1
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Kizuka Y. Regulation of intracellular activity of N-glycan branching enzymes in mammals. J Biol Chem 2024; 300:107471. [PMID: 38879010 PMCID: PMC11328876 DOI: 10.1016/j.jbc.2024.107471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 06/01/2024] [Accepted: 06/06/2024] [Indexed: 07/07/2024] Open
Abstract
Most proteins in the secretory pathway are glycosylated, and N-glycans are estimated to be attached to over 7000 proteins in humans. As structural variation of N-glycans critically regulates the functions of a particular glycoprotein, it is pivotal to understand how structural diversity of N-glycans is generated in cells. One of the major factors conferring structural variation of N-glycans is the variable number of N-acetylglucosamine branches. These branch structures are biosynthesized by dedicated glycosyltransferases, including GnT-III (MGAT3), GnT-IVa (MGAT4A), GnT-IVb (MGAT4B), GnT-V (MGAT5), and GnT-IX (GnT-Vb, MGAT5B). In addition, the presence or absence of core modification of N-glycans, namely, core fucose (included as an N-glycan branch in this manuscript), synthesized by FUT8, also confers large structural variation on N-glycans, thereby crucially regulating many protein-protein interactions. Numerous biochemical and medical studies have revealed that these branch structures are involved in a wide range of physiological and pathological processes. However, the mechanisms regulating the activity of the biosynthetic glycosyltransferases are yet to be fully elucidated. In this review, we summarize the previous findings and recent updates regarding regulation of the activity of these N-glycan branching enzymes. We hope that such information will help readers to develop a comprehensive overview of the complex system regulating mammalian N-glycan maturation.
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Affiliation(s)
- Yasuhiko Kizuka
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu, Japan.
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2
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Krishna S, Jung ST, Lee EY. Escherichia coli and Pichia pastoris: microbial cell-factory platform for -full-length IgG production. Crit Rev Biotechnol 2024:1-23. [PMID: 38797692 DOI: 10.1080/07388551.2024.2342969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 03/18/2024] [Indexed: 05/29/2024]
Abstract
Owing to the unmet demand, the pharmaceutical industry is investigating an alternative host to mammalian cells to produce antibodies for a variety of therapeutic and research applications. Regardless of some disadvantages, Escherichia coli and Pichia pastoris are the preferred microbial hosts for antibody production. Despite the fact that the production of full-length antibodies has been successfully demonstrated in E. coli, which has mostly been used to produce antibody fragments, such as: antigen-binding fragments (Fab), single-chain fragment variable (scFv), and nanobodies. In contrast, Pichia, a eukaryotic microbial host, is mostly used to produce glycosylated full-length antibodies, though hypermannosylated glycan is a major challenge. Advanced strategies, such as the introduction of human-like glycosylation in endotoxin-edited E. coli and cell-free system-based glycosylation, are making progress in creating human-like glycosylation profiles of antibodies in these microbes. This review begins by explaining the structural and functional requirements of antibodies and continues by describing and analyzing the potential of E. coli and P. pastoris as hosts for providing a favorable environment to create a fully functional antibody. In addition, authors compare these microbes on certain features and predict their future in antibody production. Briefly, this review analyzes, compares, and highlights E. coli and P. pastoris as potential hosts for antibody production.
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Affiliation(s)
- Shyam Krishna
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Sang Taek Jung
- BK21 Graduate Program, Department of Biomedical Sciences, Graduate School, Korea University, Seoul, Republic of Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
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3
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López-Cortés R, Muinelo-Romay L, Fernández-Briera A, Gil Martín E. High-Throughput Mass Spectrometry Analysis of N-Glycans and Protein Markers after FUT8 Knockdown in the Syngeneic SW480/SW620 Colorectal Cancer Cell Model. J Proteome Res 2024; 23:1379-1398. [PMID: 38507902 PMCID: PMC11002942 DOI: 10.1021/acs.jproteome.3c00833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 03/22/2024]
Abstract
Disruption of the glycosylation machinery is a common feature in many types of cancer, and colorectal cancer (CRC) is no exception. Core fucosylation is mediated by the enzyme fucosyltransferase 8 (FucT-8), which catalyzes the addition of α1,6-l-fucose to the innermost GlcNAc residue of N-glycans. We and others have documented the involvement of FucT-8 and core-fucosylated proteins in CRC progression, in which we addressed core fucosylation in the syngeneic CRC model formed by SW480 and SW620 tumor cell lines from the perspective of alterations in their N-glycosylation profile and protein expression as an effect of the knockdown of the FUT8 gene that encodes FucT-8. Using label-free, semiquantitative mass spectrometry (MS) analysis, we found noticeable differences in N-glycosylation patterns in FUT8-knockdown cells, affecting core fucosylation and sialylation, the Hex/HexNAc ratio, and antennarity. Furthermore, stable isotopic labeling of amino acids in cell culture (SILAC)-based proteomic screening detected the alteration of species involved in protein folding, endoplasmic reticulum (ER) and Golgi post-translational stabilization, epithelial polarity, and cellular response to damage and therapy. This data is available via ProteomeXchange with identifier PXD050012. Overall, the results obtained merit further investigation to validate their feasibility as biomarkers of progression and malignization in CRC, as well as their potential usefulness in clinical practice.
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Affiliation(s)
- Rubén López-Cortés
- Doctoral
Program in Methods and Applications in Life Sciences, Faculty of Biology, Universidade de Vigo, Campus Lagoas-Marcosende, 36310 Vigo, Pontevedra (Galicia), Spain
| | - Laura Muinelo-Romay
- Liquid
Biopsy Analysis Unit, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago de Compostela
(IDIS), CIBERONC, Travesía da Choupana, 15706 Santiago de Compostela, A Coruña
(Galicia), Spain
| | - Almudena Fernández-Briera
- Molecular
Biomarkers, Biomedical Research Centre (CINBIO), Universidade de Vigo, Campus Lagoas-Marcosende, 36310 Vigo, Pontevedra (Galicia), Spain
| | - Emilio Gil Martín
- Nutrition
and Food Science Group, Department of Biochemistry, Genetics and Immunology,
Faculty of Biology, Universidade de Vigo, Campus Lagoas-Marcosende, 36310 Vigo, Pontevedra (Galicia), Spain
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4
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Zhang Y, Lai Z, Yuan Z, Qu B, Li Y, Yan W, Li B, Yu W, Cai S, Zhang H. Serum disease-specific IgG Fc glycosylation as potential biomarkers for nonproliferative diabetic retinopathy using mass spectrometry. Exp Eye Res 2023:109555. [PMID: 37364630 DOI: 10.1016/j.exer.2023.109555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 06/08/2023] [Accepted: 06/23/2023] [Indexed: 06/28/2023]
Abstract
OBJECTIVE To explore the potential of serum disease-specific immunoglobulin G (DSIgG) glycosylation as a biomarker for the diagnosis of nonproliferative diabetic retinopathy (NPDR). METHODS A total of 387 consecutive diabetic patients presenting in an eye clinic without proliferative diabetic retinopathy (DR) were included and divided into those with nondiabetic retinopathy (NDR) (n = 181) and NPDR (n = 206) groups. Serum was collected from all patients for DSIgG separation. The enriched glycopeptides of the tryptic digests of DSIgG were detected using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Patients were randomly divided into discovery and validation sets (1:1). The differences in glycopeptide ratios between the groups were compared by using Student's t-test or the Mann-Whitney U test. The predictive ability of the model was assessed using the area under the receiver operating characteristic curve (AUC). RESULTS DSIgG1 G1FN/G0FN, G2N/G2, G2FN/G2N and DSIgG2 G1F/G0F, G1FN/G0FN, G2N/G1N, G2S/G2 were significantly different between NDR and NPDR patients (p < 0.05) in both the discovery and validation sets. The prediction model that was built comprising the seven glycopeptide ratios showed good NPDR prediction performance with an AUC of 0.85 in the discovery set and 0.87 in the validation set. CONCLUSION DSIgG Fc N-glycosylation ratios were associated with NPDR and can be used as potential biomarkers for the early diagnosis of DR.
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Affiliation(s)
- Yixin Zhang
- Department of Ophthalmology, The Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Zhizhen Lai
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhonghao Yuan
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bin Qu
- Traditional Chinese Medicine Hospital of Muping District of Yantai City, Yantai, Shandong, China
| | - Yan Li
- Traditional Chinese Medicine Hospital of Muping District of Yantai City, Yantai, Shandong, China
| | - Wenyu Yan
- Department of Ophthalmology, Peking Union Medical College Hospital, Beijing, China; Key Laboratory of Ocular Fundus Diseases, Chinese Academy of Medical Sciences, Beijing, China
| | - Bing Li
- Department of Ophthalmology, Peking Union Medical College Hospital, Beijing, China; Key Laboratory of Ocular Fundus Diseases, Chinese Academy of Medical Sciences, Beijing, China
| | - Weihong Yu
- Department of Ophthalmology, Peking Union Medical College Hospital, Beijing, China; Key Laboratory of Ocular Fundus Diseases, Chinese Academy of Medical Sciences, Beijing, China.
| | - Shanjun Cai
- Department of Ophthalmology, The Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China.
| | - Hua Zhang
- Continuous Education College, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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5
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Xie X, Kong S, Cao W. Targeting protein glycosylation to regulate inflammation in the respiratory tract: novel diagnostic and therapeutic candidates for chronic respiratory diseases. Front Immunol 2023; 14:1168023. [PMID: 37256139 PMCID: PMC10225578 DOI: 10.3389/fimmu.2023.1168023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/02/2023] [Indexed: 06/01/2023] Open
Abstract
Protein glycosylation is a widespread posttranslational modification that can impact the function of proteins. Dysregulated protein glycosylation has been linked to several diseases, including chronic respiratory diseases (CRDs). CRDs pose a significant public health threat globally, affecting the airways and other lung structures. Emerging researches suggest that glycosylation plays a significant role in regulating inflammation associated with CRDs. This review offers an overview of the abnormal glycoenzyme activity and corresponding glycosylation changes involved in various CRDs, including chronic obstructive pulmonary disease, asthma, cystic fibrosis, idiopathic pulmonary fibrosis, pulmonary arterial hypertension, non-cystic fibrosis bronchiectasis, and lung cancer. Additionally, this review summarizes recent advances in glycomics and glycoproteomics-based protein glycosylation analysis of CRDs. The potential of glycoenzymes and glycoproteins for clinical use in the diagnosis and treatment of CRDs is also discussed.
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Affiliation(s)
- Xiaofeng Xie
- Shanghai Fifth People’s Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Siyuan Kong
- Shanghai Fifth People’s Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Weiqian Cao
- Shanghai Fifth People’s Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China
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6
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Wu D, Guo M, Robinson CV. Connecting single-nucleotide polymorphisms, glycosylation status, and interactions of plasma serine protease inhibitors. Chem 2023; 9:665-681. [PMID: 38455847 PMCID: PMC10914678 DOI: 10.1016/j.chempr.2022.11.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 10/06/2022] [Accepted: 11/22/2022] [Indexed: 12/23/2022]
Abstract
Understanding the combined impacts of genetic variances and post-translational modifications requires new approaches. Here, we delineate proteoforms of plasma serine protease inhibitors and relate specific proteoforms to their interactions in complexes through the use of native mass spectrometry (MS). First, we dissect the proteoform repertoire of an acute-phase plasma protein, serine protease inhibitor A1 (SERPINA1), resolving four SERPINA1 variants (M1V, M1A, M2, and M3) with common single-nucleotide polymorphisms (SNPs). Investigating the glycosylation status of these variants and their ability to form complexes with a serine protease, elastase, we find that fucosylation stabilizes the interaction of the SERPINA1 M1V variant through its core fucosylation on Asn271. In contrast, antennary fucosylation on Asn271 destabilizes SERPINA1-elastase interactions. We unveil the same opposing effects of core and antennary fucosylation on SERPINA3 interactions with chymotrypsin. Together, our native MS results highlight the modulating effects of fucosylation with different linkages on glycoprotein interactions.
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Affiliation(s)
- Di Wu
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | - Manman Guo
- Botnar Research Centre, NIHR Biomedical Research Unit Oxford, Nuffield Department of Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
| | - Carol V. Robinson
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
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7
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Yamaguchi Y, Yamaguchi T, Kato K. Structural Analysis of Oligosaccharides and Glycoconjugates Using NMR. ADVANCES IN NEUROBIOLOGY 2023; 29:163-184. [PMID: 36255675 DOI: 10.1007/978-3-031-12390-0_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Carbohydrate chains play critical roles in cellular recognition and subsequent signal transduction in the nervous system. Furthermore, gangliosides are targets for various amyloidogenic proteins associated with neurodegenerative disorders. To better understand the molecular mechanisms underlying these biological phenomena, atomic views are essential to delineate dynamic biomolecular interactions. Nuclear magnetic resonance (NMR) spectroscopy provides powerful tools for studying structures, dynamics, and interactions of biomolecules at the atomic level. This chapter describes the basics of solution NMR techniques and their applications to the analysis of 3D structures and interactions of glycoconjugates in the nervous system.
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Affiliation(s)
- Yoshiki Yamaguchi
- Division of Structural Biology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Sendai, Japan.
| | - Takumi Yamaguchi
- School of Materials Science, Japan Advanced Institute of Science and Technology, Nomi, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Mizuho-ku, Nagoya, Japan
| | - Koichi Kato
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Mizuho-ku, Nagoya, Japan.
- Exploratory Research Center on Life and Living Systems and Institute for Molecular Science, Okazaki, Japan.
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8
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Roy R, Poddar S, Kar P. Comparison of the conformational dynamics of an N-glycan in implicit and explicit solvents. Carbohydr Res 2022; 522:108700. [DOI: 10.1016/j.carres.2022.108700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/28/2022]
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9
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Grothaus IL, Bussi G, Colombi Ciacchi L. Exploration, Representation, and Rationalization of the Conformational Phase Space of N-Glycans. J Chem Inf Model 2022; 62:4992-5008. [PMID: 36179122 DOI: 10.1021/acs.jcim.2c01049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Despite their fundamental biological relevance, structure-property relationships in N-glycans are fundamentally lacking, and their highly multidimensional compositional and conformational phase spaces remain largely unexplored. The torsional flexibility of the glycosidic linkages and the ring dynamics result in wide, rugged free-energy landscapes that are difficult to sample in molecular dynamics simulations. We show that a novel enhanced-sampling scheme combining replica exchange with solute and collective-variable tempering, enabling transitions over all relevant energy barriers, delivers converged distributions of solvated N-glycan conformers. Several dimensionality-reduction algorithms are compared and employed to generate conformational free-energy maps in two dimensions. Together with an originally developed conformation-based nomenclature scheme that uniquely identifies glycan conformers, our modeling procedure is applied to reveal the effect of chemical substitutions on the conformational ensemble of selected high-mannose-type and complex glycans. Moreover, the structure-prediction capabilities of two commonly used glycan force fields are assessed via the theoretical prediction of experimentally available nuclear magnetic resonance J-coupling constants. The results especially confirm the key role of ω and ψ torsion angles in discriminating between different conformational states and suggest an intriguing correlation between the torsional and ring-puckering degrees of freedom that may be biologically relevant.
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Affiliation(s)
- Isabell Louise Grothaus
- Hybrid Materials Interfaces Group, Bremen Center for Computational Materials Science and MAPEX Center for Materials and Processes, University of Bremen, 28359Bremen, Germany
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136Trieste, Italy
| | - Lucio Colombi Ciacchi
- Hybrid Materials Interfaces Group, Bremen Center for Computational Materials Science and MAPEX Center for Materials and Processes, University of Bremen, 28359Bremen, Germany
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10
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Manabe N, Ohno S, Matsumoto K, Kawase T, Hirose K, Masuda K, Yamaguchi Y. A Data Set of Ion Mobility Collision Cross Sections and Liquid Chromatography Retention Times from 71 Pyridylaminated N-Linked Oligosaccharides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1772-1783. [PMID: 35997275 PMCID: PMC9460764 DOI: 10.1021/jasms.2c00165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/28/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
Determination of the glycan structure is an essential step in understanding structure-function relationships of glycans and glycoconjugates including biopharmaceuticals. Mass spectrometry, because of its high sensitivity and mass resolution, is an excellent means of analyzing glycan structures. We previously proposed a method for rapid and precise identification of N-glycan structures by ultraperformance liquid chromatography-connected ion mobility mass spectrometry (UPLC/IM-MS). To substantiate this methodology, we here examine 71 pyridylaminated (PA-) N-linked oligosaccharides including isomeric pairs. A data set on collision drift times, retention times, and molecular mass was collected for these PA-oligosaccharides. For standardization of the observables, LC retention times were normalized into glucose units (GU) using pyridylaminated α-1,6-linked glucose oligomers as reference, and drift times in IM-MS were converted into collision cross sections (CCS). To evaluate the CCS value of each PA-oligosaccharide, we introduced a CCS index which is defined as a CCS ratio of a target PA-glycan to the putative standard PA-glucose oligomer of the same m/z. We propose a strategy for practical structural analysis of N-linked glycans based on the database of m/z, CCS index, and normalized retention time (GU).
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Affiliation(s)
- Noriyoshi Manabe
- Division
of Structural Glycobiology, Institute of Molecular Biomembrane and
Glycobiology, Tohoku Medical and Pharmaceutical
University, 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi981-8558, Japan
| | - Shiho Ohno
- Division
of Structural Glycobiology, Institute of Molecular Biomembrane and
Glycobiology, Tohoku Medical and Pharmaceutical
University, 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi981-8558, Japan
| | - Kana Matsumoto
- Structural
Glycobiology Team, RIKEN-Max Planck Joint Research Center, Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako, Saitama351-0198, Japan
| | - Taiji Kawase
- Nihon
Waters KK, Kitashinagawa, Shinagawa, Tokyo140-0001, Japan
| | - Kenji Hirose
- Nihon
Waters KK, Kitashinagawa, Shinagawa, Tokyo140-0001, Japan
| | - Katsuyoshi Masuda
- Graduate
School of Engineering, Osaka University, Suita, Osaka565-0871, Japan
| | - Yoshiki Yamaguchi
- Division
of Structural Glycobiology, Institute of Molecular Biomembrane and
Glycobiology, Tohoku Medical and Pharmaceutical
University, 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi981-8558, Japan
- Structural
Glycobiology Team, RIKEN-Max Planck Joint Research Center, Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako, Saitama351-0198, Japan
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11
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Abstract
Glycoscience assembles all the scientific disciplines involved in studying various molecules and macromolecules containing carbohydrates and complex glycans. Such an ensemble involves one of the most extensive sets of molecules in quantity and occurrence since they occur in all microorganisms and higher organisms. Once the compositions and sequences of these molecules are established, the determination of their three-dimensional structural and dynamical features is a step toward understanding the molecular basis underlying their properties and functions. The range of the relevant computational methods capable of addressing such issues is anchored by the specificity of stereoelectronic effects from quantum chemistry to mesoscale modeling throughout molecular dynamics and mechanics and coarse-grained and docking calculations. The Review leads the reader through the detailed presentations of the applications of computational modeling. The illustrations cover carbohydrate-carbohydrate interactions, glycolipids, and N- and O-linked glycans, emphasizing their role in SARS-CoV-2. The presentation continues with the structure of polysaccharides in solution and solid-state and lipopolysaccharides in membranes. The full range of protein-carbohydrate interactions is presented, as exemplified by carbohydrate-active enzymes, transporters, lectins, antibodies, and glycosaminoglycan binding proteins. A final section features a list of 150 tools and databases to help address the many issues of structural glycobioinformatics.
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Affiliation(s)
- Serge Perez
- Centre de Recherche sur les Macromolecules Vegetales, University of Grenoble-Alpes, Centre National de la Recherche Scientifique, Grenoble F-38041, France
| | - Olga Makshakova
- FRC Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, Kazan 420111, Russia
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12
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Fadda E. Molecular simulations of complex carbohydrates and glycoconjugates. Curr Opin Chem Biol 2022; 69:102175. [PMID: 35728307 DOI: 10.1016/j.cbpa.2022.102175] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 11/17/2022]
Abstract
Complex carbohydrates (glycans) are the most abundant and versatile biopolymers in nature. The broad diversity of biochemical functions that carbohydrates cover is a direct consequence of the variety of 3D architectures they can adopt, displaying branched or linear arrangements, widely ranging in sizes, and with the highest diversity of building blocks of any other natural biopolymer. Despite this unparalleled complexity, a common denominator can be found in the glycans' inherent flexibility, which hinders experimental characterization, but that can be addressed by high-performance computing (HPC)-based molecular simulations. In this short review, I present and discuss the state-of-the-art of molecular simulations of complex carbohydrates and glycoconjugates, highlighting methodological strengths and weaknesses, important insights through emblematic case studies, and suggesting perspectives for future developments.
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Affiliation(s)
- Elisa Fadda
- Department of Chemistry and Hamilton Institute, Maynooth University, Ireland.
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13
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Rao RM, Dauchez M, Baud S. How molecular modelling can better broaden the understanding of glycosylations. Curr Opin Struct Biol 2022; 75:102393. [PMID: 35679802 DOI: 10.1016/j.sbi.2022.102393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/31/2022] [Accepted: 04/18/2022] [Indexed: 11/03/2022]
Abstract
Glycosylations are among the most ubiquitous post-translational modifications (PTMs) in proteins, and the effects of their perturbations are seen in various diseases such as cancers, diabetes and arthritis to name a few. Yet they remain one of the most enigmatic aspects of protein structure and function. On the other hand, molecular modelling techniques have been rapidly bridging this knowledge gap since the last decade. In this review, we discuss how these techniques have proven to be indispensable for a better understanding of the role of glycosylations in glycoprotein structure and function.
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Affiliation(s)
- Rajas M Rao
- Université de Reims Champagne Ardenne, CNRS UMR 7369, MEDyC, Reims, 51687, France
| | - Manuel Dauchez
- Université de Reims Champagne Ardenne, CNRS UMR 7369, MEDyC, Reims, 51687, France.
| | - Stéphanie Baud
- Université de Reims Champagne Ardenne, CNRS UMR 7369, MEDyC, Reims, 51687, France
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14
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Vattepu R, Sneed SL, Anthony RM. Sialylation as an Important Regulator of Antibody Function. Front Immunol 2022; 13:818736. [PMID: 35464485 PMCID: PMC9021442 DOI: 10.3389/fimmu.2022.818736] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/17/2022] [Indexed: 12/14/2022] Open
Abstract
Antibodies play a critical role in linking the adaptive immune response to the innate immune system. In humans, antibodies are categorized into five classes, IgG, IgM, IgA, IgE, and IgD, based on constant region sequence, structure, and tropism. In serum, IgG is the most abundant antibody, comprising 75% of antibodies in circulation, followed by IgA at 15%, IgM at 10%, and IgD and IgE are the least abundant. All human antibody classes are post-translationally modified by sugars. The resulting glycans take on many divergent structures and can be attached in an N-linked or O-linked manner, and are distinct by antibody class, and by position on each antibody. Many of these glycan structures on antibodies are capped by sialic acid. It is well established that the composition of the N-linked glycans on IgG exert a profound influence on its effector functions. However, recent studies have described the influence of glycans, particularly sialic acid for other antibody classes. Here, we discuss the role of glycosylation, with a focus on terminal sialylation, in the biology and function across all antibody classes. Sialylation has been shown to influence not only IgG, but IgE, IgM, and IgA biology, making it an important and unappreciated regulator of antibody function.
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Affiliation(s)
- Ravi Vattepu
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Sunny Lyn Sneed
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Robert M Anthony
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
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15
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Conformational preferences of triantennary and tetraantennary hybrid N-glycans in aqueous solution: Insights from 20 μs long atomistic molecular dynamic simulations. J Biomol Struct Dyn 2022; 41:3305-3320. [PMID: 35262462 DOI: 10.1080/07391102.2022.2047109] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In the current study, we have investigated the conformational dynamics of a triantennary (N-glycan1) and tetraantennary (N-glycan2) hybrid N-glycans found on the surface of the HIV glycoprotein using 20 μs long all-atom molecular dynamics (MD) simulations. The main objective of the present study is to elucidate the influence of adding a complex branch on the overall glycan structural dynamics. Our investigation suggests that the average RMSD value increases when a complex branch is added to N-glycan1. However, the RMSD distribution is relatively wider in the case of N-glycan1 compared to N-glycan2, which indicates that multiple complex branches restrict the conformational variability of glycans. A similar observation is obtained from the principal component analysis of both glycans. All the puckering states (4C1 to 1C4) of each monosaccharide except mannose are sampled in our simulations, although the 4C1 chair form is energetically more favorable than 1C4. In N-glycan1, the 1-6 linkage in the mannose branch [Man(9)-α(1-6)-Man(5)] stays in the gauche-gauche cluster, whereas it moves towards trans-gauche in N-glycan2. For both glycans, mannose branches are more flexible than the complex branches, and adding a complex branch does not influence the dynamics of the mannose branches. We have noticed that the end-to-end distance of the complex branch shortens by ∼ 10 Å in the presence of another complex branch. This suggests that in the presence of an additional complex branch, the other complex branch adopts a close folded structure. All these conformational changes involve the selective formation of inter-residue and water-mediated hydrogen-bond networks.
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16
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Abstract
Glycosylation, one of the most common post-translational modifications in mammalian cells, impacts many biological processes such as cell adhesion, proliferation and differentiation. As the most abundant glycoprotein in human serum, immunoglobulin G (IgG) plays a vital role in immune response and protection. There is a growing body of evidence suggests that IgG structure and function are modulated by attached glycans, especially N-glycans, and aberrant glycosylation is associated with disease states. In this chapter, we review IgG glycan repertoire and function, strategies for profiling IgG N-glycome and recent studies. Mass spectrometry (MS) based techniques are the most powerful tools for profiling IgG glycome. IgG glycans can be divided into high-mannose, biantennary complex and hybrid types, modified with mannosylation, core-fucosylation, galactosylation, bisecting GlcNAcylation, or sialylation. Glycosylation of IgG affects antibody half-life and their affinity and avidity for antigens, regulates crystallizable fragment (Fc) structure and Fcγ receptor signaling, as well as antibody effector function. Because of their critical roles, IgG N-glycans appear to be promising biomarkers for various disease states. Specific IgG glycosylation can convert a pro-inflammatory response to an anti-inflammatory activity. Accordingly, IgG glycoengineering provides a powerful approach to potentially develop effective drugs and treat disease. Based on the understanding of the functional role of IgG glycans, the development of vaccines with enhanced capacity and long-term protection are possible in the near future.
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17
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Shirakawa A, Manabe Y, Marchetti R, Yano K, Masui S, Silipo A, Molinaro A, Fukase K. Chemical Synthesis of Sialyl
N
‐Glycans and Analysis of Their Recognition by Neuraminidase. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202111035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Asuka Shirakawa
- Department of Chemistry Graduate School of Science Osaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
| | - Yoshiyuki Manabe
- Department of Chemistry Graduate School of Science Osaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
- Core for Medicine and Science Collaborative Research and Education Project Research Center for Fundamental Sciences Graduate School of Science Osaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
| | - Roberta Marchetti
- Department of Chemical Science University of Naples Federico II Via Cinthia 4 80126 Naples Italy
| | - Kumpei Yano
- Department of Chemistry Graduate School of Science Osaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
| | - Seiji Masui
- Department of Chemistry Graduate School of Science Osaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
| | - Alba Silipo
- Department of Chemistry Graduate School of Science Osaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
- Department of Chemical Science University of Naples Federico II Via Cinthia 4 80126 Naples Italy
| | - Antonio Molinaro
- Department of Chemistry Graduate School of Science Osaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
- Department of Chemical Science University of Naples Federico II Via Cinthia 4 80126 Naples Italy
| | - Koichi Fukase
- Department of Chemistry Graduate School of Science Osaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
- Core for Medicine and Science Collaborative Research and Education Project Research Center for Fundamental Sciences Graduate School of Science Osaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
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18
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Shirakawa A, Manabe Y, Marchetti R, Yano K, Masui S, Silipo A, Molinaro A, Fukase K. Chemical Synthesis of Sialyl N-Glycans and Analysis of Their Recognition by Neuraminidase. Angew Chem Int Ed Engl 2021; 60:24686-24693. [PMID: 34520098 DOI: 10.1002/anie.202111035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Indexed: 11/07/2022]
Abstract
The chemical synthesis of a fully sialylated tetraantennary N-glycan has been achieved for the first time by using the diacetyl strategy, in which NHAc is protected as NAc2 to improve reactivity by preventing intermolecular hydrogen bonds. Another key was the glycosylation to the branched mannose in an ether solvent, which promoted the desired glycosylation by stabilizing the oxocarbenium ion intermediate. Furthermore, high α-selectivity of these glycosylation reactions was realized by utilizing remote participation. Two asymmetrically deuterium labeled sialyl N-glycans were also synthesized by the same strategy. The synthesized N-glycans were used to probe the molecular basis of H1N1 neuraminidase recognition. The asymmetrically deuterated N-glycans revealed a difference in the recognition of sialic acid on each branch. Meanwhile, the tetraantennary N-glycan was used to evaluate the effects of multivalency and steric hinderance by forming branching structures.
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Affiliation(s)
- Asuka Shirakawa
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Yoshiyuki Manabe
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan.,Core for Medicine and Science Collaborative Research and Education, Project Research Center for Fundamental Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Roberta Marchetti
- Department of Chemical Science, University of Naples Federico II, Via Cinthia 4, 80126, Naples, Italy
| | - Kumpei Yano
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Seiji Masui
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Alba Silipo
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan.,Department of Chemical Science, University of Naples Federico II, Via Cinthia 4, 80126, Naples, Italy
| | - Antonio Molinaro
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan.,Department of Chemical Science, University of Naples Federico II, Via Cinthia 4, 80126, Naples, Italy
| | - Koichi Fukase
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan.,Core for Medicine and Science Collaborative Research and Education, Project Research Center for Fundamental Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
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19
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Smith J, Millán-Martín S, Mittermayr S, Hilborne V, Davey G, Polom K, Roviello F, Bones J. 2-Dimensional ultra-high performance liquid chromatography and DMT-MM derivatization paired with tandem mass spectrometry for comprehensive serum N-glycome characterization. Anal Chim Acta 2021; 1179:338840. [PMID: 34535264 DOI: 10.1016/j.aca.2021.338840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/02/2021] [Accepted: 07/04/2021] [Indexed: 12/25/2022]
Abstract
Glycosylation is a prominent co- and post-translational modification which contributes to a variety of important biological functions. Protein glycosylation characteristics, particularly N-glycosylation, are influenced by changes in one's pathological state, such as through the presence of disease, and as such, there is great interest in N-glycans as potential disease biomarkers. Human serum is an attractive source for N-glycan based biomarker studies as circulatory proteins are representative of one's physiology, with many serum proteins containing N-glycosylation. The difficulty in comprehensively characterizing the serum N-glycome arises from the absence of a biosynthetic template resulting in great structural heterogeneity and complexity. To help overcome these challenges we developed a 2-dimensional liquid chromatography platform which utilizes offline weak anion exchange (WAX) chromatography in the first dimension and hydrophilic interaction liquid chromatography (HILIC) in the second dimension to separate N-glycans by charge, corresponding to degree of sialylation, and size, respectively. Performing these separations offline enables subsequent derivatization with 4-(4,6-Dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium chloride (DMT-MM) for sialic acid linkage determination and the identification of sialic acid linkage isomers. Subsequent tandem mass spectrometry analysis revealed the identification of 212 complete and partial N-glycan structures including low abundant N-glycans containing acetyl and sulphate modifications. The identifications obtained through this platform were then applied to N-glycans released from a set of stage 3 gastric cancer serum samples obtained from patients before (pre-op) and after (post-op) tumour resection to investigate how the serum N-glycome can facilitate differentiation between the two pathological states.
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Affiliation(s)
- Josh Smith
- Characterisation and Comparability Laboratory, The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Co. Dublin, A94 X099, Ireland; School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, D02 R590, Ireland
| | - Silvia Millán-Martín
- Characterisation and Comparability Laboratory, The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Co. Dublin, A94 X099, Ireland
| | - Stefan Mittermayr
- Characterisation and Comparability Laboratory, The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Co. Dublin, A94 X099, Ireland
| | - Vivian Hilborne
- Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, USA
| | - Gavin Davey
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, D02 R590, Ireland
| | - Karol Polom
- Department of General Surgery and Surgical Oncology, University of Siena, Siena, Italy; Department of Surgical Oncology, Medical University of Gdansk, Gdansk, Poland
| | - Franco Roviello
- Department of Medicine, Surgery and Neurosciences, University of Siena, Siena, Italy
| | - Jonathan Bones
- Characterisation and Comparability Laboratory, The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Co. Dublin, A94 X099, Ireland; School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, D04 V1W8, Ireland.
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20
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Re S, Mizuguchi K. Glycan Cluster Shielding and Antibody Epitopes on Lassa Virus Envelop Protein. J Phys Chem B 2021; 125:2089-2097. [PMID: 33606939 DOI: 10.1021/acs.jpcb.0c11516] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
An understanding of how an antiviral monoclonal antibody recognizes its target is vital for the development of neutralizing antibodies and vaccines. The extensive glycosylation of viral proteins almost certainly affects the antibody response, but the investigation of such effects is hampered by the huge range of structures and interactions of surface glycans through their inherent complexity and flexibility. Here, we built an atomistic model of a fully glycosylated envelope protein complex of the Lassa virus and performed molecular dynamics simulations to characterize the impact of surface glycans on the antibody response. The simulations attested to the variety of conformations and interactions of surface glycans. The results show that glycosylation nonuniformly shields the surface of the complex and only marginally affects protein dynamics. The glycans gather in distinct clusters through interaction with protein residues, and only a few regions are left accessible by an antibody. We successfully recovered known protein epitopes by integrating the simulation results with existing sequence- and structure-based epitope prediction methods. The results emphasize the rich structural environment of glycans and demonstrate that shielding is not merely envelopment by a uniform blanket of sugars. This work provides a molecular basis for integrating otherwise elusive structural properties of glycans into vaccine and neutralizing antibody developments.
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Affiliation(s)
- Suyong Re
- Center for Drug Design Research, National Institutes of Biomedical Innovation, Health, and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan.,RIKEN Center for Biosystems Dynamics Research, Integrated Innovation Building 7F, 6-7-1 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Kenji Mizuguchi
- Center for Drug Design Research, National Institutes of Biomedical Innovation, Health, and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan.,Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health, and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan.,Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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21
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Shirakawa A, Manabe Y, Fukase K. Recent Advances in the Chemical Biology of N-Glycans. Molecules 2021; 26:molecules26041040. [PMID: 33669465 PMCID: PMC7920464 DOI: 10.3390/molecules26041040] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/08/2021] [Accepted: 02/14/2021] [Indexed: 12/19/2022] Open
Abstract
Asparagine-linked N-glycans on proteins have diverse structures, and their functions vary according to their structures. In recent years, it has become possible to obtain high quantities of N-glycans via isolation and chemical/enzymatic/chemoenzymatic synthesis. This has allowed for progress in the elucidation of N-glycan functions at the molecular level. Interaction analyses with lectins by glycan arrays or nuclear magnetic resonance (NMR) using various N-glycans have revealed the molecular basis for the recognition of complex structures of N-glycans. Preparation of proteins modified with homogeneous N-glycans revealed the influence of N-glycan modifications on protein functions. Furthermore, N-glycans have potential applications in drug development. This review discusses recent advances in the chemical biology of N-glycans.
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Affiliation(s)
- Asuka Shirakawa
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan;
| | - Yoshiyuki Manabe
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan;
- Core for Medicine and Science Collaborative Research and Education, Project Research Center for Fundamental Sciences, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
- Correspondence: (Y.M.); (K.F.); Tel.: +81-6-6850-5391 (Y.M.); +81-6-6850-5388 (K.F.)
| | - Koichi Fukase
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan;
- Core for Medicine and Science Collaborative Research and Education, Project Research Center for Fundamental Sciences, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
- Correspondence: (Y.M.); (K.F.); Tel.: +81-6-6850-5391 (Y.M.); +81-6-6850-5388 (K.F.)
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22
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Schust DJ, Bonney EA, Sugimoto J, Ezashi T, Roberts RM, Choi S, Zhou J. The Immunology of Syncytialized Trophoblast. Int J Mol Sci 2021; 22:ijms22041767. [PMID: 33578919 PMCID: PMC7916661 DOI: 10.3390/ijms22041767] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/02/2021] [Accepted: 02/06/2021] [Indexed: 02/06/2023] Open
Abstract
Multinucleate syncytialized trophoblast is found in three forms in the human placenta. In the earliest stages of pregnancy, it is seen at the invasive leading edge of the implanting embryo and has been called primitive trophoblast. In later pregnancy, it is represented by the immense, multinucleated layer covering the surface of placental villi and by the trophoblast giant cells found deep within the uterine decidua and myometrium. These syncytia interact with local and/or systemic maternal immune effector cells in a fine balance that allows for invasion and persistence of allogeneic cells in a mother who must retain immunocompetence for 40 weeks of pregnancy. Maternal immune interactions with syncytialized trophoblast require tightly regulated mechanisms that may differ depending on the location of fetal cells and their invasiveness, the nature of the surrounding immune effector cells and the gestational age of the pregnancy. Some specifically reflect the unique mechanisms involved in trophoblast cell–cell fusion (aka syncytialization). Here we will review and summarize several of the mechanisms that support healthy maternal–fetal immune interactions specifically at syncytiotrophoblast interfaces.
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Affiliation(s)
- Danny J. Schust
- Department of Obstetrics, Gynecology, University of Missouri School of Medicine, Columbia, MO 65202, USA; (T.E.); (R.M.R.); (S.C.); (J.Z.)
- Correspondence:
| | - Elizabeth A. Bonney
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Vermont College of Medicine, Burlington, VT 05405, USA;
| | - Jun Sugimoto
- Department of Obstetrics and Gynecology, Hiroshima University, Hiroshima 734-8551, Japan;
| | - Toshi Ezashi
- Department of Obstetrics, Gynecology, University of Missouri School of Medicine, Columbia, MO 65202, USA; (T.E.); (R.M.R.); (S.C.); (J.Z.)
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - R. Michael Roberts
- Department of Obstetrics, Gynecology, University of Missouri School of Medicine, Columbia, MO 65202, USA; (T.E.); (R.M.R.); (S.C.); (J.Z.)
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Sehee Choi
- Department of Obstetrics, Gynecology, University of Missouri School of Medicine, Columbia, MO 65202, USA; (T.E.); (R.M.R.); (S.C.); (J.Z.)
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Jie Zhou
- Department of Obstetrics, Gynecology, University of Missouri School of Medicine, Columbia, MO 65202, USA; (T.E.); (R.M.R.); (S.C.); (J.Z.)
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
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23
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Sastre Toraño J, Aizpurua‐Olaizola O, Wei N, Li T, Unione L, Jiménez‐Osés G, Corzana F, Somovilla VJ, Falcon‐Perez JM, Boons G. Identification of Isomeric N-Glycans by Conformer Distribution Fingerprinting using Ion Mobility Mass Spectrometry. Chemistry 2021; 27:2149-2154. [PMID: 33047840 PMCID: PMC7898647 DOI: 10.1002/chem.202004522] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Indexed: 12/14/2022]
Abstract
Glycans possess unparalleled structural complexity arising from chemically similar monosaccharide building blocks, configurations of anomeric linkages and different branching patterns, potentially giving rise to many isomers. This level of complexity is one of the main reasons that identification of exact glycan structures in biological samples still lags behind that of other biomolecules. Here, we introduce a methodology to identify isomeric N-glycans by determining gas phase conformer distributions (CDs) by measuring arrival time distributions (ATDs) using drift-tube ion mobility spectrometry-mass spectrometry. Key to the approach is the use of a range of well-defined synthetic glycans that made it possible to investigate conformer distributions in the gas phase of isomeric glycans in a systematic manner. In addition, we have computed CD fingerprints by molecular dynamics (MD) simulation, which compared well with experimentally determined CDs. It supports that ATDs resemble conformational populations in the gas phase and offer the prospect that such an approach can contribute to generating a library of CCS distributions (CCSDs) for structure identification.
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Affiliation(s)
- Javier Sastre Toraño
- Department of Chemical Biology and Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUtrecht UniversityUtrechtThe Netherlands
| | - Oier Aizpurua‐Olaizola
- Department of Chemical Biology and Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUtrecht UniversityUtrechtThe Netherlands
- Exosomes LabCIC bioGUNE, CIBERehdDerioSpain
| | - Na Wei
- The University of GeorgiaComplex Carbohydrate Research CenterAthensGAUSA
| | - Tiehai Li
- The University of GeorgiaComplex Carbohydrate Research CenterAthensGAUSA
| | - Luca Unione
- Department of Chemical Biology and Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUtrecht UniversityUtrechtThe Netherlands
| | - Gonzalo Jiménez‐Osés
- Center for Cooperative Research in Biosciences (CIC bioGUNEBasque Research and Technology Alliance (BRTA)Bizkaia Technology Park, Building 801A48160DerioSpain
| | - Francisco Corzana
- Departamento de Química, Centro de Investigación en Síntesis QuímicaUniversidad de La Rioja26006LogroñoSpain
| | - Victor J. Somovilla
- Department of Chemical Biology and Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUtrecht UniversityUtrechtThe Netherlands
| | | | - Geert‐Jan Boons
- Department of Chemical Biology and Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUtrecht UniversityUtrechtThe Netherlands
- The University of GeorgiaComplex Carbohydrate Research CenterAthensGAUSA
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24
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Irvine EB, Alter G. Understanding the role of antibody glycosylation through the lens of severe viral and bacterial diseases. Glycobiology 2020; 30:241-253. [PMID: 32103252 PMCID: PMC7109349 DOI: 10.1093/glycob/cwaa018] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 01/31/2020] [Accepted: 02/12/2020] [Indexed: 01/12/2023] Open
Abstract
Abundant evidence points to a critical role for antibodies in protection and pathology across infectious diseases. While the antibody variable domain facilitates antibody binding and the blockade of infection, the constant domain (Fc) mediates cross talk with the innate immune system. The biological activity of the Fc region is controlled genetically via class switch recombination, resulting in the selection of distinct antibody isotypes and subclasses. However, a second modification is made to all antibodies, via post-translational changes in antibody glycosylation. Studies from autoimmunity and oncology have established the role of immunoglobulin G (IgG) Fc glycosylation as a key regulator of humoral immune activity. However, a growing body of literature, exploring IgG Fc glycosylation through the lens of infectious diseases, points to the role of inflammation in shaping Fc-glycan profiles, the remarkable immune plasticity in antibody glycosylation across pathogen-exposed populations, the canonical and noncanonical functions of glycans and the existence of antigen-specific control over antibody Fc glycosylation. Ultimately, this work provides critical new insights into the functional roles for antibody glycosylation as well as lays the foundation for leveraging antibody glycosylation to drive prevention or control across diseases.
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Affiliation(s)
- Edward B Irvine
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
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25
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Multiscale Simulations Examining Glycan Shield Effects on Drug Binding to Influenza Neuraminidase. Biophys J 2020; 119:2275-2289. [PMID: 33130120 DOI: 10.1016/j.bpj.2020.10.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/08/2020] [Accepted: 10/21/2020] [Indexed: 12/18/2022] Open
Abstract
Influenza neuraminidase is an important drug target. Glycans are present on neuraminidase and are generally considered to inhibit antibody binding via their glycan shield. In this work, we studied the effect of glycans on the binding kinetics of antiviral drugs to the influenza neuraminidase. We created all-atom in silico systems of influenza neuraminidase with experimentally derived glycoprofiles consisting of four systems with different glycan conformations and one system without glycans. Using Brownian dynamics simulations, we observe a two- to eightfold decrease in the rate of ligand binding to the primary binding site of neuraminidase due to the presence of glycans. These glycans are capable of covering much of the surface area of neuraminidase, and the ligand binding inhibition is derived from glycans sterically occluding the primary binding site on a neighboring monomer. Our work also indicates that drugs preferentially bind to the primary binding site (i.e., the active site) over the secondary binding site, and we propose a binding mechanism illustrating this. These results help illuminate the complex interplay between glycans and ligand binding on the influenza membrane protein neuraminidase.
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26
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Taniguchi N, Ohkawa Y, Maeda K, Harada Y, Nagae M, Kizuka Y, Ihara H, Ikeda Y. True significance of N-acetylglucosaminyltransferases GnT-III, V and α1,6 fucosyltransferase in epithelial-mesenchymal transition and cancer. Mol Aspects Med 2020; 79:100905. [PMID: 33010941 DOI: 10.1016/j.mam.2020.100905] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 09/02/2020] [Indexed: 12/13/2022]
Abstract
It is well known that numerous cancer-related changes occur in glycans that are attached to glycoproteins, glycolipids and proteoglycans on the cell surface and these changes in structure and the expression of the glycans are largely regulated by glycosyl-transferases, glycosidases, nucleotide sugars and their related genes. Such structural changes in glycans on cell surface proteins may accelerate the progression, invasion and metastasis of cancer cells. Among the over 200 known glycosyltransferases and related genes, β 1,6 N-acetylglucosaminyltransferase V (GnT-V) (the MGAT5 gene) and α 1,6 fucosyltransferase (FUT8) (the FUT8 gene) are representative enzymes in this respect because changes in glycans caused by these genes appear to be related to cancer metastasis and invasion in vitro as well as in vivo, and a number of reports on these genes in related to epithelial-mesenchymal transition (EMT) have also appeared. Another enzyme, one of the N-glycan branching enzymes, β1,4 N-acetylglucosaminyltransferase III (GnT-III) (the MGAT3 gene) has been reported to suppress EMT. However, there are intermediate states between EMT and mesenchymal-epithelial transition (MET) and some of these genes have been implicated in both EMT and MET and are also probably in an intermediate state. Therefore, it would be difficult to clearly define which specific glycosyltransferase is involved in EMT or MET or an intermediate state. The significance of EMT and N-glycan branching glycosyltransferases needs to be reconsidered and the inhibition of their corresponding genes would also be desirable in therapeutics. This review mainly focuses on GnT-III, GnT-V and FUT8, major players as N-glycan branching enzymes in cancer in relation to EMT programs, and also discusses the catalytic mechanisms of GnT-V and FUT8 whose crystal structures have now been obtained.
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Affiliation(s)
- Naoyuki Taniguchi
- Department of Glyco-Oncology and Medical Biochemistry, Osaka International Cancer Institute, Osaka, Japan.
| | - Yuki Ohkawa
- Department of Glyco-Oncology and Medical Biochemistry, Osaka International Cancer Institute, Osaka, Japan.
| | - Kento Maeda
- Department of Glyco-Oncology and Medical Biochemistry, Osaka International Cancer Institute, Osaka, Japan.
| | - Yoichiro Harada
- Department of Glyco-Oncology and Medical Biochemistry, Osaka International Cancer Institute, Osaka, Japan.
| | - Masamichi Nagae
- Department of Molecular Immunology, RIMD, Osaka University, Osaka, Japan.
| | - Yasuhiko Kizuka
- Glyco-biochemistry Laboratory, G-Chain, Gifu University, Gifu, Japan.
| | - Hideyuki Ihara
- Division of Molecular Cell Biology, Department of Biomolecular Sciences, Saga University Faculty of Medicine, Saga, Japan.
| | - Yoshitaka Ikeda
- Division of Molecular Cell Biology, Department of Biomolecular Sciences, Saga University Faculty of Medicine, Saga, Japan.
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27
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Cioce A, Thépaut M, Fieschi F, Reichardt N. Rapid On‐Chip Synthesis of Complex Glycomimetics from N‐Glycan Scaffolds for Improved Lectin Targeting. Chemistry 2020; 26:12809-12817. [DOI: 10.1002/chem.202000026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 05/10/2020] [Indexed: 02/03/2023]
Affiliation(s)
- Anna Cioce
- CIC biomaGUNE Paseo Miramón 182 20009 San Sebastian Spain
| | - Michel Thépaut
- CNRS, CEA Institut de Biologie Structurale Université Grenoble Alpes 38100 Grenoble France
| | - Franck Fieschi
- CNRS, CEA Institut de Biologie Structurale Université Grenoble Alpes 38100 Grenoble France
| | - Niels‐Christian Reichardt
- CIC biomaGUNE Paseo Miramón 182 20009 San Sebastian Spain
- CIBER-BBN Paseo Miramón 182 20009 San Sebastian Spain
- Basque Research and Technology Alliance (BRTA) Paseo Miramón 182 20009 San Sebastian Spain
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28
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Wang SH, Wu TJ, Lee CW, Yu J. Dissecting the conformation of glycans and their interactions with proteins. J Biomed Sci 2020; 27:93. [PMID: 32900381 PMCID: PMC7487937 DOI: 10.1186/s12929-020-00684-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/26/2020] [Indexed: 12/20/2022] Open
Abstract
The use of in silico strategies to develop the structural basis for a rational optimization of glycan-protein interactions remains a great challenge. This problem derives, in part, from the lack of technologies to quantitatively and qualitatively assess the complex assembling between a glycan and the targeted protein molecule. Since there is an unmet need for developing new sugar-targeted therapeutics, many investigators are searching for technology platforms to elucidate various types of molecular interactions within glycan-protein complexes and aid in the development of glycan-targeted therapies. Here we discuss three important technology platforms commonly used in the assessment of the complex assembly of glycosylated biomolecules, such as glycoproteins or glycosphingolipids: Biacore analysis, molecular docking, and molecular dynamics simulations. We will also discuss the structural investigation of glycosylated biomolecules, including conformational changes of glycans and their impact on molecular interactions within the glycan-protein complex. For glycoproteins, secreted protein acidic and rich in cysteine (SPARC), which is associated with various lung disorders, such as chronic obstructive pulmonary disease (COPD) and lung cancer, will be taken as an example showing that the core fucosylation of N-glycan in SPARC regulates protein-binding affinity with extracellular matrix collagen. For glycosphingolipids (GSLs), Globo H ceramide, an important tumor-associated GSL which is being actively investigated as a target for new cancer immunotherapies, will be used to demonstrate how glycan structure plays a significant role in enhancing angiogenesis in tumor microenvironments.
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Affiliation(s)
- Sheng-Hung Wang
- Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, and Chang Gung University, Taoyuan, 333, Taiwan
| | - Tsai-Jung Wu
- Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, and Chang Gung University, Taoyuan, 333, Taiwan
| | - Chien-Wei Lee
- Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, and Chang Gung University, Taoyuan, 333, Taiwan
| | - John Yu
- Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, and Chang Gung University, Taoyuan, 333, Taiwan. .,Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan.
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29
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Roy R, Ghosh B, Kar P. Investigating Conformational Dynamics of Lewis Y Oligosaccharides and Elucidating Blood Group Dependency of Cholera Using Molecular Dynamics. ACS OMEGA 2020; 5:3932-3942. [PMID: 32149220 PMCID: PMC7057322 DOI: 10.1021/acsomega.9b03398] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 02/11/2020] [Indexed: 05/08/2023]
Abstract
Cholera is caused by Vibrio cholerae and is an example of a blood-group-dependent disease. Recent studies suggest that the receptor-binding B subunit of the cholera toxin (CT) binds histo-blood group antigens at a secondary binding site. Herein, we studied the conformational dynamics of Lewis Y (LeY) oligosaccharides, H-tetrasaccharides and A-pentasaccharides, in aqueous solution by conducting accelerated molecular dynamics (aMD) simulations. The flexible nature of both oligosaccharides was displayed in aMD simulations. Furthermore, aMD simulations revealed that for both oligosaccharides in the free form, 4C1 and 1C4 puckers were sampled for all but GalNAc monosaccharides, while either the 4C1 (GlcNAc, Gal, GalNAc) or 1C4 (Fuc2, Fuc3) pucker was sampled in the CT-bound forms. In aMD, the complete transition from the 4C1 to 1C4 pucker was sampled for GlcNAc and Gal in both oligosaccharides. Further, we have observed a transition from the open to closed conformer in the case of A-pentasaccharide, while H-tetrasaccharide remains in the open conformation throughout the simulation. Both oligosaccharides adopted an open conformation in the CT binding site. Moreover, we have investigated the molecular basis of recognition of LeY oligosaccharides by the B subunit of the cholera toxin of classical and El Tor biotypes using the molecular mechanics generalized Born surface area (MM/GBSA) scheme. The O blood group determinant, H-tetrasaccharide, exhibits a stronger affinity to both biotypes compared to the A blood group determinant, A-pentasaccharide, which agrees with the experimental data. The difference in binding free energy between O and A blood group determinants mainly arises due to the increased entropic cost and desolvation energy in the case of A-pentasaccharide compared to that of H-tetrasaccharide. Our study also reveals that the terminal Fuc3 contributes most to the binding free energy compared to other carbohydrate residues as it forms multiple hydrogen bonds with CT. Overall, our study might help in designing glycomimetic drugs targeting the cholera toxin.
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Affiliation(s)
- Rajarshi Roy
- Discipline
of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Indore 453552, India
| | - Biplab Ghosh
- High
Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Parimal Kar
- Discipline
of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Indore 453552, India
- E-mail: . Phone: +91 731 2438700 (ext. 550)
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30
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Structural basis for substrate specificity and catalysis of α1,6-fucosyltransferase. Nat Commun 2020; 11:973. [PMID: 32080177 PMCID: PMC7033129 DOI: 10.1038/s41467-020-14794-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 01/30/2020] [Indexed: 12/22/2022] Open
Abstract
Core-fucosylation is an essential biological modification by which a fucose is transferred from GDP-β-L-fucose to the innermost N-acetylglucosamine residue of N-linked glycans. A single human enzyme α1,6-fucosyltransferase (FUT8) is the only enzyme responsible for this modification via the addition of an α-1,6-linked fucose to N-glycans. To date, the details of substrate recognition and catalysis by FUT8 remain unknown. Here, we report the crystal structure of FUT8 complexed with GDP and a biantennary complex N-glycan (G0), which provides insight into both substrate recognition and catalysis. FUT8 follows an SN2 mechanism and deploys a series of loops and an α-helix which all contribute in forming the binding site. An exosite, formed by one of these loops and an SH3 domain, is responsible for the recognition of branched sugars, making contacts specifically to the α1,3 arm GlcNAc, a feature required for catalysis. This information serves as a framework for inhibitor design, and helps to assess its potential as a therapeutic target.
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31
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Nagae M, Yamaguchi Y, Taniguchi N, Kizuka Y. 3D Structure and Function of Glycosyltransferases Involved in N-glycan Maturation. Int J Mol Sci 2020; 21:E437. [PMID: 31936666 PMCID: PMC7014118 DOI: 10.3390/ijms21020437] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/06/2020] [Accepted: 01/08/2020] [Indexed: 12/21/2022] Open
Abstract
Glycosylation is the most ubiquitous post-translational modification in eukaryotes. N-glycan is attached to nascent glycoproteins and is processed and matured by various glycosidases and glycosyltransferases during protein transport. Genetic and biochemical studies have demonstrated that alternations of the N-glycan structure play crucial roles in various physiological and pathological events including progression of cancer, diabetes, and Alzheimer's disease. In particular, the formation of N-glycan branches regulates the functions of target glycoprotein, which are catalyzed by specific N-acetylglucosaminyltransferases (GnTs) such as GnT-III, GnT-IVs, GnT-V, and GnT-IX, and a fucosyltransferase, FUT8s. Although the 3D structures of all enzymes have not been solved to date, recent progress in structural analysis of these glycosyltransferases has provided insights into substrate recognition and catalytic reaction mechanisms. In this review, we discuss the biological significance and structure-function relationships of these enzymes.
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Affiliation(s)
- Masamichi Nagae
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yoshiki Yamaguchi
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Miyagi 981-8558, Japan;
| | - Naoyuki Taniguchi
- Department of Glyco-Oncology and Medical Biochemistry, Osaka International Cancer Institute, 3-1-69 Otemae, Chuo-ku, Osaka 541-8567, Japan;
| | - Yasuhiko Kizuka
- Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN), Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
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32
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Manabe Y, Marchetti R, Takakura Y, Nagasaki M, Nihei W, Takebe T, Tanaka K, Kabayama K, Chiodo F, Hanashima S, Kamada Y, Miyoshi E, Dulal HP, Yamaguchi Y, Adachi Y, Ohno N, Tanaka H, Silipo A, Fukase K, Molinaro A. The Core Fucose on an IgG Antibody is an Endogenous Ligand of Dectin‐1. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201911875] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yoshiyuki Manabe
- Department of ChemistryGraduate School of ScienceOsaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
- Core for Medicine and Science Collaborative Research and EducationProject Research Center for Fundamental SciencesGraduate School of ScienceOsaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
| | - Roberta Marchetti
- Department of Chemical SciencesUniversity of Naples Federico II Via Cinthia 4 80126 Napoli Italy
| | - Yohei Takakura
- Department of ChemistryGraduate School of ScienceOsaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
| | - Masahiro Nagasaki
- Department of ChemistryGraduate School of ScienceOsaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
| | - Wataru Nihei
- Department of ChemistryGraduate School of ScienceOsaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
| | - Tomoyuki Takebe
- Department of ChemistryGraduate School of ScienceOsaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
| | - Katsunori Tanaka
- Department of ChemistryGraduate School of ScienceOsaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
- Biofunctional Synthetic Chemistry LaboratoryRIKEN 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Kazuya Kabayama
- Department of ChemistryGraduate School of ScienceOsaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
- Core for Medicine and Science Collaborative Research and EducationProject Research Center for Fundamental SciencesGraduate School of ScienceOsaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
| | - Fabrizio Chiodo
- Amsterdam UMCVrije Universiteit AmsterdamDept. of Molecular Cell Biology and ImmunologyAmsterdam Infection and Immunity Institute Amsterdam The Netherlands
| | - Shinya Hanashima
- Department of ChemistryGraduate School of ScienceOsaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
| | - Yoshihiro Kamada
- Department of Molecular Biochemistry & Clinical InvestigationGraduate School of MedicineOsaka University 1–7 Yamada-oka, Suita Osaka 565-0871 Japan
| | - Eiji Miyoshi
- Department of Molecular Biochemistry & Clinical InvestigationGraduate School of MedicineOsaka University 1–7 Yamada-oka, Suita Osaka 565-0871 Japan
| | - Hari Prasad Dulal
- Structural Glycobiology TeamSystems Glycobiology Research GroupRIKEN 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Yoshiki Yamaguchi
- Laboratory of Pharmaceutical Physical ChemistryTohoku Medical and Pharmaceutical University 4-4-1 Komatsushima Aoba-ku, Sendai Miyagi 981-8558 Japan
| | - Yoshiyuki Adachi
- Laboratory for Immunopharmacology of Microbial ProductsSchool of PharmacyTokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi, Hachioji Tokyo 192-0392 Japan
| | - Naohito Ohno
- Laboratory for Immunopharmacology of Microbial ProductsSchool of PharmacyTokyo University of Pharmacy and Life Sciences 1432-1 Horinouchi, Hachioji Tokyo 192-0392 Japan
| | - Hiroshi Tanaka
- Department of Chemical Science and EngineeringTokyo Institute of Technology 2-12-1-H-101, Ookayama, Meguro Tokyo 152-8552 Japan
| | - Alba Silipo
- Department of Chemical SciencesUniversity of Naples Federico II Via Cinthia 4 80126 Napoli Italy
| | - Koichi Fukase
- Department of ChemistryGraduate School of ScienceOsaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
- Core for Medicine and Science Collaborative Research and EducationProject Research Center for Fundamental SciencesGraduate School of ScienceOsaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
| | - Antonio Molinaro
- Department of ChemistryGraduate School of ScienceOsaka University 1-1 Machikaneyama, Toyonaka Osaka 560-0043 Japan
- Department of Chemical SciencesUniversity of Naples Federico II Via Cinthia 4 80126 Napoli Italy
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33
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Manabe Y, Marchetti R, Takakura Y, Nagasaki M, Nihei W, Takebe T, Tanaka K, Kabayama K, Chiodo F, Hanashima S, Kamada Y, Miyoshi E, Dulal HP, Yamaguchi Y, Adachi Y, Ohno N, Tanaka H, Silipo A, Fukase K, Molinaro A. The Core Fucose on an IgG Antibody is an Endogenous Ligand of Dectin-1. Angew Chem Int Ed Engl 2019; 58:18697-18702. [PMID: 31625659 DOI: 10.1002/anie.201911875] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Indexed: 01/07/2023]
Abstract
The core fucose, a major modification of N-glycans, is implicated in immune regulation, such as the attenuation of the antibody-dependent cell-mediated cytotoxicity of antibody drugs and the inhibition of anti-tumor responses via the promotion of PD-1 expression on T cells. Although the core fucose regulates many biological processes, no core fucose recognition molecule has been identified in mammals. Herein, we report that Dectin-1, a known anti-β-glucan lectin, recognizes the core fucose on IgG antibodies. A combination of biophysical experiments further suggested that Dectin-1 recognizes aromatic amino acids adjacent to the N-terminal asparagine at the glycosylation site as well as the core fucose. Thus, Dectin-1 appears to be the first lectin-like molecule involved in the heterovalent and specific recognition of characteristic N-glycans on antibodies.
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Affiliation(s)
- Yoshiyuki Manabe
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan.,Core for Medicine and Science Collaborative Research and Education, Project Research Center for Fundamental Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Roberta Marchetti
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Napoli, Italy
| | - Yohei Takakura
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Masahiro Nagasaki
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Wataru Nihei
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Tomoyuki Takebe
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Katsunori Tanaka
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan.,Biofunctional Synthetic Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Kazuya Kabayama
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan.,Core for Medicine and Science Collaborative Research and Education, Project Research Center for Fundamental Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Fabrizio Chiodo
- Amsterdam UMC, Vrije Universiteit Amsterdam, Dept. of Molecular Cell Biology and Immunology, Amsterdam Infection and Immunity Institute, Amsterdam, The Netherlands
| | - Shinya Hanashima
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Yoshihiro Kamada
- Department of Molecular Biochemistry & Clinical Investigation, Graduate School of Medicine, Osaka University, 1-7 Yamada-oka, Suita, Osaka, 565-0871, Japan
| | - Eiji Miyoshi
- Department of Molecular Biochemistry & Clinical Investigation, Graduate School of Medicine, Osaka University, 1-7 Yamada-oka, Suita, Osaka, 565-0871, Japan
| | - Hari Prasad Dulal
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Yoshiki Yamaguchi
- Laboratory of Pharmaceutical Physical Chemistry, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi, 981-8558, Japan
| | - Yoshiyuki Adachi
- Laboratory for Immunopharmacology of Microbial Products, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Naohito Ohno
- Laboratory for Immunopharmacology of Microbial Products, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Hiroshi Tanaka
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1-H-101, Ookayama, Meguro, Tokyo, 152-8552, Japan
| | - Alba Silipo
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Napoli, Italy
| | - Koichi Fukase
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan.,Core for Medicine and Science Collaborative Research and Education, Project Research Center for Fundamental Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Antonio Molinaro
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan.,Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Napoli, Italy
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34
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Characterisation of the Dynamic Interactions between Complex
N
‐Glycans and Human CD22. Chembiochem 2019; 21:129-140. [DOI: 10.1002/cbic.201900295] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Indexed: 12/21/2022]
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35
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Nakano M, Mishra SK, Tokoro Y, Sato K, Nakajima K, Yamaguchi Y, Taniguchi N, Kizuka Y. Bisecting GlcNAc Is a General Suppressor of Terminal Modification of N-glycan. Mol Cell Proteomics 2019; 18:2044-2057. [PMID: 31375533 PMCID: PMC6773561 DOI: 10.1074/mcp.ra119.001534] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 08/01/2019] [Indexed: 12/18/2022] Open
Abstract
Glycoproteins are decorated with complex glycans for protein functions. However, regulation mechanisms of complex glycan biosynthesis are largely unclear. Here we found that bisecting GlcNAc, a branching sugar residue in N-glycan, suppresses the biosynthesis of various types of terminal epitopes in N-glycans, including fucose, sialic acid and human natural killer-1. Expression of these epitopes in N-glycan was elevated in mice lacking the biosynthetic enzyme of bisecting GlcNAc, GnT-III, and was conversely suppressed by GnT-III overexpression in cells. Many glycosyltransferases for N-glycan terminals were revealed to prefer a nonbisected N-glycan as a substrate to its bisected counterpart, whereas no up-regulation of their mRNAs was found. This indicates that the elevated expression of the terminal N-glycan epitopes in GnT-III-deficient mice is attributed to the substrate specificity of the biosynthetic enzymes. Molecular dynamics simulations further confirmed that nonbisected glycans were preferentially accepted by those glycosyltransferases. These findings unveil a new regulation mechanism of protein N-glycosylation.
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Affiliation(s)
- Miyako Nakano
- Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashihiroshima, Hiroshima 739-8530, Japan
| | - Sushil K Mishra
- Glycoscience Group, National University of Ireland, Galway, Ireland; Structural Glycobiology Team, RIKEN-Max Planck Joint Research Center, Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yuko Tokoro
- Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN), Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Keiko Sato
- Disease Glycomics Team, RIKEN-Max Planck Joint Research Center, Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kazuki Nakajima
- Division of Clinical Research Promotion and Support, Center for Research Promotion, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan.
| | - Yoshiki Yamaguchi
- Structural Glycobiology Team, RIKEN-Max Planck Joint Research Center, Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Synthetic Cellular Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Naoyuki Taniguchi
- Disease Glycomics Team, RIKEN-Max Planck Joint Research Center, Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Department of Glyco-Oncology and Medical Biochemistry, Osaka International Cancer Institute, 3-1-69 Otemae, Chuoku, Osaka 541-8567, Japan
| | - Yasuhiko Kizuka
- Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN), Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan; Disease Glycomics Team, RIKEN-Max Planck Joint Research Center, Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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36
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Oshima H, Re S, Sugita Y. Replica-Exchange Umbrella Sampling Combined with Gaussian Accelerated Molecular Dynamics for Free-Energy Calculation of Biomolecules. J Chem Theory Comput 2019; 15:5199-5208. [PMID: 31539245 DOI: 10.1021/acs.jctc.9b00761] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We have developed an enhanced conformational sampling method combining replica-exchange umbrella sampling (REUS) with Gaussian accelerated molecular dynamics (GaMD). REUS enhances the sampling along predefined reaction coordinates, while GaMD accelerates the conformational dynamics by adding a boost potential to the system energy. The method, which we call GaREUS (Gaussian accelerated replica-exchange umbrella sampling), enhances the sampling more efficiently than REUS or GaMD, while the computational resource for GaREUS is the same as that required for REUS. The two-step reweighting procedure using the multistate Bennett acceptance ratio method and the cumulant expansion for the exponential average is applied to the simulation trajectories for obtaining the unbiased free-energy landscapes. We apply GaREUS to the calculations of free-energy landscapes for three different cases: conformational equilibria of N-glycan, folding of chignolin, and conformational change of adenyl kinase. We show that GaREUS speeds up the convergences of free-energy calculations using the same amount of computational resources as REUS. The free-energy landscapes reweighted from the trajectories of GaREUS agree with previously reported ones. GaREUS is applicable to free-energy calculations of various biomolecular dynamics and functions with reasonable computational costs.
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Affiliation(s)
- Hiraku Oshima
- Laboratory for Biomolecular Function Simulation , RIKEN Center for Biosystems Dynamics Research , Integrated Innovation Building N702, 6-7-1 Minatojima-minamimachi, Chuo-ku , Kobe , Hyogo 650-0047 , Japan
| | - Suyong Re
- Laboratory for Biomolecular Function Simulation , RIKEN Center for Biosystems Dynamics Research , Integrated Innovation Building N702, 6-7-1 Minatojima-minamimachi, Chuo-ku , Kobe , Hyogo 650-0047 , Japan
| | - Yuji Sugita
- Laboratory for Biomolecular Function Simulation , RIKEN Center for Biosystems Dynamics Research , Integrated Innovation Building N702, 6-7-1 Minatojima-minamimachi, Chuo-ku , Kobe , Hyogo 650-0047 , Japan.,Theoretical Molecular Science Laboratory , RIKEN Cluster for Pioneering Research , 2-1 Hirosawa, Wako-shi , Saitama 351-0198 , Japan.,Computational Biophysics Research Team , RIKEN Center for Computational Science , Integrated Innovation Building N702, 6-7-1 Minatojima-minamimachi, Chuo-ku , Kobe , Hyogo 650-0047 , Japan
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37
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Chandler KB, Mehta N, Leon DR, Suscovich TJ, Alter G, Costello CE. Multi-isotype Glycoproteomic Characterization of Serum Antibody Heavy Chains Reveals Isotype- and Subclass-Specific N-Glycosylation Profiles. Mol Cell Proteomics 2019; 18:686-703. [PMID: 30659065 PMCID: PMC6442369 DOI: 10.1074/mcp.ra118.001185] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/16/2019] [Indexed: 01/16/2023] Open
Abstract
Antibodies are critical glycoproteins that bridge the innate and adaptive immune systems to provide protection against infection. The isotype/subclass of the antibody, the co-translational N-glycosylation on the CH2 domain, and the remodeling of the N-linked glycans during passage through the ER and Golgi are the known variables within the Fc domain that program antibody effector function. Through investigations of monoclonal therapeutics, it has been observed that addition or removal of specific monosaccharide residues from antibody N-glycans can influence the potency of antibodies, highlighting the importance of thoroughly characterizing antibody N-glycosylation. Although IgGs usually have a single N-glycosylation site and are well studied, other antibody isotypes, e.g. IgA and IgM, that are the first responders in certain diseases, have two to five sites/monomer of antibody, and little is known about their N-glycosylation. Here we employ a nLC-MS/MS method using stepped-energy higher energy collisional dissociation to characterize the N-glycan repertoire and site occupancy of circulating serum antibodies. We simultaneously determined the site-specific N-linked glycan repertoire for IgG1, IgG4, IgA1, IgA2, and IgM in individual healthy donors. Compared with IgG1, IgG4 displayed a higher relative abundance of G1S1F and a lower relative abundance of G1FB. IgA1 and IgA2 displayed mostly biantennary N-glycans. IgA2 variants with the either serine (S93) or proline (P93) were detected. In digests of the sera from a subset of donors, we detected an unmodified peptide containing a proline residue at position 93; this substitution would strongly disfavor N-glycosylation at N92. IgM sites N46, N209, and N272 displayed mostly complex glycans, whereas sites N279 and N439 displayed higher relative abundances of high-mannose glycoforms. This multi-isotype approach is a crucial step toward developing a platform to define disease-specific N-glycan signatures for different isotypes to help tune antibodies to induce protection. Data are available via ProteomeXchange with identifier PXD010911.
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Affiliation(s)
- Kevin Brown Chandler
- From the ‡Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts
| | - Nickita Mehta
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts
| | - Deborah R Leon
- From the ‡Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts
| | - Todd J Suscovich
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts
| | - Catherine E Costello
- From the ‡Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts;.
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38
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Sugita Y, Kamiya M, Oshima H, Re S. Replica-Exchange Methods for Biomolecular Simulations. Methods Mol Biol 2019; 2022:155-177. [PMID: 31396903 DOI: 10.1007/978-1-4939-9608-7_7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In this study, a replica-exchange method was developed to overcome conformational sampling difficulties in computer simulations of spin glass or other systems with rugged free-energy landscapes. This method was then applied to the protein-folding problem in combination with molecular dynamics (MD) simulation. Owing to its simplicity and sampling efficiency, the replica-exchange method has been applied to many other biological problems and has been continuously improved. The method has often been combined with other sampling techniques, such as umbrella sampling, free-energy perturbation, metadynamics, and Gaussian accelerated MD (GaMD). In this chapter, we first summarize the original replica-exchange molecular dynamics (REMD) method and discuss how new algorithms related to the original method are implemented to add new features. Heterogeneous and flexible structures of an N-glycan in a solution are simulated as an example of applications by REMD, replica exchange with solute tempering, and GaMD. The sampling efficiency of these methods on the N-glycan system and the convergence of the free-energy changes are compared. REMD simulation protocols and trajectory analysis using the GENESIS software are provided to facilitate the practical use of advanced simulation methods.
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Affiliation(s)
- Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Saitama, Japan. .,Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Japan. .,Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.
| | - Motoshi Kamiya
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Japan
| | - Hiraku Oshima
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Suyong Re
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
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39
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Tachi Y, Okamoto Y, Okumura H. Conformational properties of an artificial GM1 glycan cluster based on a metal-ligand complex. J Chem Phys 2018; 149:135101. [PMID: 30292198 DOI: 10.1063/1.5045310] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
An artificial glycan cluster, in which 24 monosialotetrahexosylganglioside (GM1) glycans are transplanted to the interface of a metal-ligand complex, was recently proposed to investigate the interaction between GM1 glycan clusters and amyloidogenic proteins by NMR analysis. In this study, all-atom molecular dynamics simulations were performed to characterize the conformational properties of the artificial GM1 glycan cluster. We found that more than 65% of GM1 glycans are clustered by interchain hydrogen bonds. Interchain hydrogen bonds are mainly formed between Neu5Ac and Gal'. Pentamers were most frequently observed in the metal-ligand complex. GM1 glycans are tilted and hydrophobically interact with ligand moieties. The hydrophobic surface of the metal-ligand complex increases intrachain hydrogen bonds in each conformation of the GM1 glycans. The increase of intrachain hydrogen bonds stabilizes the local minimum conformations of the GM1 glycan in comparison with the monomeric one. Interchain hydrogen bonding between glycans and glycan-ligand hydrophobic interactions also contribute to this conformational stabilization. Our results provide the physicochemical properties of the new artificial GM1 glycan cluster under the thermal fluctuations for understanding its protein recognition and designing the drug material for amyloidogenic proteins.
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Affiliation(s)
- Yuhei Tachi
- Department of Physics, Graduate school of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Yuko Okamoto
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Hisashi Okumura
- Research Center for Computational Science, Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan
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40
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Structure and mechanism of cancer-associated N-acetylglucosaminyltransferase-V. Nat Commun 2018; 9:3380. [PMID: 30140003 PMCID: PMC6107550 DOI: 10.1038/s41467-018-05931-w] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 07/31/2018] [Indexed: 12/31/2022] Open
Abstract
N-acetylglucosaminyltransferase-V (GnT-V) alters the structure of specific N-glycans by modifying α1-6-linked mannose with a β1-6-linked N-acetylglucosamine branch. β1-6 branch formation on cell surface receptors accelerates cancer metastasis, making GnT-V a promising target for drug development. However, the molecular basis of GnT-V's catalytic mechanism and substrate specificity are not fully understood. Here, we report crystal structures of human GnT-V luminal domain with a substrate analog. GnT-V luminal domain is composed of a GT-B fold and two accessary domains. Interestingly, two aromatic rings sandwich the α1-6 branch of the acceptor N-glycan and restrain the global conformation, partly explaining the fine branch specificity of GnT-V. In addition, interaction of the substrate N-glycoprotein with GnT-V likely contributes to protein-selective and site-specific glycan modification. In summary, the acceptor-GnT-V complex structure suggests a catalytic mechanism, explains the previously observed inhibition of GnT-V by branching enzyme GnT-III, and provides a basis for the rational design of drugs targeting N-glycan branching.
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41
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Ma J, Sanda M, Wei R, Zhang L, Goldman R. Quantitative analysis of core fucosylation of serum proteins in liver diseases by LC-MS-MRM. J Proteomics 2018; 189:67-74. [PMID: 29427759 DOI: 10.1016/j.jprot.2018.02.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/30/2018] [Accepted: 02/02/2018] [Indexed: 12/22/2022]
Abstract
Aberrant core fucosylation of proteins has been linked to liver diseases. In this study, we carried out multiple reaction monitoring (MRM) quantification of core fucosylated N-glycopeptides of serum proteins partially deglycosylated by a combination of endoglycosidases (endoF1, endoF2, and endoF3). To minimize variability associated with the preparatory steps, the analysis was performed without enrichment of glycopeptides or fractionation of serum besides the nanoRP chromatography. Specifically, we quantified core fucosylation of 22 N-glycopeptides derived from 17 proteins together with protein abundance of these glycoproteins in a cohort of 45 participants (15 disease-free control, 15 fibrosis and 15 cirrhosis patients) using a multiplex nanoUPLC-MS-MRM workflow. We find increased core fucosylation of 5 glycopeptides at the stage of liver fibrosis (i.e., N630 of serotransferrin, N107 of alpha-1-antitrypsin, N253 of plasma protease C1 inhibitor, N397 of ceruloplasmin, and N86 of vitronectin), increase of additional 6 glycopeptides at the stage of cirrhosis (i.e., N138 and N762 of ceruloplasmin, N354 of clusterin, N187 of hemopexin, N71 of immunoglobulin J chain, and N127 of lumican), while the degree of core fucosylation of 10 glycopeptides did not change. Interestingly, although we observe an increase in the core fucosylation at N86 of vitronectin in liver fibrosis, core fucosylation decreases on the N169 glycopeptide of the same protein. Our results demonstrate that the changes in core fucosylation are protein and site specific during the progression of fibrotic liver disease and independent of the changes in the quantity of N-glycoproteins. It is expected that the fully optimized multiplex LC-MS-MRM assay of core fucosylated glycopeptides will be useful for the serologic assessment of the fibrosis of liver. BIOLOGICAL SIGNIFICANCE: We have quantified the difference in core fucosylation among three comparison groups (healthy control, fibrosis and cirrhosis patients) using a sensitive and selective LC-MS-MRM method. Despite an overall increase in core fucosylation of many of the glycoproteins that we examined, core fucosylation changed in a protein- and site-specific manner. Moreover, increased and decreased fucosylation was observed on different N-glycopeptides of the same protein. Altered core fucosylation of N-glycopeptides might be used as an alternative serologic assay for the evaluation of fibrotic liver disease.
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Affiliation(s)
- Junfeng Ma
- Proteomics and Metabolomics Shared Resource, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Miloslav Sanda
- Proteomics and Metabolomics Shared Resource, Georgetown University Medical Center, Washington, DC 20057, USA; Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | - Renhuizi Wei
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | - Lihua Zhang
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | - Radoslav Goldman
- Proteomics and Metabolomics Shared Resource, Georgetown University Medical Center, Washington, DC 20057, USA; Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA; Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC 20057, USA.
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42
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Hanashima S, Suga A, Yamaguchi Y. Bisecting GlcNAc restricts conformations of branches in model N-glycans with GlcNAc termini. Carbohydr Res 2018; 456:53-60. [PMID: 29274553 DOI: 10.1016/j.carres.2017.12.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 12/10/2017] [Indexed: 01/23/2023]
Abstract
Bisected N-glycans play significant roles in tumor migration and Alzheimer's disease through modulating the action and localization of their carrier proteins. Such biological functions are often discussed in terms of the conformation of the attached N-glycans with or without bisecting GlcNAc. To obtain insights into the effects of bisecting GlcNAc on glycan conformation, a systematic NMR structural analysis was performed on two pairs of synthetic N-glycans, with and without bisecting GlcNAc. The analysis reveals that terminal GlcNAcs and bisecting GlcNAc cooperate to restrict the conformations of both the α1-3 and α1-6 branches of N-glycans. 1H and 13C chemical shift comparisons suggest that bisecting GlcNAc directly modulates local conformation. Unique NOE correlations between core-mannose and the α1-3 branch mannose as well as the 3JC-H constant of the glycoside linkage indicate that bisecting GlcNAc restricts the conformation of the 1-3 branch. The angles of the glycosidic bonds between core-mannose and α1-6 branch mannose derived from 3JC-H and 3JH-H coupling constants show that terminal GlcNAcs restrict the distribution of the ψ angle to 180° and the bisecting GlcNAc increases the distribution of the ω angle +60° in the presence of terminal GlcNAcs. It is feasible that restriction of branch conformations by bisecting GlcNAc has important consequences for protein-glycan interplay and following biological events.
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Affiliation(s)
- Shinya Hanashima
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center for Systems Chemical Biology, RIKEN Global Research Cluster, Wako, Saitama, 351-0198, Japan; Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Akitsugu Suga
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center for Systems Chemical Biology, RIKEN Global Research Cluster, Wako, Saitama, 351-0198, Japan
| | - Yoshiki Yamaguchi
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center for Systems Chemical Biology, RIKEN Global Research Cluster, Wako, Saitama, 351-0198, Japan.
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43
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Re S, Watabe S, Nishima W, Muneyuki E, Yamaguchi Y, MacKerell AD, Sugita Y. Characterization of Conformational Ensembles of Protonated N-glycans in the Gas-Phase. Sci Rep 2018; 8:1644. [PMID: 29374210 PMCID: PMC5786100 DOI: 10.1038/s41598-018-20012-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 01/10/2018] [Indexed: 12/18/2022] Open
Abstract
Ion mobility mass spectrometry (IM-MS) is a technique capable of investigating structural changes of biomolecules based on their collision cross section (CCS). Recent advances in IM-MS allow us to separate carbohydrate isomers with subtle conformational differences, but the relationship between CCS and atomic structure remains elusive. Here, we characterize conformational ensembles of gas-phase N-glycans under the electrospray ionization condition using molecular dynamics simulations with enhanced sampling. We show that the separation of CCSs between isomers reflects folding features of N-glycans, which are determined both by chemical compositions and protonation states. Providing a physicochemical basis of CCS for N-glycans helps not only to interpret IM-MS measurements but also to estimate CCSs of complex glycans.
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Affiliation(s)
- Suyong Re
- RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Shigehisa Watabe
- RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Graduate School of Science and Engineering, Chuo University, 1-13-27, Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan
| | - Wataru Nishima
- RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,RIKEN iTHES, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Eiro Muneyuki
- Graduate School of Science and Engineering, Chuo University, 1-13-27, Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan
| | - Yoshiki Yamaguchi
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN Global Research Cluster, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland, 21201, USA
| | - Yuji Sugita
- RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. .,RIKEN iTHES, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
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44
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Nagae M, Mishra SK, Hanashima S, Tateno H, Yamaguchi Y. Distinct roles for each N-glycan branch interacting with mannose-binding type Jacalin-related lectins Orysata and Calsepa. Glycobiology 2017; 27:1120-1133. [DOI: 10.1093/glycob/cwx081] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 09/06/2017] [Indexed: 12/17/2022] Open
Affiliation(s)
- Masamichi Nagae
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN Global Research Cluster, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Sushil K Mishra
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN Global Research Cluster, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Shinya Hanashima
- Department of Chemistry, Osaka University, Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Hiroaki Tateno
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 2, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Yoshiki Yamaguchi
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN Global Research Cluster, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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45
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Conformational Heterogeneity of the HIV Envelope Glycan Shield. Sci Rep 2017; 7:4435. [PMID: 28667249 PMCID: PMC5493700 DOI: 10.1038/s41598-017-04532-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/16/2017] [Indexed: 01/08/2023] Open
Abstract
To better understand the conformational properties of the glycan shield covering the surface of the HIV gp120/gp41 envelope (Env) trimer, and how the glycan shield impacts the accessibility of the underlying protein surface, we performed enhanced sampling molecular dynamics (MD) simulations of a model glycosylated HIV Env protein and related systems. Our simulation studies revealed a conformationally heterogeneous glycan shield with a network of glycan-glycan interactions more extensive than those observed to date. We found that partial preorganization of the glycans potentially favors binding by established broadly neutralizing antibodies; omission of several specific glycans could increase the accessibility of other glycans or regions of the protein surface to antibody or CD4 receptor binding; the number of glycans that can potentially interact with known antibodies is larger than that observed in experimental studies; and specific glycan conformations can maximize or minimize interactions with individual antibodies. More broadly, the enhanced sampling MD simulations described here provide a valuable tool to guide the engineering of specific Env glycoforms for HIV vaccine design.
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46
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Jennewein MF, Alter G. The Immunoregulatory Roles of Antibody Glycosylation. Trends Immunol 2017; 38:358-372. [DOI: 10.1016/j.it.2017.02.004] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 01/03/2017] [Accepted: 02/10/2017] [Indexed: 12/12/2022]
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47
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Gimeno A, Reichardt NC, Cañada FJ, Perkams L, Unverzagt C, Jiménez-Barbero J, Ardá A. NMR and Molecular Recognition of N-Glycans: Remote Modifications of the Saccharide Chain Modulate Binding Features. ACS Chem Biol 2017; 12:1104-1112. [PMID: 28192664 PMCID: PMC5435455 DOI: 10.1021/acschembio.6b01116] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Glycans
play a key role as recognition elements in the communication
of cells and other organisms. Thus, the analysis of carbohydrate–protein
interactions has gained significant importance. In particular, nuclear
magnetic resonance (NMR) techniques are considered powerful tools
to detect relevant features in the interaction between sugars and
their natural receptors. Here, we present the results obtained in
the study on the molecular recognition of different mannose-containing
glycans by Pisum sativum agglutinin. NMR experiments
supported by Corcema-ST analysis, isothermal titration calorimetry
(ITC) experiments, and molecular dynamics (MD) protocols have been
successfully applied to unmask important binding features and especially
to determine how a remote branching substituent significantly alters
the binding mode of the sugar entity. These results highlight the
key influence of common structural modifications in natural glycans
on molecular recognition processes and underscore their importance
for the development of biomedical applications.
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Affiliation(s)
- Ana Gimeno
- Molecular Recognition & Host−Pathogen Interactions Unit, CIC bioGUNE, Bizkaia Technology Park, Building 801A, 48170 Derio, Spain
| | - Niels-Christian Reichardt
- Glycotechnology
Laboratory, CIC biomaGUNE, Paseo Miramón 182, 20014 San Sebastián, Spain
- CIBER-BBN, Paseo Miramón 182, 20014 San Sebastián, Spain
| | - F. Javier Cañada
- Chemical
and Physical Biology, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Lukas Perkams
- Bioorganic
Chemistry, Gebäude NWI, Universität Bayreuth, 95440 Bayreuth, Germany
| | - Carlo Unverzagt
- Bioorganic
Chemistry, Gebäude NWI, Universität Bayreuth, 95440 Bayreuth, Germany
| | - Jesús Jiménez-Barbero
- Molecular Recognition & Host−Pathogen Interactions Unit, CIC bioGUNE, Bizkaia Technology Park, Building 801A, 48170 Derio, Spain
- Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 13, 48009 Bilbao, Spain
- Department of Organic Chemistry II, Faculty of Science & Technology, University of the Basque Country, 48940 Leioa, Bizkaia, Spain
| | - Ana Ardá
- Molecular Recognition & Host−Pathogen Interactions Unit, CIC bioGUNE, Bizkaia Technology Park, Building 801A, 48170 Derio, Spain
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48
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Galvelis R, Re S, Sugita Y. Enhanced Conformational Sampling of N-Glycans in Solution with Replica State Exchange Metadynamics. J Chem Theory Comput 2017; 13:1934-1942. [DOI: 10.1021/acs.jctc.7b00079] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Raimondas Galvelis
- RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako-shi,
Saitama 351-0198, Japan
| | - Suyong Re
- RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako-shi,
Saitama 351-0198, Japan
- RIKEN Quantitative Biology Center, Integrated Innovation Building 7F, 6-7-1 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Yuji Sugita
- RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako-shi,
Saitama 351-0198, Japan
- RIKEN iTHES, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
- RIKEN Advanced Institute for Computational Science, Integrated Innovation Building 7F, 6-7-1 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- RIKEN Quantitative Biology Center, Integrated Innovation Building 7F, 6-7-1 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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49
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Hirano M, Totani K, Fukuda T, Gu J, Suzuki A. N-Glycoform-dependent interactions of megalin with its ligands. Biochim Biophys Acta Gen Subj 2017; 1861:3106-3118. [DOI: 10.1016/j.bbagen.2016.10.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 09/30/2016] [Accepted: 10/19/2016] [Indexed: 12/18/2022]
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50
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Kanjanatanin P, Pichyangkura R, Chunsrivirot S. Replica exchange molecular dynamics simulations reveal the structural and molecular properties of levan-type fructo-oligosaccharides of various chain lengths. BMC Bioinformatics 2016; 17:306. [PMID: 27534934 PMCID: PMC4989353 DOI: 10.1186/s12859-016-1182-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 08/12/2016] [Indexed: 12/17/2022] Open
Abstract
Background Levan and levan-type fructo-oligosaccharides (LFOs) have various potential applications in pharmaceutical and food industries due to their beneficial properties such as their low intrinsic viscosity and high water solubility. Previous studies showed that they exhibited prebiotic effects, anti-inflammatory and anti-tumor activities against Sarcoma-180 tumor cells of human. Despite their various potential applications, the structural and molecular properties of LFOs of various chain lengths are not well understood. Results We employed the replica-exchange molecular dynamics simulations method (REMD) in AMBER14 to elucidate structural and molecular properties of LFOs with chain lengths of 5 (LFO5), 10 (LFO10) and 15 (LFO15) residues in two models of generalized Born implicit solvent (GBHCT and GBOBC1). For LFO10 and LFO15, four distinct conformations (helix-like, partial helix, zig-zag and random structures) were characterized by their upper-middle and lower-middle torsions. For LFO5, two distinct conformations (partial helix and random structures) were characterized by their middle torsion and molecular angle of residues 1, 3 and 5. To determine hydrogen bonds important for the formation of helix-like structures of LFO10 and LFO15, occurrence frequencies of hydrogen bonds were analyzed, and the O6(i)--H3O(i+1) hydrogen bond was found with the highest frequency, suggesting its importance in helix formation. Among three dihedral angles between two fructosyl units [ϕ (O5’-C2’-O6-C6), ψ (C2’-O6-C6-C5) and ω (O6-C6-C5-C4)], dihedral angle distributions showed that ω was the most flexible dihedral angle and probably responsible for conformational differences of LFOs. Conclusions Our study provides important insights into the structural and molecular properties of LFOs, which tend to form helical structures as the chain length increases from 5 to 15 residues. This information could be beneficial for the selection of LFOs with appropriate lengths and properties for pharmaceutical and biological applications. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1182-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pongsakorn Kanjanatanin
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Phaya Thai road, Pathumwan, Bangkok, 10330, Thailand.,Structural and Computational Biology Research Group, Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Phaya Thai road, Pathumwan, Bangkok, 10330, Thailand
| | - Rath Pichyangkura
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Phaya Thai road, Pathumwan, Bangkok, 10330, Thailand
| | - Surasak Chunsrivirot
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Phaya Thai road, Pathumwan, Bangkok, 10330, Thailand. .,Structural and Computational Biology Research Group, Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Phaya Thai road, Pathumwan, Bangkok, 10330, Thailand.
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