Review
Immunology
Irini Evnouchidou, Despoina Koumantou, Mathilde Nugue, Loredana Saveanu
Summary: Antigen-trimming aminopeptidases, belonging to the oxytocinase subfamily of M1 metallopeptidases, have been extensively studied for their ability to modify antigenic precursors and generate major histocompatibility class-I ligands. These enzymes have been associated with autoimmune diseases, cancers, and infections, and recent research has raised new questions about their functions.
CURRENT OPINION IN IMMUNOLOGY
(2023)
Article
Chemistry, Applied
Nani Wang, Pingcui Xu, Weixuan Yao, Jiali Zhang, Shufen Liu, Yongjun Wang, Yan Zhang
Summary: PPCP-1, an arabinogalactan isolated from Phellodendron chinense Schneid., shows potential in protecting against diabetic osteoporosis through various mechanisms, making it a potential functional food or drug for bone health.
CARBOHYDRATE POLYMERS
(2021)
Article
Plant Sciences
Jelena Bozunovic, Milica Milutinovic, Neda Anicic, Marijana Skoric, Dragana Matekalo, Suzana Zivkovic, Milan Dragicevic, Biljana Filipovic, Tijana Banjanac, Luka Petrovic, Danijela Misic
Summary: Secoiridoid glucosides (SGs) are bitter tasting monoterpenoids that play a key role in plant defense. This study found that SGs can undergo hydrolysis mediated by enzymes, leading to different metabolic pathways in plants. Transient overexpression of two beta-D-glucosidases can alter the metabolite profiles of SGs, potentially impacting the overall phytochemistry of the plant.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Kiminori Toyooka, Yumi Goto, Kei Hashimoto, Mayumi Wakazaki, Mayuko Sato, Masami Yokota Hirai
Summary: In this study, the ultrastructure of lateral root cap (LRC) cells in Arabidopsis was investigated using advanced microscopy techniques. The researchers discovered sausage-shaped structures in the ER that were identified as ER bodies using fluorescence markers. The fusion of ER bodies with vacuoles and subsequent vacuolar collapse were observed, suggesting a direct transport of beta-glucosidases and release of protective substances in LRC cells.
PLANT AND CELL PHYSIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Anjali Purohit, Lata Pawar, Sudesh Kumar Yadav
Summary: A gene, glu1 (WP_243232135.1), coding for beta-glucosidase from Microbacterium sp. CIAB417 was studied for its cold adaptive nature and tolerance to high levels of glucose and ethanol. The phylogenetic analysis revealed its close association with a similar gene from Microbacterium indicum. The purified recombinant GLU1 enzyme displayed optimal activity and stability at pH 5 and temperature 30 degrees C, and showed high efficiency in hydrolyzing celloologosaccharides and other substrates. This cold adaptive GLU1 with high glucose and ethanol tolerance could have significant applications in various industries.
ENZYME AND MICROBIAL TECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Lilei Xu, Yu Xiao, Jie Zhang, Xianyang Fang
Summary: In bacteria, the expression of folate-related genes is controlled by different types of riboswitches, including the THF-I and recently discovered THF-II riboswitches. In this study, the crystal structures of THF-II riboswitch from Mesorhizobium loti were determined, revealing a unique architecture stabilized by continuous base pair stacking. The ligand binding pocket of the riboswitch accommodates the pterin moiety and its binding is influenced by Mg2+ ions. Ligand binding reduces accessibility of the ribosome binding site, regulating the expression of downstream genes. These findings provide mechanistic insights into translation regulation by THF-II riboswitch.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Astronomy & Astrophysics
M. Gatto, V Ripepi, M. Bellazzini, M. Tosi, M. Cignoni, C. Tortora, S. Leccia, G. Clementini, E. K. Grebel, G. Longo, M. Marconi, I Musella
Summary: This study derived surface brightness profiles and structural parameters for 170 star clusters in the Small Magellanic Cloud, providing ages for a subsample of 134 clusters. The results indicate a dynamic evolution of the SMC star cluster system in terms of sizes, luminosities, and masses, with a relationship between cluster mass and inner expansion detected. The data suggest an increase in core radius after a certain period and a mass-size relationship across the investigated range of cluster masses.
MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY
(2021)
Article
Biochemistry & Molecular Biology
In Jung Kim, Uwe T. Bornscheuer, Ki Hyun Nam
Summary: In this study, the biochemical and structural analysis of a Bgl enzyme (TsaBgl) from the hemicellulose-degrading bacterium Thermoanaerobacterium saccharolyticum was reported. TsaBgl exhibited maximum hydrolase activity at pH 6.0 and 55°C and showed a unique structure compared to other known Bgls. The study improved our understanding of the inhibition and glucose tolerance mechanisms of Bgl enzymes, which is crucial for their industrial application.
Article
Engineering, Aerospace
Marco Evangelos Biancolini, Corrado Groth, Stefano Porziani, Andrea Chiappa, Francesco Giorgetti, Fabrizio Nicolosi, Ubaldo Cella
Summary: The coupling of finite-element method solutions and fluid dynamic solvers for high-fidelity fluid-structure interaction numerical methods involves challenges that impact both the robustness and accuracy of the tools. The European research project aimed to enhance the accuracy of numerical FSI procedures by addressing critical issues like interpolation errors in mapping and developing a mapping procedure, along with validating FSI methodologies in aeronautical structural modeling. Using radial basis functions, the project addressed solver coupling problems and developed a mesh morphing technique to adapt the CFD domain, showcasing the tool's capability to capture a typical wing box structure's stress state and deformation under aerodynamic loads.
JOURNAL OF AEROSPACE ENGINEERING
(2021)
Article
Biochemistry & Molecular Biology
Xin Jiang, Nieng Yan, Dong Deng, Chuangye Yan
Summary: The Warburg effect refers to the phenomenon in which cancer cells shift their glucose metabolism from aerobic respiration to lactic fermentation even in the presence of oxygen. Elevated expression levels of human glucose transporters (GLUTs) and human monocarboxylate transporters (MCTs) are observed to maintain metabolic homeostasis and prevent lactate accumulation. Inhibition of GLUTs and/or MCTs shows potential as therapeutic strategies for cancer treatment. Recent advances in the structural characterization of GLUTs and MCTs provide a comprehensive understanding of their transport and inhibition mechanisms, contributing to the development of anticancer therapies.
Article
Chemistry, Inorganic & Nuclear
Irina Kuznetcova, Felix Bacher, Samah Mutasim Alfadul, Max Jing Rui Tham, Wee Han Ang, Maria V. Babak, Peter Rapta, Vladimir B. Arion
Summary: A small library of novel indolo[3,2-d][2]benzazepine-derived ligands and their copper complexes was prepared, and their antiproliferative activity in vitro was tested. The compounds showed high anticancer activity in breast cancer and hepatocellular carcinoma cell lines, with important structure-activity relationships observed.
INORGANIC CHEMISTRY
(2022)
Article
Chemistry, Applied
Dong-Dong Yang, Han-Wen Zheng, Qiong-Fang Liang, Xiang-Jun Zheng
Summary: In this study, a new viologen-based Zn complex was presented, which underwent single-crystal-to-single-crystal transformation under external stimuli. The complex exhibited a two-step color change upon UV irradiation. These findings provide insights into the multiple photochromism and variations of crystal structures via single-crystal-to-single-crystal transformations.
Article
Biochemical Research Methods
Mehari Muuz Weldemariam, Putty-Reddy Sudhir, Jongmin Woo, Qibin Zhang
Summary: Pancreatic β-cell dysfunction is an early hallmark of type 1 diabetes mellitus. This study aimed to uncover the molecular mechanisms underlying this dysfunction using cytokines and chemical inducers to mimic the conditions experienced by dysfunctional β-cells. Proteomics analysis identified differentially expressed proteins associated with immune pathways, respiratory electron transport chains, protein processing in the endoplasmic reticulum, lipid synthesis, peroxisomal protein import, energy metabolism, and vesicle secretion. High glucose was found to alleviate the inhibition of complex I induced by one of the chemical inducers. These findings contribute to a better understanding of the molecular events involved in β-cell dysfunction.
Article
Chemistry, Physical
Adalberto Vasconcelos Sanches de Araujo, Antonio Carlos Borin
Summary: Understanding the role of metal ions in living organisms and their interactions with biological compounds is crucial for developing bioinorganic applications. In this study, the luminescence of the Zn(II)-guanine complex in water was investigated using computational quantum chemical methods. The results provide molecular-level explanations for the experimental findings, showing that Zn(II) ions preferentially bind to the N7 position and that three water molecules are sufficient for describing the photophysical properties.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Biochemistry & Molecular Biology
Yoel A. Klug, Roland Schwarzer, Thirupathi Ravula, Etai Rotem, Ayyalusamy Ramamoorthy, Yechiel Shai
Summary: In this study, calcium interaction motifs (CIMs) in the gp41 CHR and NHR regions were discovered via NMR spectroscopy. The assembly of CHR-NHR SHB was found to be facilitated in Ca2+-containing media and impaired in CIM mutants. The clinically approved fusion inhibitor T20 exhibited reduced inhibitory efficiency when challenged with calcium, which could have implications for the development of better fusion inhibitors for HIV.
Article
Biochemistry & Molecular Biology
Saeko Yanaka, Shigetaka Nishiguchi, Rina Yogo, Hiroki Watanabe, Jiana Shen, Hirokazu Yagi, Takayuki Uchihashi, Koichi Kato
Summary: This study employed high-speed atomic force microscopy to quantitatively visualize the interaction between mouse IgG and the C1 complex. The results showed that C1q is restricted in terms of internal motion and has a stronger binding affinity for IgG2b assemblages. Additionally, a 1:1 stoichiometric interaction between C1/C1q and an IgG2a variant was observed in the absence of an antigen.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Saeko Yanaka, Hirokazu Yagi, Rina Yogo, Masayoshi Onitsuka, Koichi Kato
Summary: Mammalian cells are commonly used for producing recombinant glycoproteins, but the high production costs are a drawback. We developed a cost-saving method by culturing the cells under glutamine-free conditions for uniform isotope labeling.
JOURNAL OF BIOMOLECULAR NMR
(2022)
Article
Biochemistry & Molecular Biology
Siriluk Ratanabunyong, Supaphorn Seetaha, Supa Hannongbua, Saeko Yanaka, Maho Yagi-Utsumi, Koichi Kato, Atchara Paemanee, Kiattawee Choowongkomon
Summary: This research identified the KY44 aptamer as a potential inhibitor of both wildtype and mutant forms of HIV-RT. The aptamer showed low cytotoxicity and inhibited pseudo-HIV particle infection.
Article
Biotechnology & Applied Microbiology
Yuki Yoshida, Tadashi Satoh, Chise Ota, Sae Tanaka, Daiki D. Horikawa, Masaru Tomita, Koichi Kato, Kazuharu Arakawa
Summary: A novel Mn-dependent peroxidase has been identified as an important factor in the anhydrobiosis of tardigrades. It enhances oxidative stress tolerance and is mainly localized in the Golgi apparatus, suggesting the crucial role of the Golgi stress response in desiccation tolerance.
Review
Biochemistry & Molecular Biology
Koichi Kato, Takumi Yamaguchi, Maho Yagi-Utsumi
Summary: Carbohydrate chains on cell surfaces play important roles in mediating various biological functions through both carbohydrate-protein and carbohydrate-carbohydrate interactions. The combination of nuclear magnetic resonance spectroscopy and molecular dynamics simulation allows for the investigation of the dynamical structures of these carbohydrate chains. This approach has been used to improve protein-binding affinity by remodeling the conformational space of oligosaccharides and to visualize dynamic carbohydrate-carbohydrate interactions. Understanding and controlling these processes have implications for designing molecular systems with improved glycofunctions.
GLYCOCONJUGATE JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Kiyotaka Kondo, Yoichiro Harada, Miyako Nakano, Takehiro Suzuki, Tomoko Fukushige, Ken Hanzawa, Hirokazu Yagi, Koichi Takagi, Keiko Mizuno, Yasuhide Miyamoto, Naoyuki Taniguchi, Koichi Kato, Takuro Kanekura, Naoshi Dohmae, Kentaro Machida, Ikuro Maruyama, Hiromasa Inoue
Summary: Protein N-glycosylation in lung cancer sEVs may potentially reflect the histology of lung cancers.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Medicine, Research & Experimental
Yuki Yamaguchi, Natsumi Wakaizumi, Mine Irisa, Takahiro Maruno, Mari Shimada, Koya Shintani, Haruka Nishiumi, Rina Yogo, Saeko Yanaka, Daisuke Higo, Tetsuo Torisu, Koichi Kato, Susumu Uchiyama
Summary: This study investigates the interaction between IgG and Fc gamma receptor IIIa (FcγRIIIa). The results show that the Fab of IgG facilitates the interaction by slowing dissociation and increasing enthalpy gain. The CL domain of Fab specifically interacts with the D1 and D2 domains of FcγRIIIa. Additionally, antigen binding plays a role in stabilizing the IgG-FcγRIIIa interactions.
Article
Biology
Yasuhiro Yunoki, Atsushi Matsumoto, Ken Morishima, Anne Martel, Lionel Porcar, Nobuhiro Sato, Rina Yogo, Taiki Tominaga, Rintaro Inoue, Maho Yagi-Utsumi, Aya Okuda, Masahiro Shimizu, Reiko Urade, Kazuki Terauchi, Hidetoshi Kono, Hirokazu Yagi, Koichi Kato, Masaaki Sugiyama
Summary: The overall structure of the fully assembled cyanobacterial circadian clock system composed of KaiA, KaiB and KaiC was determined using an integrated approach of experimental and computational methods. This approach provides a useful tool to resolve large complex structures with dynamically fluctuating domains.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Fumiko Umezawa, Makoto Natsume, Shigeki Fukusada, Kazuki Nakajima, Fumiya Yamasaki, Hiroto Kawashima, Chu-Wei Kuo, Kay-Hooi Khoo, Takaya Shimura, Hirokazu Yagi, Koichi Kato
Summary: This study suggests that the GroP modification, mediated by PCYT2, is positively correlated with cancer progression and migration ability. These findings provide a potential novel approach for cancer treatment targeting PCYT2.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Kunihiro Kuwajima, Maho Yagi-Utsumi, Saeko Yanaka, Koichi Kato
Summary: Hydrogen/deuterium (H/D) exchange combined with two-dimensional (2D) NMR spectroscopy is widely used for studying the structure, stability, and dynamics of proteins. This article introduces the dimethylsulfoxide (DMSO)-quenched H/D-exchange method and its applications in protein science. The method involves replacing the H/D-exchange buffer with an aprotic DMSO solution, which quenches the exchange reaction. The improved DMSO-quenched method allows for monitoring the H/D exchange of proteins at high concentrations of salts or denaturants.
Article
Biology
Taiki Saito, Hirokazu Yagi, Chu-Wei Kuo, Kay-Hooi Khoo, Koichi Kato
Summary: A 29-amino acid sequence in the N-terminal domain of LAMP-1 promotes its Lewis X glycosylation and can be embedded into other proteins for Lewis X glycoengineering, opening up new possibilities for protein and cell engineering.
COMMUNICATIONS BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Shinnosuke Horiuchi, Takumi Yamaguchi, Jacopo Tessarolo, Hirotaka Tanaka, Eri Sakuda, Yasuhiro Arikawa, Eric Meggers, Guido H. Clever, Keisuke Umakoshi
Summary: In this study, we achieved symmetry-breaking self-assembly of a defined C-1-symmetric supramolecular structure by the synergistic effects of weak binding forces. The flexible capsule framework undergoes a large structural change upon guest binding, forming a distorted resorcin[4]arene hexameric capsule with an asymmetric cavity. The location of the chiral guest in the anisotropic environment leads to modulation of its Electric Dipole (ED) and Magnetic Dipole (MD) transition moments, resulting in increased emission quantum yield and circularly polarized luminescence.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Methanee Hiranyakorn, Maho Yagi-Utsumi, Saeko Yanaka, Naoya Ohtsuka, Norie Momiyama, Tadashi Satoh, Koichi Kato
Summary: We characterized the dynamic conformational interconversions of Lys48-linked ubiquitin chains, which involve both intermolecular and intramolecular interactions. The hydrophobic Ub-Ub interaction in diUb was reinforced by cysteine substitution of Lys48 of the distal Ub unit. Additionally, the mutational modification impacted the exposure of the most distal Ub unit in triUb.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
