Review
Biochemistry & Molecular Biology
Kaori Kanemaru, Yoshikazu Nakamura
Summary: Phospholipase C (PLC) metabolizes phosphatidylinositol 4,5-bisphosphate in the plasma membrane and generates inositol 1,4,5-trisphosphate and diacylglycerol, which regulate cellular functions. Mammalian PLC consists of six typical classes and one atypical class, and dysregulation of PLC activity is associated with various diseases. Therefore, the review focuses on the structure, activation mechanisms, and physiological functions of mammalian PLC.
Article
Microbiology
Hao-Yu Zheng, Liang Yang, Tao Dong
Summary: The type VI secretion system injects a rigid inner tube into cells using a contractile outer sheath, with the tip often decorated by a PAAR-repeat protein. PAAR proteins have diverse functions, acting as toxins or carriers for interacting toxins, highlighting the need for future research on their functions.
Article
Biochemical Research Methods
Tielin Wang, Wei Guan, Yongxi Du, Yang Xu, Zhen He, Yan Zhang, Chuanzhi Kang, Xiufu Wan, Xiulian Chi, Kai Sun, Xiaobo Zhang
Summary: The study identified 1909 modification sites on 940 proteins in N. crassa using LC-MS/MS qualitative proteomics strategies. The functions of these proteins were analyzed using GO enrichment, KEGG pathway, and subcellular location experiments, revealing their involvement in diverse pathways and forming a complex protein-protein interaction (PPI) network with both similar and distinct regulatory mechanisms.
Review
Biochemistry & Molecular Biology
Susanna Tornroth-Horsefield, Clara Chivasso, Helin Strandberg, Claudia D'Agostino, Carla V. T. O'Neale, Kevin L. Schey, Christine Delporte
Summary: This review provides a comprehensive overview of the current knowledge of AQP interactomes and discusses the molecular basis and functional significance of these protein-protein interactions in health and diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Jialei Ji, Limei Yang, Zhiyuan Fang, Yangyong Zhang, Mu Zhuang, Honghao Lv, Yong Wang
Summary: This review focuses on the advances of the plant SWEETs, including their discovery, protein structure characteristics, evolution, physiological functions, and applications in plant breeding. It provides more in-depth and comprehensive information to elucidate the molecular basis of SWEETs' function in plants.
Article
Biochemistry & Molecular Biology
Pavlina Pokorna, Miroslav Krepl, Jiri Sponer
Summary: The study shows that the HP1 chromodomain (CD) interacts with its target peptides dynamically, with the target sequence ranging from positions -7 to +3. The CD's anionic clamp can be neutralized by not only the -3 and -1 residues, but also by -7, -6, -5 and +3 residues. Structural dynamics play a significant role in molecular recognition between the HP1 CD domain and its targets, increasing target sequence flexibility through mutual replaceability of target residues.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2021)
Article
Microbiology
Annie Lebreton, Francois Bonnardel, Yu-Cheng Dai, Anne Imberty, Francis M. Martin, Frederique Lisacek
Summary: Fungal lectins are a type of carbohydrate-binding protein that play important roles in the interactions of fungi with their environment and defense against feeders. Research shows that fungal lectins have highly similar amino acid sequences, indicating an evolutionary relationship among them.
Review
Chemistry, Physical
Marcos Lopez Hernandez, Jan Skov Pedersen, Daniel E. Otzen
Summary: The synergies between surfactants and proteins are widely utilized in various fields, but there is still room for improvement in terms of sustainability. Biosurfactants offer an attractive alternative, and understanding their interactions with proteins can open up new opportunities. This review focuses on the self-assembly of protein:BS complexes and the effects of BS on enzymatic activity.
CURRENT OPINION IN COLLOID & INTERFACE SCIENCE
(2023)
Article
Multidisciplinary Sciences
James Mark Wagstaff, Vicente Jose Planelles-Herrero, Grigory Sharov, Aisha Alnami, Frank Kozielski, Emmanuel Derivery, Jan Lowe
Summary: Protein filaments are used to organize other molecules within cells, and some of them can generate movement by coupling nucleotide hydrolysis to their polymerization cycle. Actin and tubulin proteins are capable of forming cytomotive filaments. In this study, the polymerization cycles of actin and tubulin homologs were analyzed to understand the basis of cytomotivity. Shared subunit polymerization switches were found in cytomotive actins and tubulins, indicating conformational changes of subunits upon filament assembly. These cytomotive switches contribute to filament robustness and ensure their stability.
Review
Microbiology
Nicole J. Curtis, Krupa J. Patel, Amina Rizwan, Constance J. Jeffery
Summary: This mini-review discusses examples of moonlighting proteins in fungi, revealing their roles in transcription and DNA metabolism, translation and RNA metabolism, protein folding, regulation of protein function, and their interaction with other cell types and host proteins.
Review
Biochemistry & Molecular Biology
Kevin Reinle, Axel Mogk, Bernd Bukau
Summary: The protein quality control system maintains protein homeostasis through substrate degradation, refolding, and sequestration activities, in which small heat shock proteins play a crucial role and adapt to different tasks and stress conditions.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Chemistry, Physical
Rebecca F. Alford, Rituparna Samanta, Jeffrey J. Gray
Summary: Energy functions are crucial for biomolecular modeling, with membrane protein energy functions lagging behind soluble protein ones due to sparse data and overfitting issues. To address this challenge, a suite of 12 tests on diverse independent data sets was conducted, evaluating the ability of energy functions to capture membrane protein orientation, stability, sequence, and structure. Findings point out areas for improvement in energy functions and potential integration with machine-learning-based optimization methods in the future.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Multidisciplinary Sciences
Ilya A. Vakser, Sergei Grudinin, Nathan W. Jenkins, Petras J. Kundrotas, Eric J. Deeds
Summary: Computational methodologies are being used to model the entire cell at the molecular level. This study combines protein docking and molecular simulations to develop an approach that can simulate cellular processes at unprecedented timescales and all-atom resolution. The approach successfully captures the dynamics of protein interactions and has been validated across various protein systems.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Biochemistry & Molecular Biology
Camilla Faoro, Sandro F. Ataide
Summary: SRP plays a crucial role in co-translational delivery of proteins, but recent studies have revealed its involvement in various cellular and molecular pathways. Understanding the noncanonical functions of SRP components could pave the way for targeted therapies in diseases associated with SRP dysregulation.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Ting Huang, Dan Yu, Xiuqin Wang
Summary: WRKY transcription factors are a crucial regulator family in plants, with VvWRKY22 playing a significant role in sugar accumulation in grapes. By interacting with sugar-related genes and kinases, VvWRKY22 regulates sugar metabolism in grapes.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Review
Biochemistry & Molecular Biology
Naoyuki Taniguchi, Yuki Ohkawa, Kento Maeda, Yoichiro Harada, Masamichi Nagae, Yasuhiko Kizuka, Hideyuki Ihara, Yoshitaka Ikeda
Summary: Cancer-related changes in glycans on cell surface proteins are regulated by glycosyltransferases and related genes, which play key roles in cancer metastasis and invasion. The significance of EMT and N-glycan branching glycosyltransferases needs to be reconsidered for potential therapeutic strategies. Specific glycosyltransferases involved in EMT or MET pathways may be difficult to define due to their roles in intermediate states.
MOLECULAR ASPECTS OF MEDICINE
(2021)
Article
Biophysics
Saeko Yanaka, Yoshiki Yamaguchi, Takeshi Takizawa, Yohei Miyanoiri, Rina Yogo, Ichio Shimada, Koichi Kato
Summary: The N-glycosylation at the Fc portion of IgG plays a critical role in defensive effector functions. Degalactosylation was found to structurally perturb the Fc region in a solution-based analysis.
BIOMOLECULAR NMR ASSIGNMENTS
(2021)
Article
Biochemistry & Molecular Biology
Sushil K. Mishra, Yoshiki Yamaguchi, Makoto Higuchi, Naruhiko Sahara
Summary: This study utilized molecular modeling to investigate the binding of PET probes to tau filaments from patients with Pick's disease, identifying binding sites, modes, and energies. Among the probes tested, PM-PBB3 showed the strongest binding affinity, suggesting potential for the rational design of PET tracers specific to Pick's disease in the future.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Masamichi Nagae, Kei Suzuki, Norihisa Yasui, Terukazu Nogi, Takao Kohno, Mitsuharu Hattori, Junichi Takagi
Summary: Reelin is a glycoprotein that regulates embryonic brain development and adult brain functions. Its N-terminal region is crucial for multimer formation and efficient signal transduction.
JOURNAL OF BIOCHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Shiho Ohno, Noriyoshi Manabe, Takumi Yamaguchi, Jun Uzawa, Yoshiki Yamaguchi
Summary: Ribitol, an acyclic sugar alcohol found in mammalian alpha-dystroglycan, exhibits conformational asymmetry influenced by hydrogen bonds and steric hinderance. Solid-state and solution NMR spectra show differences in chemical shifts. Molecular dynamics simulations reveal the presence of asymmetric conformations in ribitol.
Article
Biochemistry & Molecular Biology
Kyoka Hoshi, Hiromi Ito, Eriko Abe, Takashi J. Fuwa, Mayumi Kanno, Yuta Murakami, Mitsunari Abe, Takenobu Murakami, Akioh Yoshihara, Yoshikazu Ugawa, Takashi Saito, Takaomi C. Saido, Kana Matsumoto, Yoshiki Yamaguchi, Katsutoshi Furukawa, Hiroyuki Arai, Mitsuyasu Kanai, Masakazu Miyajima, Hajime Arai, Norihiro Ogawa, Hiroyasu Akatsu, Yoshio Hashizume, Hiroaki Tateno, Takashi Honda, Yasuhiro Hashimoto
Summary: The study explored glycan-biomarkers on Tf in cerebrospinal fluid, finding that Man-Tf levels were significantly increased in patients with AD and MCI, correlating well with p-tau levels. Man-Tf could be a new biomarker for AD.
Review
Biochemistry & Molecular Biology
Shunli Pan, Noriyoshi Manabe, Yoshiki Yamaguchi
Summary: IgG is the most studied immunoglobin class currently, while IgA and IgM play a crucial role in mucosal immunity. These immunoglobulins have complex structures, but with emerging technologies, there is increasing understanding of the 3D structures and structure-function relationships of IgA and IgM.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Reina F. Osuka, Tetsuya Hirata, Masamichi Nagae, Miyako Nakano, Hiroyuki Shibata, Ryo Okamoto, Yasuhiko Kizuka
Summary: The N-terminal domain of N-acetylglucosaminyltransferase-V (GnT-V) is crucial for efficient glycosylation and plays a key role in the recognition of glycoprotein substrates. This study revealed that the N domain interacts directly with the substrate polypeptide, providing new insights into the mechanism of substrate-selective biosynthesis of N-glycans.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Immunology
Xiuyuan Lu, Yuki Hosono, Masamichi Nagae, Shigenari Ishizuka, Eri Ishikawa, Daisuke Motooka, Yuki Ozaki, Nicolas Sax, Yuichi Maeda, Yasuhiro Kato, Takayoshi Morita, Ryo Shinnakasu, Takeshi Inoue, Taishi Onodera, Takayuki Matsumura, Masaharu Shinkai, Takashi Sato, Shota Nakamura, Shunsuke Mori, Teru Kanda, Emi E. Nakayama, Tatsuo Shioda, Tomohiro Kurosaki, Kiyoshi Takeda, Atsushi Kumanogoh, Hisashi Arase, Hironori Nakagami, Kazuo Yamashita, Yoshimasa Takahashi, Sho Yamasaki
Summary: Through single-cell TCR and RNA sequencing, researchers identified public cTfh clonotypes expanded in recovered COVID-19 patients, determined their epitopes in the conserved regions of spike protein, and found that these epitopes may be valuable candidates for booster antigens to enhance adaptive immunity against the virus.
JOURNAL OF EXPERIMENTAL MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Amol M. Vibhute, Hide-nori Tanaka, Sushil K. Mishra, Reina F. Osuka, Masamichi Nagae, Chizuko Yonekawa, Hiroaki Korekane, Robert J. Doerksen, Hiromune Ando, Yasuhiko Kizuka
Summary: This study aims to design novel inhibitors for GnT-V by chemically synthesizing a series of UDP-GlcNAc analogs and testing their inhibitory effects on GnT-V. The results show that although these analogs have modest inhibition potency, they exhibit a certain selectivity for GnT-V. Additionally, the docking models provide insights into the interactions and inhibitory mechanisms between these analogs and GnT-V.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2022)
Article
Biochemistry & Molecular Biology
Kyoka Hoshi, Mayumi Kanno, Mitsunari Abe, Takenobu Murakami, Yoshikazu Ugawa, Aya Goto, Takashi Honda, Takashi Saito, Takaomi C. Saido, Yoshiki Yamaguchi, Masakazu Miyajima, Katsutoshi Furukawa, Hiroyuki Arai, Yasuhiro Hashimoto
Summary: CSF protein levels may be associated with neurodegenerative diseases, particularly Alzheimer's disease. Increased CSF protein levels in CN subjects are positively correlated with AD markers, while correlations decline in MCI and AD patients with AD markers.
Article
Biology
Masamichi Nagae, Tetsuya Hirata, Hiroaki Tateno, Sushil K. Mishra, Noriyoshi Manabe, Naoko Osada, Yuko Tokoro, Yoshiki Yamaguchi, Robert J. Doerksen, Toshiyuki Shimizu, Yasuhiko Kizuka
Summary: X-ray crystallography, NMR, and computer modeling were used to investigate the structure and catalytic mechanism of GnTIVa, an enzyme involved in the synthesis of GlcNAc branches. The enzyme contains a C-terminal lectin domain that regulates its activity. The lectin domain was found to interact selectively with N-glycans having a beta 1-4 GlcNAc branch. Our findings provide insights into the biosynthesis of branching structures in N-glycans.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Naoko Osada, Masamichi Nagae, Miyako Nakano, Tetsuya Hirata, Yasuhiko Kizuka
Summary: In this study, the authors found that GnT-IVa and GnT-IVb have different preferences for glycoprotein substrates in both cells and in vitro. They discovered that the noncatalytic C-terminal lectin domain regulates the substrate selectivity of these enzymes, providing a new mechanism for the formation of N-glycan branches on glycoproteins.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Noriyoshi Manabe, Shiho Ohno, Kana Matsumoto, Taiji Kawase, Kenji Hirose, Katsuyoshi Masuda, Yoshiki Yamaguchi
Summary: The determination of glycan structures is crucial for understanding the relationship between structure and function of glycans and glycoconjugates. Mass spectrometry is an effective method for analyzing glycan structures due to its high sensitivity and mass resolution. In this study, we propose a rapid and precise method for identifying N-glycan structures using ultraperformance liquid chromatography-connected ion mobility mass spectrometry (UPLC/IM-MS). We validate this methodology by examining 71 pyridylaminated (PA-) N-linked oligosaccharides, including isomeric pairs. By establishing a database of m/z, CCS index, and normalized retention time (GU), we provide a practical strategy for structural analysis of N-linked glycans.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Multidisciplinary Sciences
Kensuke Shibata, Chihiro Motozono, Masamichi Nagae, Takashi Shimizu, Eri Ishikawa, Daisuke Motooka, Daisuke Okuzaki, Yoshihiro Izumi, Masatomo Takahashi, Nao Fujimori, James B. Wing, Takahide Hayano, Yoshiyuki Asai, Takeshi Bamba, Yoshihiro Ogawa, Makoto Furutani-Seiki, Mutsunori Shirai, Sho Yamasaki
Summary: By studying a Bcl11b-deficient mouse model, the authors found that MR1-reactive T cells have pathogenic potential and that MR1 functions as an antigen presenting protein on cells other than MAIT cells.
NATURE COMMUNICATIONS
(2022)
