Article
Multidisciplinary Sciences
Lucy I. Crouch, Paulina A. Urbanowicz, Arnaud Basle, Zhi-Peng Cai, Li Liu, Josef Voglmeir, Javier M. Melo Diaz, Samuel T. Benedict, Daniel I. R. Spencer, David N. Bolam
Summary: The human colonic microbiota can utilize complex glycans as a source of nutrients. Gut microbes have a diverse array of carbohydrate-active enzymes that can degrade plant N-glycans. The discovery of these enzymes provides a potential tool for modifying plant N-glycans for various applications.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Genetics & Heredity
Yohana Camila Garay, Romina Beatriz Cejas, Virginia Lorenz, Natacha Zlocowski, Pedro Parodi, Franco Alejandro Ferrero, Genaro Angeloni, Valentina Alfonso Garcia, Victor German Sendra, Ricardo Dante Lardone, Fernando Jose Irazoqui
Summary: ppGalNAc-T3 is a key enzyme in human O-GalNAc glycans biosynthesis, regulated by PTMs, lectin domain, and protein-protein interactions. It is located in the human Golgi apparatus and cell nucleus, playing a central role in cell physiology and various pathologies. Biotechnological tools are proposed as new therapeutic options for managing pathologies.
JOURNAL OF MOLECULAR MEDICINE-JMM
(2022)
Review
Biotechnology & Applied Microbiology
Luis Izquierdo
Summary: Like other microorganisms, pathogenic protozoan parasites rely on glycoconjugates and glycan binding proteins to survive and interact with their hosts. Understanding how glycobiology contributes to their survival and virulence can reveal new aspects of their biology and lead to the development of new strategies against them.
BIOTECHNOLOGY ADVANCES
(2023)
Review
Microbiology
Felix Goerdeler, Peter H. Seeberger, Oren Moscovitz
Summary: Malaria pathogenesis is closely linked to glycans on the surface of Plasmodium parasites and host cells, with complex glycosylphosphatidylinositol (GPI) glycolipids playing a crucial role in parasite survival. Meanwhile, host cell glycocalyx and lectin expression serve as the first line of defense against parasites, directly impacting susceptibility to Plasmodium infection.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Endocrinology & Metabolism
Elham Memarian, Ralph Heijmans, Roderick C. Slieker, Adriana Sierra, Olga Gornik, Joline W. J. Beulens, Maja Hanic, Petra Elders, Julio Pascual, Eric Sijbrands, Gordan Lauc, Viktoria Dotz, Clara Barrios, Leen M. 't Hart, Manfred Wuhrer, Mandy van Hoek
Summary: Inflammation plays an important role in the development of type 2 diabetes complications, and the N-glycosylation of IgG affects its role in inflammation. This study found that IgG N-glycosylation, particularly galactosylation and to a lesser extent sialylation, is associated with a higher prevalence and future development of macro- and microvascular complications of diabetes.
DIABETES-METABOLISM RESEARCH AND REVIEWS
(2023)
Article
Microbiology
Tanya R. McKitrick, Margaret E. Ackerman, Robert M. Anthony, Clay S. Bennett, Michael Demetriou, Gregory A. Hudalla, Katharina Ribbeck, Stefan Ruhl, Christina M. Woo, Loretta Yang, Seth J. Zost, Ronald L. Schnaar, Tamara L. Doering
Summary: Advancements in glycoscience research have revealed the crucial roles of glycan structures in microbial infections and host immune responses, leading to potential improvements in the diagnosis and treatment of infections and immune dysregulation. Ongoing efforts in exploring these roles are expected to enhance fundamental scientific understanding in these fields.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Agriculture, Multidisciplinary
Haiyan Wang, Ximei Zhang, Peng Kang, Xiuxiu Cui, Guo Hao, Zhongfu Wang, Bei Han, Xin Lv, Jing Zhang, Wupeng Ge
Summary: Oligosaccharides and N/O-glycans are abundant in human milk, with variations observed during lactation. Colostrum has the highest levels of oligosaccharides, which decrease as lactation progresses. Sialylated oligosaccharides and N/O-glycans are highly abundant in colostrum.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Review
Oncology
Nora Berois, Alvaro Pittini, Eduardo Osinaga
Summary: Aberrant glycosylation is a common feature of cancer and can lead to changes that affect tumor behavior. Glycans can serve as a source of new clinical biomarkers, providing specific targets for therapeutic intervention. Different mechanisms of aberrant glycosylation lead to the formation of tumor-associated carbohydrate antigens (TACAs) suitable for selective cancer-targeting therapy.
Article
Biochemistry & Molecular Biology
Chie Morikawa, Kanako Sugiura, Keina Kondo, Yurie Yamamoto, Yuma Kojima, Yurika Ozawa, Hiroki Yoshioka, Nobuaki Miura, Jinhua Piao, Kazue Okada, Hisatoshi Hanamatsu, Masumi Tsuda, Shinya Tanaka, Jun-ichi Furukawa, Yasuro Shinohara
Summary: In this study, the alterations in N and free N-glycomic upon addition of SWA to HepG2 cells were analyzed. The results showed specific glycomic alterations induced by SWA, including unique fucosylated hybrid-type and fucosylated M5 (M5F) N-glycans, and a remarkable increase in all classes of Gn1 FNGs. The dynamic nature of glycomic alterations and the accumulation of free N-glycans occurring earlier than that of hybrid-type N-glycans were also observed.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2022)
Article
Biochemistry & Molecular Biology
Marie Petit, Marie-Laure Walet-Balieu, Damien Schapman, Marie-Laure Golinski, Carole Burel, Marion Barray, Laurent Drouot, Maud Maho-Vaillant, Vivien Hebert, Olivier Boyer, Muriel Bardor, Pascal Joly, Sebastien Calbo
Summary: The pathogenicity of serum IgG in pemphigus patients is correlated with disease activity, and alterations in N-glycan structure can affect the in vitro pathogenicity of autoantibodies. The pathogenic properties of pemphigus IgG do not seem to be related to variations in IgG N-glycans during the course of the disease.
Article
Chemistry, Physical
Ana Garcia-Garcia, Sonia Serna, Zhang Yang, Ignacio Delso, Victor Taleb, Thomas Hicks, Raik Artschwager, Sergey Y. Vakhrushev, Henrik Clausen, Jesus Angulo, Francisco Corzana, Niels C. Reichardt, Ramon Hurtado-Guerrero
Summary: Core fucosylation by FUT8 is affected by the underlying peptide sequence for paucimannose and high-mannose N-glycans, but not for complex-type N-glycans. FUT8 recognizes all sugar units and most amino acid residues of the G0 N-glycan, with optimal recognition requiring prior binding to GDP-Fuc. Genetic engineering in CHO cells demonstrated that core fucosylation mainly occurs on complex-type N-glycans, but certain glycosites can acquire Fuc on high-mannose N-glycans.
Article
Chemistry, Analytical
Rui Zhang, Wenjing Peng, Yifan Huang, Sakshi Gautam, Junyao Wang, Yehia Mechref, Haixu Tang
Summary: This paper presents a novel reciprocal best-hit glycan-spectrum matching (RB-GSM) approach for characterizing N-glycans. By evaluating the MS/MS spectra and glycans, this method is capable of accurately distinguishing isomeric glycans.
ANALYTICAL CHEMISTRY
(2022)
Review
Biochemistry & Molecular Biology
Ruben Warkentin, David H. Kwan
Summary: This review provides information on available methods for engineering glycan-binding proteins (GBPs) and highlights the importance of glycans in physiological functions and their applications. Recent advances in glycobiology have largely overcome challenges in developing GBPs.
Article
Chemistry, Multidisciplinary
Aron Gyorgypal, Oscar G. Potter, Antash Chaturvedi, David N. Powers, Shishir P. S. Chundawat
Summary: With the shift towards continuous bioprocessing, process analytical technology (PAT) becomes necessary for real-time monitoring in biotherapeutics manufacturing. The integration of PAT-enabled process control is crucial for ensuring drug product quality attributes, such as protein N-glycosylation, which can change during bioprocessing. However, there is currently no method to measure N-glycosylation using on-line PAT, limiting the effectiveness of upstream process control strategies.
REACTION CHEMISTRY & ENGINEERING
(2023)
Review
Spectroscopy
Alba Hykollari, Katharina Paschinger, Iain B. H. Wilson
Summary: In the past 20 years, the approaches for N-glycan analysis have undergone significant changes, with mass spectrometry emerging as the predominant method in modern glycomics. Improved resolution and detection using MALDI-TOF MS have greatly contributed to the discovery of a wide range of N-glycan structures, aiding in distinguishing glycan variations.
MASS SPECTROMETRY REVIEWS
(2022)
Review
Biochemistry & Molecular Biology
Robbie P. Joosten, Robert A. Nicholls, Jon Agirre
Summary: Macromolecular restrained refinement is a commonly used method to improve the agreement between an atomic structural model and experimental data. This study discusses the functional differences between restraint generators and the process of achieving consistent results. Practical considerations and recommendations for generating new restraint dictionaries are provided.
CURRENT MEDICINAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Ida de Vries, Tim Kwakman, Xiang-Jun Lu, Maarten L. Hekkelman, Mandar Deshpande, Sameer Velankar, Anastassis Perrakis, Robbie P. Joosten
Summary: This article introduces new nucleic acid-specific approaches in PDB-REDO, including a new restraint model using noncovalent geometries as refinement targets, and new validation routines. Overall, applying the PDB-REDO pipeline to the Protein Data Bank has a positive effect on the quality of nucleic acid-containing structure models.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2021)
Article
Biochemical Research Methods
Mihaela Atanasova, Robert A. Nicholls, Robbie P. Joosten, Jon Agirre
Summary: Restraint dictionaries are used in macromolecular structure refinement to preserve intramolecular connectivity and geometric information. Their importance is particularly notable in refining crystal structures of glycosylated proteins. New dictionaries with improved restraints, reflecting the lowest-energy ring pucker and updated geometry, have been developed and evaluated for improved accuracy and will be released with CCP4 version 8.0.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Marjon S. van Ruiten, Demi van Gent, Angela Sedeno Cacciatore, Astrid Fauster, Laureen Willems, Maarten L. Hekkelman, Liesbeth Hoekman, Maarten Altelaar, Judith H. I. Haarhuis, Thijn R. Brummelkamp, Elzo de Wit, Benjamin D. Rowland
Summary: The acetylation of cohesin's SMC3 subunit controls the three-dimensional genome structure in human cells. ESCO1 restricts the length of chromatin loops and architectural stripes, while HDAC8 promotes their extension. Acetylation also controls the interaction of cohesin with PDS5A to limit chromatin loop length.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Editorial Material
Biochemical Research Methods
Jon Agirre, Robbie P. Joosten, Alan Roseman
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Maarten L. Hekkelman, Ida de Vries, Robbie P. Joosten, Anastassis Perrakis
Summary: Artificial intelligence-based protein structure prediction has greatly impacted biomolecular sciences. However, the predicted protein models in the AlphaFold database lack coordinates for small molecules and ions necessary for structure and function. The AlphaFill algorithm addresses this issue by transplanting missing small molecules and ions from experimentally determined structures to predicted protein models.
Article
Biology
Ida de Vries, Danique Ammerlaan, Tatjana Heidebrecht, Patrick H. N. Celie, Daan P. Geerke, Robbie P. Joosten, Anastassis Perrakis
Summary: Base-J (β-D-glucopyranosyloxymethyluracil) is a modified DNA nucleotide that replaces 1% of thymine in kinetoplastid flagellates. The biosynthesis and maintenance of base-J depends on the base-J-binding protein 1 (JBP1) that has a thymidine hydroxylase domain and a J-DNA-binding domain (JDBD). This study presents a crystal structure of the JDBD and proposes recognition models for JDBD binding to J-DNA, which were confirmed by mutagenesis experiments. The findings provide insights into the molecular mechanism of base-J replication.
LIFE SCIENCE ALLIANCE
(2023)
