, 162, 162, MDPI AG, 2019年04月27日, ［査読有り］, ［筆頭著者］, ［国際誌］
英語, 研究論文（学術雑誌）, Hydration is crucial for a function and a ligand recognition of a protein. The hydration shell constructed on an antifreeze protein (AFP) contains many organized waters, through which AFP is thought to bind to specific ice crystal planes. For a Ca2+-dependent species of AFP, however, it has not been clarified how 1 mol of Ca2+-binding is related with the hydration and the ice-binding ability. Here we determined the X-ray crystal structure of a Ca2+-dependent AFP (jsAFP) from Japanese smelt, Hypomesus nipponensis, in both Ca2+-bound and -free states. Their overall structures were closely similar (Root mean square deviation (RMSD) of Cα = 0.31 Å), while they exhibited a significant difference around their Ca2+-binding site. Firstly, the side-chains of four of the five Ca2+-binding residues (Q92, D94 E99, D113, and D114) were oriented to be suitable for ice binding only in the Ca2+-bound state. Second, a Ca2+-binding loop consisting of a segment D94–E99 becomes less flexible by the Ca2+-binding. Third, the Ca2+-binding induces a generation of ice-like clathrate waters around the Ca2+-binding site, which show a perfect position-match to the waters constructing the first prism plane of a single ice crystal. These results suggest that generation of ice-like clathrate waters induced by Ca2+-binding enables the ice-binding of this protein. - Ice‐binding proteins from the fungusAntarctomyces psychrotrophicuspossibly originate from two different bacteria through horizontal gene transfer
Tatsuya Arai; Daichi Fukami; Tamotsu Hoshino; Hidemasa Kondo; Sakae Tsuda
The FEBS Journal, 286, 5, 946, 962, Wiley, 2019年03月, ［査読有り］, ［筆頭著者］, ［国際誌］
英語, 研究論文（学術雑誌）, Various microbes, including fungi and bacteria, that live in cold environments produce ice-binding proteins (IBPs) that protect them from freezing. Ascomycota and Basidiomycota are two major phyla of fungi, and Antarctomyces psychrotrophicus is currently designated as the sole ascomycete that produces IBP (AnpIBP). However, its complete amino acid sequence, ice-binding property, and evolutionary history have not yet been clarified. Here, we determined the peptide sequences of three new AnpIBP isoforms by total cDNA analysis and compared them with those of other microbial IBPs. The AnpIBP isoforms and ascomycete-putative IBPs were found to be phylogenetically close to the bacterial ones but far from the basidiomycete ones, which is supported by the higher sequence identities to bacterial IBPs than basidiomycete IBPs, although ascomycetes are phylogenetically distant from bacteria. In addition, two of the isoforms of AnpIBP share low sequence identity and are not close in the phylogenetic tree. It is hence presumable that these two AnpIBP isoforms were independently acquired from different bacteria through horizontal gene transfer (HGT), which implies that ascomycetes and bacteria frequently exchange their IBP genes. The non-colligative freezing-point depression ability of AnpIBP was not very high, whereas it exhibited significant abilities of ice recrystallization inhibition, ice shaping, and cryo-protection against freeze-thaw cycles even at submicromolar concentrations. These results suggest that HGT is crucial for the cold-adaptive evolution of ascomycetes, and their IBPs offer freeze resistance to organisms to enable them to inhabit the icy environments of Antarctica. DATABASES: Nucleotide sequence data are available in the DDBJ database under the accession numbers LC378707, LC378707, LC378707 for AnpIBP1a, AnpIBP1b, AnpIBP2, respectively. - Polypentagonal ice-like water networks emerge solely in an activity-improved variant of ice-binding protein
Sheikh Mahatabuddin; Daichi Fukami; Tatsuya Arai; Yoshiyuki Nishimiya; Rumi Shimizu; Chie Shibazaki; Hidemasa Kondo; Motoyasu Adachi; Sakae Tsuda
Proceedings of the National Academy of Sciences, 115, 21, 5456, 5461, Proceedings of the National Academy of Sciences, 2018年05月22日, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）, Significance
This study expands our knowledge of protein hydration, which is highly related to the macromolecular antifreeze property of proteins. We examined a polypentagonal network formation of waters for a series of artificial variants of a 65-residue ice-binding protein. The polypentagonal waters were created solely on the surface of an activity-improved variant, which appeared to contain two sets of water clusters exhibiting a perfect position match to the waters constructing the first prism and pyramidal ice planes. These data suggest that a minute structural change in a protein organizes the surface waters into a polypentagonal arrangement, which merges with the intrinsically disordered ice surface and freezes to specific ice crystal planes. - Temperature Dynamics of Single Molecular Antifreeze Protein
Okada Rio; Arai Tatsuya; Fukami Daichi; Matsushita Yuhuku; Chang Jae-won; Sekiguchi Hiroshi; Ohta Noboru; Mori Tadashi; Nishijima Masaki; Miyazawa Keisuke; Fukuma Takeshi; Ikezaki Keigo; Tsuda Sakae; Sasaki Yuji C
BIOPHYSICAL JOURNAL, 112, 3, 323A, 2017年02月03日, ［査読有り］
- X線1分子計測法を用いたエボラウイルスVP40導入細胞の形質膜動態計測
谷中慶三郎; 新井達也; 野澤俊介; 関口博史; 古山若呼; 南保明日香; 三尾和弘; 佐々木裕次; 佐々木裕次, 量子ビームサイエンスフェスタ(Web), 2023, 2024年 - 氷結合タンパク質は個体生物の凍結・非凍結低温環境における生存率を改善する
倉持昌弘; 新井達也; 三尾和弘; 津田栄; 佐々木裕次, アグリバイオ, 6, 14, 2023年 - 凍結低温環境下での生命活動維持を実現する氷晶結合タンパク質
倉持昌弘; 新井達也; 三尾和弘; 津田栄; 佐々木裕次, アグリバイオ, 7, 5, 2023年 - 回折X線明滅法を用いた劣化ポリマーの内部動態計測
坂口正紀; 新井達也; 引田理英; 三尾和弘; 佐々木裕次, Photon Factory News, 41, 2, 2023年 - 氷晶結合タンパク質分子の構造特異機能に起因した凍結・低温耐性獲得メカニズム
倉持昌弘; 新井達也; 三尾和弘; 津田栄; 佐々木裕次, アグリバイオ, 7, 10, 2023年
- 温度ストレスによる生体応答ダイナミクス (永島 計 監修)
新井達也; 佐々木裕次, 第1章 環境温度ストレスによる生体応答 第4節 不凍タンパク質による低温耐性メカニズム
エヌ・ティー・エス, 2023年05月, 9784860438302, 2, 8, 337, 10p, 図版 21p, 日本語, ［共著］ - 不凍タンパク質の機能と応用
津田 栄, 第８章 微生物由来不凍タンパク質、その発見と多様性
シーエムシー出版, 2018年08月, 9784781313399, viii, 289p, 日本語, ［共著］
- Discovery and characterization of beetle-type antifreeze proteins in distantly related snakeflies
Tatsuya Arai; Kosuke Maeda; Kaho Uchizawa; Tomoyasu Aizawa; Sakae Tsuda
5th Ice-Binding Proteins Conference, 2025年09月04日, 英語, 口頭発表（一般）
46471129;40627476 - Structural diversity of ice-binding proteins observed with X-ray crystallography
Tatsuya Arai; Sakae Tsuda; Tomoyasu Aizawa
9th ISQBS, 2024年10月21日, 英語, 口頭発表（招待・特別）
2024年10月19日 - 2024年10月22日, 46471129;40627476, ［招待講演］ - Ca2+-induced formation of ice-like water network on the surface of type II antifreeze protein from Japanese smelt
Tatsuya ARAI; Yue YANG; Sakae TSUDA; Kazuhiro MIO; Yuji C. SASAKI
IUPAB2024, 2024年06月25日, 英語, ポスター発表
2024年06月24日 - 2024年06月28日, 46471129;40627476 - ワカサギ由来不凍タンパク質はCa2+結合時にのみ氷結晶結合部位に水和ネットワークを形成する
新井達也; 山内彩加林; 津田栄; 三尾和弘; 佐々木裕次
第24回日本蛋白質科学年会, 2024年06月13日, 日本語, ポスター発表
2024年06月11日 - 2024年06月13日, 46471129 - Rotational dynamics of nanoparticles in polymer nanocomposites observed with diffracted X-ray blinking
Tatsuya Arai; Masahiro Kuramochi; Kazuhiro Mio; Hiroshi Sekiguchi; Yuji C. Sasaki
MRM2023, 2023年12月14日, 英語, ポスター発表
2023年12月11日 - 2023年12月16日, 43926675 - X線回折で見る高分子材料内部フィラーの回転ダイナミクス
新井達也; 倉持昌弘; 三尾和弘; 関口博史; 佐々木裕次
第72回高分子討論会, 2023年09月28日, 日本語, 口頭発表（一般） - 回折X線明滅法で見る不凍タンパク質分子表面の凍結水和層のダイナミクス
Tatsuya Arai; Yang Yue; Sakae Tsuda; Kazuhiro Mio; Yuji. C. Sasaki
第23回日本蛋白質科学年会, 2023年07月06日, 英語, ポスター発表 - 回折X線明滅法を用いた加硫天然ゴム内部の粒子動態解析
新井達也; 坂口正紀; 三尾和弘; 佐々木裕次
2022年度量子ビームサイエンスフェスタ, 2023年03月15日, 日本語, ポスター発表
2023年03月13日 - 2023年03月15日 - ナノ結晶をプローブとした高分子のX線動態計測
新井達也; 坂口正紀; 三尾和弘; 関口博史; 佐々木裕次
第37回日本放射光学会年会, 2023年01月08日, 日本語, 口頭発表（一般）
2023年01月07日 - 2023年01月09日 - オペランド計測に基づく不凍タンパク質応用技術の開発
新井達也; 三尾和弘; 佐々木 裕次
2022年度OPERANDO-OIL・COMS・量子ビーム計測クラブ合同研究会, 2022年11月29日, ポスター発表
2022年11月29日 - 2022年11月29日, ［招待講演］ - Elucidating the molecular mechanism of cell protective function of ice-binding proteins at non-freezing temperature
Tatsuya Arai; Yue Yang; Akari Yamauchi; Sakae Tsuda; Kazuhiro Mio; Yuji C. Sasaki
第60回日本生物物理学会年会, 2022年09月29日, 英語, ポスター発表
2022年09月28日 - 2022年09月30日 - Elucidating the molecular mechanism of cell protective function of ice-binding proteins at non-freezing temperature
Tatsuya Arai
Ice Binding Protein conference 2022, 2022年08月01日, 英語, 口頭発表（一般）
2022年07月29日 - 2022年08月01日 - 氷と細胞の双方に結合するタンパク質の分子機能解析
新井 達也; 楊 越; 津田 栄; 三尾 和弘; 佐々木 裕次
第22回日本蛋白質科学会年会, 2022年06月08日, 日本語, 口頭発表（一般）
2022年06月07日 - 2022年06月09日 - "Cell-adsorption and -protection of ice-binding protein at non-freezing temperature"
Tatsuya Arai
IBP international seminar series, 2022年05月06日, 英語, 口頭発表（招待・特別）
2021年06月21日 - 2022年05月06日, ［招待講演］ - 回折X線明滅法を用いた天然ゴム内分子動態の解析
新井達也; 増井友美; 引田理英; 岸本浩通; 佐々木裕次
2021年度量子ビームサイエンスフェスタ, 2021年03月08日, 日本語, ポスター発表
2021年03月07日 - 2021年03月09日 - DXB法を用いた不凍タンパク質結晶の内部分子動態計測
新井達也; 倉持昌弘; 三尾和弘; 佐々木裕次
2020年度量子ビームサイエンスフェスタ, 2020年03月10日, 日本語, ポスター発表
2020年03月09日 - 2020年03月11日
- スギ・ヒノキ由来ペプチドGRPによる花粉－食物アレルギー症候群発症の分子機構解析
科学研究費助成事業
2025年04月01日 - 2028年03月31日
相沢 智康; 新井 達也; 久米田 博之; 菊川 峰志; 門間 敬子
日本学術振興会, 基盤研究(B), 北海道大学, 25K02233 - X線回折ゆらぎを活用した高分子材料の時空間ゆらぎ測定基盤の構築
2025年 - 2028年
新井 達也
高分子複合材料開発において、材料内部におけるナノ粒子ダイナミクスとマクロ物性との相関を可視化する手法が求められています。本研究ではX線回折強度の揺らぎからナノ粒子の回転揺らぎを測定するDXB法を基盤として、これを発展させた新奇計測手法の開発を目的とします。具体的には、DXB法と既存のX線手法を融合した新規手法により、粒子の動的挙動と材料機能の相関を多角的に解析し、高機能材料設計指針を創出します。
科学技術振興機構, 戦略的な研究開発の推進/戦略的創造研究推進事業/さきがけ, 25144879 - 水の凍結を制御する水分子凝集層の開発
科学研究費助成事業
2024年04月 - 2027年03月
津田 栄; 佐々木 裕次; 三尾 和弘; 新井 達也
日本学術振興会, 基盤研究(C), 東京大学, 研究分担者, 24K08487 - X線回折で見る高分子複合材料のリアルタイム内部運動
2023年 - 2025年
新井 達也
高分子複合材料において、ナノスケールのダイナミクスがマクロな物性と関連していることは広く知られています。そのため、ダイナミクスの直接観察手法の発展が期待されています。本研究では、時分割X線回折強度の揺らぎの速さからダイナミクスを推定する新たな手法としてDXB法を考案しました。DXB法を用いて様々なゴムやゲルのダイナミクスを測定し、マクロな物性との関係性を明らかにする事を本研究の最終目的とします。
科学技術振興機構, 戦略的な研究開発の推進/戦略的創造研究推進事業/ACT-X, 23827366 - 氷と細胞に結合する天然多機能性タンパク質の分子メカニズム解明
科学研究費助成事業 若手研究
2022年04月01日 - 2024年03月31日
新井 達也
日本学術振興会, 若手研究, 東京大学, 22K15071
