Article
Biochemical Research Methods
Jiechen Shen, Li Jia, Liuyi Dang, Yuanjie Su, Jie Zhang, Yintai Xu, Bojing Zhu, Zexuan Chen, Jingyu Wu, Rongxia Lan, Zhifang Hao, Chen Ma, Ting Zhao, Ni Gao, Jieyun Bai, Yuan Zhi, Jun Li, Junying Zhang, Shisheng Sun
Summary: This study introduces a modularization strategy and an algorithm named StrucGP for automated interpretation of N-glycan structures using tandem mass spectrometry, enabling detailed glycan structure determination on thousands of glycosites. The approach aids in identifying rare/new glycan structures and facilitates in-depth structural and functional study of glycoproteins in the biomedical research field. StrucGP offers a novel de novo glycan mapping method for determining detailed N-glycan structures at the site-specific level.
Article
Biochemical Research Methods
Jiangming Huang, Shouzeng Hou, Jiao An, Chenliang Zhou
Summary: In this study, a full characterization of N-glycosylation was performed for a Chinese Hamster Ovary (CHO) cell expressed variant-designed spike protein. The study revealed 19 N-glycosites at intact N-glycopeptide level and identified 31 high-abundance N-glycans through quantitative analysis by LC-MS/MS. Sequencing analysis of glycans confirmed the glycan structure. The results showed good batch-to-batch consistency, providing valuable information for SARS-CoV-2 spike protein analysis and quality studies.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Luyao Liu, Bin Zhu, Zheng Fang, Na Zhang, Hongqiang Qin, Zhimou Guo, Xinmiao Liang, Zhenzhen Yao, Mingliang Ye
Summary: Bottom-up proteomics is increasingly used in clinical research, but glycoproteomic analysis has been a bottleneck. An automated glycopeptide enrichment method was developed for site-specific N-glycoproteome analysis, showing higher efficiency and reliability.
ANALYTICAL CHEMISTRY
(2021)
Review
Food Science & Technology
Boyuan Guan, Zhenghan Zhang, Yuxia Chai, Xiakouna Amantai, Xinping Chen, Xueyan Cao, Xiqing Yue
Summary: This article summarizes the synthetic pathways, types, and distribution characteristics of protein N-glycosylation in milk, exploring further research supported by mass spectrometry and bioinformatics algorithms. N-glycosylation of milk proteins plays a crucial role in dairy processing and metabolism, impacting intestinal microbiota, immune function, and brain development.
TRENDS IN FOOD SCIENCE & TECHNOLOGY
(2022)
Article
Chemistry, Analytical
Myung Jin Oh, Unyong Kim, Sol Kim, Dae Sik Cho, Jung-A Seo, Nari Seo, Joo An
Summary: Glycosylation plays a crucial role in the quality, stability, safety, immunogenicity, pharmacokinetics, and efficacy of biotherapeutics. Various methods have been used for glyco-characterization at different levels. Intact protein analysis is considered a rapid glycoform monitoring approach; however, it can be challenging for biotherapeutics with multiple glycosylation sites. A new strategy using two-step intact glycoform mass spectrometry has been developed to address this challenge, providing rapid and accurate information on the degree of glycosylation. This method can be used to assess glycosylation similarity between batches and between biosimilar and reference during development and production.
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
(2023)
Review
Biochemical Research Methods
Elli Makrydaki, Pavlos Kotidis, Karen M. Polizzi, Cleo Kontoravdi
Summary: N-glycosylation is crucial for understanding human disease mechanisms and ensuring the safety and efficacy of biotherapeutics. Capillary electrophoresis is emerging as a versatile and adaptable method for glycan analysis due to its speed, sensitivity, and complementarity with standard techniques, making it increasingly used in academia and industry for glycomics and glycoproteomics.
CURRENT OPINION IN BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Chunqun Wang, Wenjie Gao, Shi Yan, Xing-Quan Zhu, Xun Suo, Xin Liu, Nishith Gupta, Min Hu
Summary: N-glycosylation is a physiologically vital post-translational modification in eukaryotic organisms, and Haemonchus contortus has exclusive chitobiose modifications in its N-glycans. Immunogenic proteins like peptidases are N-glycosylated in the parasite, with glycan-rich conjugates primarily located in the intestine and gonads of adult worms, evading host immune responses. This comprehensive atlas of N-glycosylation in the prevalent parasitic nematode highlights its importance for infection, immunity, and prevention.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Chemistry, Analytical
Chia Yen Liew, Hong-Sheng Luo, Ting-Yi Yang, An-Ti Hung, Bryan John Abel Magoling, Charles Pin-Kuang Lai, Chi-Kung Ni
Summary: This study re-examines high mannose N-glycans in multicellular eukaryotes using a new mass spectrometry method, and identifies many previously unreported isomers. A database is constructed for rapid identification of high mannose N-glycan isomers.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Tomoki Himiyama, Yuko Tsuchiya, Yasushige Yonezawa, Tsutomu Nakamura
Summary: This study successfully disrupted and reconstituted the quaternary structure of ApPrx through amino acid mutations and chemical modifications. The research demonstrates a facile method to regulate the protein assembly state.
BIOCONJUGATE CHEMISTRY
(2021)
Article
Biochemical Research Methods
Dinko Soic, Toma Keser, Jerko Stambuk, Domagoj Kifer, Flemming Pociot, Gordan Lauc, Grant Morahan, Mislav Novokmet, Olga Gornik
Summary: Recent studies have shown that children with early-onset type 1 diabetes (T1D) have a higher proportion of oligomannose glycans in their plasma protein N-glycome compared to healthy siblings. This study aimed to characterize the glycosylation profile of complement component C3 in T1D and found significant changes in C3 N-glycan profiles associated with T1D. The study also confirmed the involvement of C3 N-glycome in T1D development.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Multidisciplinary Sciences
Rasia C. Li, Madeline Y. Wong, Andrew S. DiChiara, Azade S. Hosseini, Matthew D. Shoulders
Summary: The N-glycan in the C-Pro domain of procollagen plays an essential role in promoting folding and secretion, particularly under proteostatic challenge, by providing access to the ER's lectin-based chaperone machinery. This context-dependent function of the N-glycan buffers against misfolding and helps maintain proteostasis during collagen production processes such as development and wound healing.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Akos Tiboldi, Johannes Fuehrer, Wolfgang Schaubmayr, Eva Hunyadi-Gulyas, Marie Louise Zach, Beatrix Hochreiter, Andreas Spittler, Roman Ullrich, Klaus Markstaller, Friedrich Altmann, Klaus Ulrich Klein, Verena Tretter
Summary: This study investigated the effects of different oxygen conditions on the glycobiology of the pulmonary endothelium, showing that oxygen can influence glycan structures which in turn affect cell interactions and signaling.
Article
Multidisciplinary Sciences
Zheng Fang, Hongqiang Qin, Jiawei Mao, Zhongyu Wang, Na Zhang, Yan Wang, Luyao Liu, Yongzhan Nie, Mingming Dong, Mingliang Ye
Summary: The traditional site-specific glycoproteomics analysis often fails to account for glycopeptides with unusual glycans or poor peptide backbone fragmentation. In this study, a glycoproteomics tool called Glyco-Decipher is developed to address these issues. Glyco-Decipher utilizes database-independent peptide matching and the fragmentation pattern of shared peptide backbones to improve spectrum interpretation. Benchmark tests demonstrate that Glyco-Decipher identifies more peptide-spectrum matches than other existing tools, resulting in a significant increase in the number of identified glycopeptide spectra. By enabling unbiased profiling of attached glycans, Glyco-Decipher enables the discovery of modified glycans in mouse tissues, including those with chemical or biological modifications. This tool holds great promise for advancing glycoproteomics analysis in biological research.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Mingming Xu, Hong Jin, Wei Ge, Lingbo Zhao, Zhaoliang Liu, Zeyu Guo, Zhen Wu, Jing Chen, Chengjie Mao, Xumin Zhang, Chun-Feng Liu, Shuang Yang
Summary: Urine contains a wide range of glycoproteins, peptides, and free glycans, which can provide earlier and more sensitive molecular changes for biomarker discovery. Urine biomarkers have great diagnostic potential and are easy to collect and analyze non-invasively. The investigation of abnormal protein glycosylation in urine may shed light on the identification of disease-specific glycosylation biomarkers for Parkinson's disease.
ACS CHEMICAL NEUROSCIENCE
(2023)
Article
Biochemical Research Methods
Simon Ngao Mule, Livia Rosa-Fernandes, Joao V. P. Coutinho, Vinicius De Morais Gomes, Janaina Macedo-da-Silva, Veronica Feijoli Santiago, Daniel Quina, Gilberto Santos de Oliveira, Morten Thaysen-Andersen, Martin R. Larsen, Leticia Labriola, Giuseppe Palmisano
Summary: A novel method called limited deglycosylation assay (LDA) is introduced to investigate conformational changes of glycoproteins on a systems-wide scale. LDA combines site and conformation-specific PNGase F enzymatic activity with quantitative proteomics, providing avenues for studying glycoprotein structural changes in various physiological and pathophysiological conditions.
JOURNAL OF PROTEOMICS
(2021)
Article
Biochemical Research Methods
Sarah K. Osama, Edward D. Kerr, Adel M. Yousif, Toan K. Phung, Alison M. Kelly, Glen P. Fox, Benjamin L. Schulz
Summary: Germination is a critical process for flowering plant reproduction and industrial malting, while seed dormancy can lead to inefficiencies in malt production. Proteomic analysis identified significant changes during germination, including a rapid decrease in proteins involved in desiccation tolerance and germination inhibition, as well as reductions in lipid, protein, and nutrient reservoir storage. These consistent changes between laboratory and industrial scales demonstrate the utility of laboratory-scale germination as a model system for industrial malt house processes.
JOURNAL OF PROTEOMICS
(2021)
Review
Biochemical Research Methods
Shulei Liu, Benjamin L. Schulz
Summary: Mass spectrometry is a powerful technique widely used in biopharmaceutical quality control for protein identification, quantification and characterization, providing data on protein quantity, structural integrity and post-translational modifications.
Article
Multidisciplinary Sciences
Edward D. Kerr, Christopher H. Caboche, Cassandra L. Pegg, Toan K. Phung, Claudia Gonzalez Viejo, Sigfredo Fuentes, Mark T. Howes, Kate Howell, Benjamin L. Schulz
Summary: Beer is a popular beverage with high molecular complexity, where research has shown a diverse range of post-translational modifications within the proteome. Proteolysis, glycation, and glycosylation were found to be prevalent, particularly in barley and yeast proteins. Brewery origin and beer styles were found to influence the glyco/proteome profile, with distinct features identified in specific beer varieties such as darker beers. The quality properties of foam formation and stability were correlated with surface-active proteins from barley and yeast.
SCIENTIFIC REPORTS
(2021)
Article
Biology
Hugo D. Perdomo, Mazhar Hussain, Rhys Parry, Kayvan Etebari, Lauren M. Hedges, Guangmei Zhang, Benjamin L. Schulz, Sassan Asgari
Summary: The study demonstrated that human blood miRNAs can be abundantly transported into the fat body tissue of Aedes aegypti, affecting and regulating mosquito gene expression. By feeding mosquitoes with a mimic of human blood miRNA and conducting proteomics analysis, over 40 proteins were found to show differential expression in female Ae. aegypti mosquitoes after feeding. The miRNA was shown to positively regulate vitellogenin, which plays a role in egg production, potentially impacting progeny production in Ae. aegypti.
COMMUNICATIONS BIOLOGY
(2021)
Correction
Biochemical Research Methods
Rebeca Kawahara, Anastasia Chernykh, Kathirvel Alagesan, Marshall Bern, Weiqian Cao, Robert J. Chalkley, Kai Cheng, Matthew S. Choo, Nathan Edwards, Radoslav Goldman, Marcus Hoffmann, Yingwei Hu, Yifan Huang, Jin Young Kim, Doron Kletter, Benoit Liquet, Mingqi Liu, Yehia Mechref, Bo Meng, Sriram Neelamegham, Terry Nguyen-Khuong, Jonas Nilsson, Adam Pap, Gun Wook Park, Benjamin L. Parker, Cassandra L. Pegg, Josef M. Penninger, Toan K. Phung, Markus Pioch, Erdmann Rapp, Enes Sakalli, Miloslav Sanda, Benjamin L. Schulz, Nichollas E. Scott, Georgy Sofronov, Johannes Stadlmann, Sergey Y. Vakhrushev, Christina M. Woo, Hung-Yi Wu, Pengyuan Yang, Wantao Ying, Hui Zhang, Yong Zhang, Jingfu Zhao, Joseph Zaia, Stuart M. Haslam, Giuseppe Palmisano, Jong Shin Yoo, Goran Larson, Kai-Hooi Khoo, Katalin F. Medzihradszky, Daniel Kolarich, Nicolle H. Packer, Morten Thaysen-Andersen
Article
Chemistry, Multidisciplinary
Aoife M. Harbison, Carl A. Fogarty, Toan K. Phung, Akash Satheesan, Benjamin L. Schulz, Elisa Fadda
Summary: The dense glycan shield of the SARS-CoV-2 spike plays a crucial role in immune evasion and activating the prefusion conformation. Recent studies have shown that the structures and occupancy of SARS-CoV-2 S glycans depend on both the host cell and the stability of the trimer. The type of glycosylation at specific sites greatly affects the stability of the receptor binding domain conformation, and the loss of glycosylation at another site may have contributed to increased infectivity.
Review
Biotechnology & Applied Microbiology
Aiden C. Beauglehole, Dinora Roche Recinos, Cassandra L. Pegg, Yih Yean Lee, Victor Turnbull, Susann Herrmann, Esteban Marcellin, Christopher B. Howard, Benjamin L. Schulz
Summary: Appropriate treatment of Hemophilia B is crucial, and advancements in recombinant technologies have allowed for the production of Factor IX. However, the complex post-translational modifications of Factor IX have posed challenges for large-scale recombinant production. Further research is needed to optimize the production methods.
CRITICAL REVIEWS IN BIOTECHNOLOGY
(2023)
Review
Biochemical Research Methods
Shulei Liu, Edward D. Kerr, Cassandra L. Pegg, Benjamin L. Schulz
Summary: This article reviews recent studies on proteomic and glycoproteomic analyses of beer and wine. Many grape and yeast proteins are glycosylated, while barley proteins can be glycated during the beer making process. The use of high-resolution mass spectrometry allows for the identification, quantification, and characterization of the glyco/proteomes of fermented beverages, which helps in controlling the quality of the final products.
Review
Food Science & Technology
Daniel J. Ellis, Edward D. Kerr, Gerhard Schenk, Benjamin L. Schulz
Summary: Fermented beverages are a global industry, currently dominated by Saccharomyces yeasts. However, consumer demands for alternative products with different sensory profiles and health benefits are increasing the use of non-Saccharomyces yeasts. These yeasts produce diverse secondary metabolites, leading to a variety of flavors and sensory characteristics in fermented beverages. This review explores the use of metabolomic analyses to study the impact of non-Saccharomyces yeasts on sensory characteristics, highlighting key species currently used and emphasizing the potential for their use in producing diverse fermented beverages.
Article
Chemistry, Applied
Hai-Teng Li, Edward D. Kerr, Benjamin L. Schulz, Michael J. Gidley, Sushil Dhital
Summary: The popularity of high-amylose cultivars of main crops is increasing due to their unique properties and enhanced nutritional values. This study evaluated the performance of high-amylose wheat (HAW) flours and starches with different amylose contents under high-temperature processing. The results showed that conventional RVA could not predict the pasting behaviors of HAW ingredients accurately, and the iodine colorimetry method was not a good indicator of the cooling and retrogradation process. Protein content and composition also influenced the pasting behaviors of HAW flours, and fine structural features of amylose and amylopectin played a regulatory role.
FOOD HYDROCOLLOIDS
(2022)
Article
Biochemistry & Molecular Biology
Cassandra L. Pegg, Benjamin L. Schulz, Benjamin A. Neely, Gregory F. Albery, Colin J. Carlson
Summary: Sugars that coat viruses and host cells play a crucial role in disease transmission, but their study is often neglected. Understanding glycosylation and utilizing it for predictive science can bridge the knowledge gap in zoonotic risk assessment.
Article
Multidisciplinary Sciences
Ariel Isaacs, Yu Shang Low, Kyle L. L. Macauslane, Joy Seitanidou, Cassandra L. L. Pegg, Stacey T. M. Cheung, Benjamin Liang, Connor A. P. Scott, Michael J. J. Landsberg, Benjamin L. L. Schulz, Keith J. J. Chappell, Naphak Modhiran, Daniel Watterson
Summary: In 2022, a novel henipavirus called Langya virus (LayV) was discovered in China, which is closely related to Mojiang virus (MojV) and different from bat-borne henipaviruses, such as Nipah (NiV) and Hendra (HeV) viruses. This is the first documented case of human infection with a HNV other than NiV and HeV, highlighting the potential danger of this virus genus to human health.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Medicinal
Freda E. -C. Jen, Jodie L. Abrahams, Benjamin L. Schulz, Araceli Lamelas, Gerd Pluschke, Michael P. Jennings
Summary: In the meningitis belt of sub-Saharan Africa, cyclic meningococcal epidemics coincide with clonal waves of Neisseria meningitidis. A whole-genome sequencing study with meningococcal isolates collected during outbreaks identified the pilin glycosylation (pgl) locus as a hotspot of recombination. The exchange of pgl genes in N. meningitidis results in variable glycosylation patterns of pilin and other surface glycoproteins. Investigating pilin glycosylation can shed light on bacterial adaptation and potential targets for therapies and vaccines.
ACS INFECTIOUS DISEASES
(2023)
Review
Microbiology
Kyle L. Macauslane, Cassandra L. Pegg, Kirsty R. Short, Benjamin L. Schulz
Summary: Acute respiratory infections (ARIs) are a major cause of death and disability, with the greatest impact on children, pregnant women, and the elderly. Respiratory viruses are the main culprits behind ARIs. The unfolded protein response (UPR) is a defense mechanism activated in response to viral infection, and it plays a role in the pathogenesis of respiratory diseases. Many respiratory viruses manipulate the UPR during infection, affecting both the host and the pathogens. Modulating the UPR may have therapeutic potential in virally induced respiratory diseases.
CRITICAL REVIEWS IN MICROBIOLOGY
(2023)
Meeting Abstract
Biochemistry & Molecular Biology
Carl Fogarty, Aoife M. Harbison, Toan K. Phung, Akash Satheesan, Benjamin L. Schulz, Elisa Fadda