Article
Biochemistry & Molecular Biology
Zachary L. Klamer, Chelsea M. Harris, Jonathan M. Beirne, Jessica E. Kelly, Jian Zhang, Brian B. Haab
Summary: Glycan arrays are widely used to determine the specific glycans that proteins can bind to. However, there is no common method or resource to analyze and use the increasing amount of glycan-array data. To address this issue, the researchers developed CarboGrove, a resource of analyzed glycan-array data that allows the integration and analysis of data from various sources. They demonstrated that CarboGrove can provide unprecedented access to glycan-array data and has powerful capabilities for both experimentalists and bioinformaticians.
Review
Biochemistry & Molecular Biology
Kenichi Kasai
Summary: Frontal affinity chromatography (FAC) is a versatile research method that overcomes inherent difficulties to provide accurate information on weak interactions, with great potential to solve difficult problems in general bioscience.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2021)
Review
Biochemistry & Molecular Biology
Suguru Oguri
Summary: This minireview summarizes the current literature on chitin-binding lectins in plants, focusing on the role of tomato lectin. The study found that tomato lectin has the ability to specifically recognize poly-N-acetyllactosamine and has been used for tissue staining and sugar chain fractionation.
TRENDS IN GLYCOSCIENCE AND GLYCOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Karnpob Kanhasut, Kannan Tharakaraman, Mathuros Ruchirawat, Jutamaad Satayavivad, Mayuree Fuangthong, Ram Sasisekharan
Summary: In this study, we used molecular docking and alanine scanning to predict the interaction model of FGF23-Burosumab and engineered an affinity enhanced variant of the antibody. Our findings provide insights into the mechanism of FGF23-Burosumab interaction and demonstrate the potential of this approach for optimizing therapeutic antibodies.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
James P. Tam, Jiayi Huang, Shining Loo, Yimeng Li, Antony Kam
Summary: Coffee processing waste contains novel microproteins with cell-penetrating and metal ion-binding abilities, including a ginsentide-like microprotein that can target intracellular proteins. These findings suggest that coffee by-products could be a potential source of bioactive peptides for targeting intracellular proteins.
Article
Biochemistry & Molecular Biology
Anna V. Blenda, Nourine A. Kamili, Shang-Chuen Wu, William F. Abel, Diyoly Ayona, Christian Gerner-Smidt, Alex D. Ho, Guy M. Benian, Richard D. Cummings, Connie M. Arthur, Sean R. Stowell
Summary: Galectin-9 has been found to bind various blood group antigens and microbial glycans, exhibiting antimicrobial activity against different strains of microbes and the ability to counteract molecular mimicry.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Monika Jain, Jayaraman Muthukumaran, Amit Kumar Singh
Summary: The comparative structural and functional analysis of chitin-binding lectins from S. tuberosum and S. lycopersicum revealed high percentages of proline residues and differences in binding affinity towards different chitin oligomers. The study showed that the binding of glycans significantly improved the structural stability of STL and SLL. These findings provide insights into the potential therapeutic properties of STL and SLL, laying the foundation for further experimental studies.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Biochemistry & Molecular Biology
Jennifer M. Zupancic, Alec A. Desai, John S. Schardt, Ghasidit Pornnoppadol, Emily K. Makowski, Matthew D. Smith, Andrew A. Kennedy, Mayara Garcia de Mattos Barbosa, Marilia Cascalho, Thomas M. Lanigan, Andrew W. Tai, Peter M. Tessier
Summary: There is a strong interest in developing effective methods for generating neutralizing antibodies and nanobodies against SARS-CoV-2. This study presents a simple directed evolution method for producing nanobodies with high affinities and neutralization activities, which can effectively neutralize both SARS-CoV-2 pseudovirus and live virus.
CELL CHEMICAL BIOLOGY
(2021)
Article
Biochemical Research Methods
Andrea Gottardini, Vincent Dugas, Claire Demesmay
Summary: Affinity chromatography is a powerful technique for identifying and quantifying weak ligand-protein interactions. A novel approach of protein immobilization based on streptavidin-biotin interaction was presented in this study to improve bulk density of active protein, expanding the affinity range of the technique to the millimolar range.
JOURNAL OF CHROMATOGRAPHY A
(2021)
Article
Biotechnology & Applied Microbiology
Sonalina Sahoo, Mohan R. Badhe, Anirban Paul, Pramoda Kumar Sahoo, Amol R. Suryawanshi, Debabrata Panda, Bindu R. Pillai, Bharat Bhusan Patnaik, Jyotirmaya Mohanty
Summary: The study isolated and characterized a lectin from the hepatopancreas of Macrobrachium rosenbergii. The lectin, known as lipopolysaccharide and beta-1,3-glucan binding protein (LGBP), showed hemagglutination like a lectin and exhibited antibacterial activity against certain bacteria. A sandwich ELISA system was developed to quantify LGBP in hepatopancreas and serum samples. The study revealed an increase in LGBP protein concentration in response to bacterial infection, suggesting its role in immunity.
PROBIOTICS AND ANTIMICROBIAL PROTEINS
(2023)
Article
Chemistry, Multidisciplinary
Jacob H. Forstater, Shane T. Grosser
Summary: Immobilization technology plays a significant role in commodity chemical synthesis and pharmaceutical synthesis. This study presents a data-rich approach that automates the screening and development of affinity-based enzyme immobilizations, enabling real-time process characterization and rapid decision making. The developed methodology reduces the time and resources required for immobilization process development and optimization.
REACTION CHEMISTRY & ENGINEERING
(2022)
Article
Physics, Multidisciplinary
Marc Schenkelberger, Christian Trapp, Timo Mai, Varun Giri, Mina Mohammadi-Kambs, Albrecht Ott
Summary: The specificity of molecular recognition is crucial for molecular self-organization, with better matching molecules prevailing over competitors. Fluorescence-based techniques were used to study the recognition of DNA oligonucleotide single strands, revealing reduced affinity for certain strands in the presence of a better matching competitor.
NEW JOURNAL OF PHYSICS
(2021)
Article
Biochemistry & Molecular Biology
Monika Jain, Jayaraman Muthukumaran, Amit Kumar Singh
Summary: Chitin binding lectin from Datura stramonium was studied for its evolutionary significance, structure characterization, and interaction with substrates. Sequence analysis, homology modeling, docking analysis, and MD simulation were used to explore the protein's properties and behavior towards ligands.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Chemistry, Applied
Lucile Lecas, Vincent Dugas, Claire Demesmay
Summary: Affinity chromatography, often overlooked in receptor/ligand studies, offers new perspectives with its simplicity and ability to provide diverse information. Different immobilization strategies have been developed to encompass a wide range of applications, from ligand-ranking to fragment screening and identification of active components from natural extracts.
SEPARATION AND PURIFICATION REVIEWS
(2021)
Article
Chemistry, Analytical
Frederic Jeanroy, Clothilde Comby-Zerbino, Claire Demesmay, Vincent Dugas
Summary: This study investigates the use of a new miniaturized affinity column to capture and elute high-affinity sequences from low molecular weight heparin for further characterization. Direct on-line analysis using MALDI-TOF MS was performed by applying the elution volume from the miniaturized affinity column directly to the MALDI plate.
ANALYTICA CHIMICA ACTA
(2023)
Article
Biochemistry & Molecular Biology
Shin Irumagawa, Keiko Hiemori, Sayoko Saito, Hiroaki Tateno, Ryoichi Arai
Summary: Lectins are proteins that have the ability to bind carbohydrates and they have multiple carbohydrate recognition domains and multivalent binding effects. This study developed functional protein nano-building blocks by fusing lectins to oligomeric proteins, which can self-assemble into various nanostructures. The binding avidity of the lectin nano-blocks to glycans was significantly increased through multivalent effects.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Lalhaba Oinam, Ryoma Hayashi, Keiko Hiemori, Kayo Kiyoi, Kimiyo Sage-Ono, Kenji Miura, Michiyuki Ono, Hiroaki Tateno
Summary: In this study, recombinant Concanavalin A (ConA) was successfully produced in lettuce using the Agrobacterium tumefaciens-mediated transient expression system. The recombinant ConA showed similar glycan-binding specificity and affinity to the native ConA. This study provides a new approach for the recombinant expression of ConA.
BIOTECHNOLOGY AND BIOENGINEERING
(2022)
Article
Gastroenterology & Hepatology
Haruki Odaka, Keiko Hiemori, Asako Shimoda, Kazunari Akiyoshi, Hiroaki Tateno
Summary: In this study, it was found that serum levels of CD63(+)-EVs and platelet-derived EVs (CD41(+)-EVs, CD61(+)-EVs) were significantly increased in patients with PDAC compared to healthy controls. CD63(+)-EVs showed high diagnostic performance in discriminating patients with PDAC from healthy controls and could be potential biomarkers for PDAC.
BMC GASTROENTEROLOGY
(2022)
Article
Biochemistry & Molecular Biology
Yuta Hayashi, Dilimulati Yimiti, Yohei Sanada, Chenyang Ding, Takenori Omoto, Toshihiko Ogura, Tomoyuki Nakasa, Masakazu Ishikawa, Keiko Hiemori, Hiroaki Tateno, Shigeru Miyaki, Nobuo Adachi
Summary: The therapeutic potential of MSC-derived EVs for tissue repair is being explored. The study found that early passaged MSC-EVs accelerate Achilles tendon healing compared with senescent MSC-EVs. Glycans on MSC-EVs may be useful for quality control and isolation of therapeutic MSC-EVs in regenerative medicine.
Article
Urology & Nephrology
Masayuki Tasaki, Hiroaki Tateno, Takashi Sato, Hisashi Narimatsu, Kazuhide Saito, Yuki Nakagawa, Toshinari Aoki, Masami Kamimura, Takashi Ushiki, Kota Takahashi, Yoshihiko Tomita
Summary: The study investigated the reactivity of anti-ABO antibodies detected after ABO-incompatible kidney transplantation with stable graft function to the renal graft endothelial cells, and found that the antibody reactivity was low.
CLINICAL AND EXPERIMENTAL NEPHROLOGY
(2023)
Article
Biochemistry & Molecular Biology
Kazuhiko Yamasaki, Naruhiko Adachi, Mya Myat Ngwe Tun, Akihito Ikeda, Toshio Moriya, Masato Kawasaki, Tomoko Yamasaki, Tomomi Kubota, Izuru Nagashima, Hiroki Shimizu, Hiroaki Tateno, Kouichi Morita
Summary: The N-glycosylation sites on the spike protein of SARS-CoV-2 are relatively invariant and play a crucial role in infection. Core-fucosylated N-glycans have a high affinity for the spike protein and can inhibit viral infection across different variants. Cryogenic electron microscopy revealed that the multivalence of core-fucosylated N-glycans leads to the aggregation of the spike protein. This study highlights the potential for developing specific binders targeted at the spike protein.
Article
Oncology
Yukihito Kuroda, Tatsuya Oda, Osamu Shimomura, Shinji Hashimoto, Yoshimasa Akashi, Yoshihiro Miyazaki, Kinji Furuya, Tomoaki Furuta, Hiromitsu Nakahashi, Pakavarin Louphrasitthiphol, Bryan J. Mathis, Takahito Nakajima, Hiroaki Tateno
Summary: Pancreatic ductal adenocarcinoma (PDAC) is resistant to current treatments but lectin-based phototherapy (Lec-PT) targeting cell surface glycans shows promise as a new therapy. The study combines a PDAC targeting lectin with a photoabsorber to create a near-infrared light-activated therapy. In vitro and in vivo experiments demonstrate cytotoxicity and tumor growth inhibition upon exposure to near-infrared light.
INTERNATIONAL JOURNAL OF CANCER
(2023)
Article
Oncology
Yukihito Kuroda, Tatsuya Oda, Osamu Shimomura, Pakavarin Louphrasitthiphol, Bryan J. Mathis, Hiroaki Tateno, Kentaro Hatano
Summary: By targeting cell surface glycans, a novel class of tumor-specific probes for positron emission tomography (PET) has been developed to improve the early detection of pancreatic ductal adenocarcinoma (PDAC). The PDAC-targeting ability of [F-18]FB-rBC2LCN allows for high-contrast PET imaging of tumors in a mouse model, providing an accurate and sensitive tool for early-stage pancreatic cancer detection.
Article
Cell & Tissue Engineering
Tianwei Huang, Yuya Sato, Akiko Kuramochi, Yoshio Ohba, Masayuki Sano, Makoto Miyagishi, Hiroaki Tateno, Renu Wadhwa, Kazunori Kawasaki, Takeyuki Uchida, Kristina N. Ekdahl, Bo Nilsson, Ung-il Chung, Yuji Teramura
Summary: This study aimed to improve intracellular delivery to endothelial cells by modifying the exosome surface with Tat peptide (YGRKKRRQRRR)-PEG-lipids. Tat-conjugated PEG-lipids with different spacer molecular weights and lipid types were incorporated into exosomes using fluorescein isothiocyanate labeling to optimize the number of Tat-PEG-lipids immobilized on the exosome surface. The exosomes modified with Tat-PEG-lipids showed high detection inside human umbilical vein endothelial cells (HUVECs), indicating improved intracellular delivery.
REGENERATIVE THERAPY
(2023)
Article
Biochemistry & Molecular Biology
Shuuji Mawaribuchi, Osamu Shimomura, Tatsuya Oda, Keiko Hiemori, Kayoko Shimizu, Kenya Yamase, Mutsuhiro Date, Hiroaki Tateno
Summary: Early detection for improving the survival of patients with pancreatic ductal adenocarcinoma (PDAC) is urgently needed. We identified SERPINA3 as a glycoprotein (BC2-S3) secreted from PDAC cells into the blood, which is reactive to rBC2LCN lectin. BC2-S3 exhibited higher levels in PDAC patients and showed a significantly higher detection rate for early stage PDAC than CA19-9.
Meeting Abstract
Oncology
Yukihito Kuroda, Osamu Shimomura, Hiromitsu Nakahashi, Yoshihiro Miyazaki, Takahito Nakajima, Hiroaki Tateno, Tatsuya Oda
Meeting Abstract
Urology & Nephrology
Masayuki Tasaki, Hiroaki Tateno, Takashi Sato, Azusa Tomioka, Hiroyuki Kaji, Hisashi Narimatsu, Kazuhide Saito, Toshinari Aoki, Masami Kamimura, Takashi Ushiki, Yutaka Yoshida, Kota Takahashi, Yoshihiko Tomita
JOURNAL OF UROLOGY
(2022)
Article
Surgery
Masayuki Tasaki, Hiroaki Tateno, Takashi Sato, Azusa Tomioka, Hiroyuki Kaji, Hisashi Narimatsu, Kazuhide Saito, Yuki Nakagawa, Toshinari Aoki, Masami Kamimura, Takashi Ushiki, Manabu Okada, Yuko Miwa, Kiyohiko Hotta, Yutaka Yoshida, Kota Takahashi, Yoshihiko Tomita
Summary: In this study, a new method to measure antibody titer using a microarray of recombinant CD31 linked to ABO antigens was developed. The results showed that this method had higher sensitivity and specificity in predicting antibody-mediated rejection in kidney transplantation compared to traditional isohemagglutinin assays.
TRANSPLANT INTERNATIONAL
(2022)
Meeting Abstract
Oncology
Yukihito Kuroda, Osamu Shimomura, Hiromitsu Nakahashi, Tomoaki Furuta, Yoshihiro Miyazaki, Takahito Nakajima, Hiroaki Tateno, Tatsuya Oda
Article
Biochemical Research Methods
Haruki Odaka, Haruka Ozaki, Hiroaki Tateno
Summary: The article introduces a system for combined analysis of glycan and RNA in single cells, which can reveal the cellular heterogeneity of glycans in multicellular systems. The system combines glycan profiling by sequencing and single-cell transcriptome profiling.