Article
Biochemistry & Molecular Biology
Sergio Rampino, Mirco Zerbetto, Antonino Polimeno
Summary: A new framework for describing relaxation processes in flexible macromolecules has been introduced, allowing for accurate results with minimal adjustable parameters across various molecular systems, especially in magnetic resonance experiments. By directly applying this method, successful evaluations of NMR relaxation parameters for peptides and oligosaccharides have been achieved, showing agreement with experimental data.
Article
Chemistry, Analytical
Hassiba Outilaft, Caroline Bund, Martial Piotto, Izzie J. Namer
Summary: The use of C-13-labeled molecular probes is crucial for studying altered metabolic pathways in human pathologies. Analyzing the different C-13 isotopologues resulting from these changes is essential for understanding the underlying biological processes. We propose an NMR methodology, conducted under HRMAS conditions, to explore metabolic pathways in unprocessed pathological cells and tissues. This methodology has the potential to advance the study of human pathologies and therapeutic treatments.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Hyejin Park, Shannon Eriksson, Warren S. Warren, Qiu Wang
Summary: In this study, novel N-15 and C-13-labeled NO-sensing probes were designed and developed for real-time detection of NO. These probes undergo selective and rapid reaction with NO, generating detectable AZO products that can be monitored using nuclear magnetic resonance signals. The study also compares the performance of N-15 and C-13 nuclei in hyperpolarized reaction-based probes.
BIOORGANIC & MEDICINAL CHEMISTRY
(2022)
Article
Chemistry, Organic
Matteo Borgini, Lukasz Wieteska, Cynthia S. Hinck, Troy Krzysiak, Andrew P. Hinck, Peter Wipf
Summary: Isotopic labeling of methyl-substituted proteinogenic amino acids with C-13 has revolutionized the applications of solution-based NMR spectroscopy, enabling the study of larger and more complex proteins. Methods have been established to produce methyl-labeled proteins in bacteria and yeast, but mammalian cells are preferred for the production of many human proteins. We report a cost-effective method for incorporating C-13 methyl-labeled amino acids into proteins using mammalian cells, overcoming the limitations of biosynthetic machinery in these cells.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Harri A. Heikkinen, Sofia M. Backlund, Hideo Iwai
Summary: Partially labeling samples with 20% 13C and 100% 15N can reduce chemical costs while maintaining structural information, especially for small proteins. The approach simplifies sample preparation and enhances the efficiency of NMR technology in backbone resonance assignments, structure determination, N15-relaxation analysis, and ligand-protein interactions.
Article
Biochemistry & Molecular Biology
Yan Xue, Karolina Ucieklak, Suresh Gohil, Tomasz Niedziela, Gustav Nestor, Corine Sandstrom
Summary: This study presents a method of metabolic labeling of hyaluronan (HA) using Streptococcus equi subsp. Zooepidemicus and subsequent analysis by NMR and mass spectrometry. The results provide a valid approach for the quantitative assessment of isotopically labeled glycans and will enhance detection capabilities and facilitate structure-function relationship analysis of complex glycans.
CARBOHYDRATE RESEARCH
(2023)
Article
Chemistry, Physical
Jiahui Shi, Juan Ning, Guizhen Hu, Wenzheng Guo, Yanmei Zhou
Summary: In this study, a series of panchromatic carbon dots were synthesized by using hydroxyurea and o-phenylenediamine as precursors and varying the solvents. The pink carbon dots (p-CDs) with a quantum yield of 46% were chosen for cellular research. After modifying the p-CDs with mannose, they could selectively target liver cancer cells and achieve naked-eye discrimination.
APPLIED SURFACE SCIENCE
(2023)
Article
Chemistry, Organic
Ansis Maleckis, Iresha D. Herath, Gottfried Otting
Summary: The synthesis of indoles labeled with C-13-H-1 and C-13-F-19 spin pairs is described, utilizing inexpensive carbon-C-13 dioxide as the isotope source. Key steps include ruthenium-mediated ring-closing metathesis for constructing the C-13-containing indole carbocycle. These labeled tryptophans can be incorporated into proteins for high-resolution and high-sensitivity NMR spectroscopy, and are viable precursors for in vivo and in vitro protein expression.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2021)
Article
Engineering, Multidisciplinary
Yuping Zheng, Jiawei He, Bin Li, Tonghua Wu, Wei Dai, Ye Li
Summary: This study proposes a novel single-ended DC protection strategy for multi-terminal hybrid HVDC systems, which utilizes transient information and active injection concept to detect and distinguish fault lines, showing superiority over traditional protection strategies. Results indicate that the proposed protection strategy is suitable for multi-terminal hybrid HVDC systems and not reliant on line boundary elements.
Article
Chemistry, Applied
Tianpeng Yin, Yi Yu, Qinghua Liu, Guoyuan Zhu, Liping Bai, Wei Zhang, Zhihong Jiang
Summary: Aloe vera, a popular and widely cultivated plant, is attracting increasing attention from the food industry. In this study, the secondary metabolites in Aloe vera were rapidly identified using NMR-based dereplication, and new compounds were discovered. The results demonstrate that Aloe vera is a promising natural source for the food industry, and highlight the power of NMR technology in exploring secondary metabolites from plant resources.
JOURNAL OF FOOD COMPOSITION AND ANALYSIS
(2023)
Article
Biochemical Research Methods
Philippe Lesot, Philippe Berdague, Virginie Silvestre, Gerald Remaud
Summary: This article discusses the role of chiral induction/amplification in chiral selection in living organisms, explores the method of analyzing carbon-13 isotopes in chiral molecules using NMR technology, and proposes the potential of using liquid crystals as enantiodiscriminating media. The study first explores the capabilities of anisotropic C-13-{H-1} NMR in enantiomeric position-specific C-13 isotope fractionation and demonstrates the analytical potential of using PBLG in this context.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Engineering, Electrical & Electronic
Tao Li, Yongli Li, Xiaolong Chen, Song Li, Ningning Liu
Summary: A coordinated control strategy is proposed in this paper to resist external parameter disturbances and suppress bus voltage fluctuations caused by power mutations. By integrating a nonlinear disturbance observer into the traditional passivity-based control strategy, real-time monitoring of disturbance variables can be achieved, reducing voltage fluctuation time and improving stability.
INTERNATIONAL JOURNAL OF ELECTRICAL POWER & ENERGY SYSTEMS
(2022)
Article
Polymer Science
Alexey Slobodinyuk, Vladimir Strelnikov, Valeriy Yu Senichev, Daria Slobodinyuk
Summary: This research investigates the effect of polyester oligoethylene adipate molecular weight, diisocyanate structure, and chain extender on the properties of epoxyurethane-based oligomer elastomers. The study examines the deformation and strength properties of the elastomers.
Article
Chemistry, Organic
Debobrata Paul, Joel T. Mague, Shyam Sathyamoorthi
Summary: We propose a novel approach for synthesizing protected D-galactosamine synthons. Our method involves a sulfamate-tethered aza-Wacker cyclization and starts from D-erythrono-1,4-lactone, which differs from traditional syntheses using glycals or hexoses as starting materials. This strategy can potentially be applied to the synthesis of other 2-amino-2-deoxyhexoses with challenging protection patterns.
JOURNAL OF ORGANIC CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Garry W. Buchko, Mowei Zhou, Cat Hoang Vesely, Jinhui Tao, Wendy J. Shaw, Ryan A. Mehl, Richard B. Cooley
Summary: In this study, the researchers successfully expressed and purified C-13-, N-15-labeled murine amelogenin protein with phosphorylation at Ser-16 using a modified genetic code expansion protocol. This protein will be a valuable tool for studying the process of amelogenesis and mineralization.
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)