1
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Lefèbre J, Falk T, Ning Y, Rademacher C. Secondary Sites of the C-type Lectin-Like Fold. Chemistry 2024; 30:e202400660. [PMID: 38527187 DOI: 10.1002/chem.202400660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/23/2024] [Accepted: 03/25/2024] [Indexed: 03/27/2024]
Abstract
C-type lectins are a large superfamily of proteins involved in a multitude of biological processes. In particular, their involvement in immunity and homeostasis has rendered them attractive targets for diverse therapeutic interventions. They share a characteristic C-type lectin-like domain whose adaptability enables them to bind a broad spectrum of ligands beyond the originally defined canonical Ca2+-dependent carbohydrate binding. Together with variable domain architecture and high-level conformational plasticity, this enables C-type lectins to meet diverse functional demands. Secondary sites provide another layer of regulation and are often intricately linked to functional diversity. Located remote from the canonical primary binding site, secondary sites can accommodate ligands with other physicochemical properties and alter protein dynamics, thus enhancing selectivity and enabling fine-tuning of the biological response. In this review, we outline the structural determinants allowing C-type lectins to perform a large variety of tasks and to accommodate the ligands associated with it. Using the six well-characterized Ca2+-dependent and Ca2+-independent C-type lectin receptors DC-SIGN, langerin, MGL, dectin-1, CLEC-2 and NKG2D as examples, we focus on the characteristics of non-canonical interactions and secondary sites and their potential use in drug discovery endeavors.
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Affiliation(s)
- Jonathan Lefèbre
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
- Vienna Doctoral School of Pharmaceutical, Nutritional and Sport, Sciences, University of Vienna, Vienna, Austria
- Department of Microbiology, Immunology and Genetics, University of Vienna, Max F. Perutz Labs, Vienna, Austria
| | - Torben Falk
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
- Vienna Doctoral School of Pharmaceutical, Nutritional and Sport, Sciences, University of Vienna, Vienna, Austria
- Department of Microbiology, Immunology and Genetics, University of Vienna, Max F. Perutz Labs, Vienna, Austria
| | - Yunzhan Ning
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
- Vienna Doctoral School of Pharmaceutical, Nutritional and Sport, Sciences, University of Vienna, Vienna, Austria
- Department of Microbiology, Immunology and Genetics, University of Vienna, Max F. Perutz Labs, Vienna, Austria
| | - Christoph Rademacher
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
- Department of Microbiology, Immunology and Genetics, University of Vienna, Max F. Perutz Labs, Vienna, Austria
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2
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Ma W, Xu Z, Jiang Y, Liu J, Xu D, Huang W, Li T. Divergent Enzymatic Assembly of a Comprehensive 64-Membered IgG N-Glycan Library for Functional Glycomics. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303832. [PMID: 37632720 PMCID: PMC10602528 DOI: 10.1002/advs.202303832] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/25/2023] [Indexed: 08/28/2023]
Abstract
N-Glycosylation, a main post-translational modification of Immunoglobulin G (IgG), plays a significant role in modulating the immune functions of IgG. However, the precise function elucidation of IgG N-glycosylation remains impeded due to the obstacles in obtaining comprehensive and well-defined N-glycans. Here, an easy-to-implement divergent approach is described to synthesize a 64-membered IgG N-glycan library covering all possible biantennary and bisected N-glycans by reprogramming biosynthetic assembly lines based on the inherent branch selectivity and substrate specificity of enzymes. The unique binding specificities of 64 N-glycans with different proteins are deciphered by glycan microarray technology. This unprecedented collection of synthetic IgG N-glycans can serve as standards for N-glycan structure identification in complex biological samples and the microarray data enrich N-glycan glycomics to facilitate biomedical applications.
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Affiliation(s)
- Wenjing Ma
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhuojia Xu
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuhan Jiang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Jialin Liu
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Dandan Xu
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou, 310024, China
| | - Wei Huang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou, 310024, China
| | - Tiehai Li
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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3
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Dang L, Li P, Dan W, Liu H, Shen J, Zhu B, Jia L, Sun S. Glycoproteomic analysis of regulatory effects of bisecting N-glycans on N-glycan biosynthesis and protein expressions in human HK-2 cells. Carbohydr Res 2023; 531:108894. [PMID: 37421876 DOI: 10.1016/j.carres.2023.108894] [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: 09/27/2022] [Revised: 06/02/2023] [Accepted: 07/01/2023] [Indexed: 07/10/2023]
Abstract
Bisecting N-glycan is known to be a metastasis suppressor and plays a regulatory role in the biosynthesis of N-glycans. Previous studies have shown that bisecting N-glycans are capable of modulating both the branching and terminal modifications of glycans. However, these effects have been investigated mainly by glycomic approaches and it remains unclear how they alter when glycans are attached to different glycosites of proteins. Here, we systematically investigated the regulatory roles of bisecting N-glycans in human HK-2 cells using StrucGP, a strategy we developed for structural interpretation of site-specific N-glycans on glycoproteins. The glycoproteomics analysis showed that most of bisecting N-glycans are complex type and often occur in company with core fucosylation. With the overexpression and knockdown of MGAT3, the only enzyme responsible for bisecting N-glycan synthesis, we found that bisecting N-glycans can impact the biosynthesis of N-glycans from multiple aspects, including glycan types, branching, sialylation, fucosylation (different effects for core and terminal fucosylation) as well as the presence of terminal N-acetylglucosamine. Furthermore, gene ontology analysis suggested that most proteins with bisecting N-glycans located in the extracellular region or membrane, where they function mostly in cell adhesion, extracellular matrix regulation and cell signaling. Finally, we showed that overexpression of bisecting N-glycans had a broad impact on the protein expressions of HK-2 cells, involving multiple biological processes. Taken together, our work systematically demonstrated the expression profiles of bisecting N-glycans, and their regulatory effects on the biosynthesis of N-glycans and protein expressions, which provide valuable information for the functional elucidation of bisecting N-glycans.
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Affiliation(s)
- Liuyi Dang
- College of Life Sciences, Northwest University, Xi'an, Shaanxi Province, 710069, China
| | - Pengfei Li
- College of Life Sciences, Northwest University, Xi'an, Shaanxi Province, 710069, China
| | - Wei Dan
- College of Life Sciences, Northwest University, Xi'an, Shaanxi Province, 710069, China
| | - Huanhuan Liu
- College of Life Sciences, Northwest University, Xi'an, Shaanxi Province, 710069, China
| | - Jiechen Shen
- College of Life Sciences, Northwest University, Xi'an, Shaanxi Province, 710069, China
| | - Bojing Zhu
- College of Life Sciences, Northwest University, Xi'an, Shaanxi Province, 710069, China
| | - Li Jia
- College of Life Sciences, Northwest University, Xi'an, Shaanxi Province, 710069, China
| | - Shisheng Sun
- College of Life Sciences, Northwest University, Xi'an, Shaanxi Province, 710069, China.
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4
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Leusmann S, Ménová P, Shanin E, Titz A, Rademacher C. Glycomimetics for the inhibition and modulation of lectins. Chem Soc Rev 2023; 52:3663-3740. [PMID: 37232696 PMCID: PMC10243309 DOI: 10.1039/d2cs00954d] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Indexed: 05/27/2023]
Abstract
Carbohydrates are essential mediators of many processes in health and disease. They regulate self-/non-self- discrimination, are key elements of cellular communication, cancer, infection and inflammation, and determine protein folding, function and life-times. Moreover, they are integral to the cellular envelope for microorganisms and participate in biofilm formation. These diverse functions of carbohydrates are mediated by carbohydrate-binding proteins, lectins, and the more the knowledge about the biology of these proteins is advancing, the more interfering with carbohydrate recognition becomes a viable option for the development of novel therapeutics. In this respect, small molecules mimicking this recognition process become more and more available either as tools for fostering our basic understanding of glycobiology or as therapeutics. In this review, we outline the general design principles of glycomimetic inhibitors (Section 2). This section is then followed by highlighting three approaches to interfere with lectin function, i.e. with carbohydrate-derived glycomimetics (Section 3.1), novel glycomimetic scaffolds (Section 3.2) and allosteric modulators (Section 3.3). We summarize recent advances in design and application of glycomimetics for various classes of lectins of mammalian, viral and bacterial origin. Besides highlighting design principles in general, we showcase defined cases in which glycomimetics have been advanced to clinical trials or marketed. Additionally, emerging applications of glycomimetics for targeted protein degradation and targeted delivery purposes are reviewed in Section 4.
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Affiliation(s)
- Steffen Leusmann
- Chemical Biology of Carbohydrates (CBCH), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, 66123 Saarbrücken, Germany.
- Department of Chemistry, Saarland University, 66123 Saarbrücken, Germany
- Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig, Germany
| | - Petra Ménová
- University of Chemistry and Technology, Prague, Technická 5, 16628 Prague 6, Czech Republic
| | - Elena Shanin
- Department of Pharmaceutical Sciences, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria.
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Biocenter 5, 1030 Vienna, Austria
| | - Alexander Titz
- Chemical Biology of Carbohydrates (CBCH), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, 66123 Saarbrücken, Germany.
- Department of Chemistry, Saarland University, 66123 Saarbrücken, Germany
- Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig, Germany
| | - Christoph Rademacher
- Department of Pharmaceutical Sciences, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria.
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Biocenter 5, 1030 Vienna, Austria
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5
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Mastrangeli R, Satwekar A, Bierau H. Innovative Metrics for Reporting and Comparing the Glycan Structural Profile in Biotherapeutics. Molecules 2023; 28:molecules28083304. [PMID: 37110538 PMCID: PMC10143042 DOI: 10.3390/molecules28083304] [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: 03/09/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
Glycosylation is a critical quality attribute in biotherapeutics, impacting properties such as protein stability, solubility, clearance rate, efficacy, immunogenicity, and safety. Due to the heterogenic and complex nature of protein glycosylation, comprehensive characterization is demanding. Moreover, the lack of standardized metrics for evaluating and comparing glycosylation profiles hinders comparability studies and the establishment of manufacturing control strategies. To address both challenges, we propose a standardized approach based on novel metrics for a comprehensive glycosylation fingerprint which greatly facilitates the reporting and objective comparison of glycosylation profiles. The analytical workflow is based on a liquid chromatography-mass spectrometry-based multi-attribute method. Based on the analytical data, a matrix of glycosylation-related quality attributes, both at site-specific and whole molecule level, are computed, which provide metrics for a comprehensive product glycosylation fingerprint. Two case studies illustrate the applicability of the proposed indices as a standardized and versatile approach for reporting all dimensions of the glycosylation profile. The proposed approach further facilitates the assessments of risks associated with changes in the glycosylation profile that may affect efficacy, clearance, and immunogenicity.
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Affiliation(s)
- Renato Mastrangeli
- Global CMC Development Technology & Innovation, CMC Science & Intelligence, Merck Serono SpA (An affiliate of Merck KGaA, Darmstadt, Germany), Guidonia Montecelio, 00012 Rome, Italy
| | - Abhijeet Satwekar
- Global CMC Development, Global Analytical Development, Global Analytical-Pharmaceutical Science & Innovation, Merck Serono SpA (An affiliate of Merck KGaA, Darmstadt, Germany), Guidonia Montecelio, 00012 Rome, Italy
| | - Horst Bierau
- Global CMC Development Technology & Innovation, CMC Science & Intelligence, Merck Serono SpA (An affiliate of Merck KGaA, Darmstadt, Germany), Guidonia Montecelio, 00012 Rome, Italy
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6
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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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7
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Chen Q, Zhang Y, Zhang K, Liu J, Pan H, Wang X, Li S, Hu D, Lin Z, Zhao Y, Hou G, Guan F, Li H, Liu S, Ren Y. Profiling the Bisecting N-acetylglucosamine Modification in Amniotic Membrane via Mass Spectrometry. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:648-656. [PMID: 35123071 PMCID: PMC9880894 DOI: 10.1016/j.gpb.2021.09.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 08/30/2021] [Accepted: 10/11/2021] [Indexed: 01/31/2023]
Abstract
Bisecting N-acetylglucosamine (GlcNAc), a GlcNAc linked to the core β-mannose residue via a β1,4 linkage, is a special type of N-glycosylation that has been reported to be involved in various biological processes, such as cell adhesion and fetal development. This N-glycan structure is abundant in human trophoblasts, which is postulated to be resistant to natural killer cell-mediated cytotoxicity, enabling a mother to nourish a fetus without rejection. In this study, we hypothesized that the human amniotic membrane, which serves as the last barrier for the fetus, may also express bisected-type glycans. To test this hypothesis, glycomic analysis of the human amniotic membrane was performed, and bisected N-glycans were detected. Furthermore, our proteomic data, which have been previously employed to explore human missing proteins, were analyzed and the presence of bisecting GlcNAc-modified peptides was confirmed. A total of 41 glycoproteins with 43 glycopeptides were found to possess a bisecting GlcNAc, and 25 of these glycoproteins were reported to exhibit this type of modification for the first time. These results provide insights into the potential roles of bisecting GlcNAc modification in the human amniotic membrane, and can be beneficial to functional studies on glycoproteins with bisecting GlcNAc modifications and functional studies on immune suppression in human placenta.
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Affiliation(s)
| | | | | | - Jie Liu
- BGI-Shenzhen, Shenzhen 518083, China
| | | | | | - Siqi Li
- BGI-Shenzhen, Shenzhen 518083, China
| | - Dandan Hu
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Yun Zhao
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Feng Guan
- Joint International Research Laboratory of Glycobiology and Medical Chemistry, College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Hong Li
- Shenzhen Seventh People's Hospital, Shenzhen 518081, China
| | - Siqi Liu
- BGI-Shenzhen, Shenzhen 518083, China,Corresponding authors.
| | - Yan Ren
- BGI-Shenzhen, Shenzhen 518083, China,Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China,Corresponding authors.
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8
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Brás-Costa C, Chaves AFA, Cajado-Carvalho D, da Silva Pires D, Andrade-Silva D, Serrano SMT. Profilings of subproteomes of lectin-binding proteins of nine Bothrops venoms reveal variability driven by different glycan types. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140795. [PMID: 35662639 DOI: 10.1016/j.bbapap.2022.140795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Snake venom proteomes have long been investigated to explore a multitude of biologically active components that are used for prey capture and defense, and are involved in the pathological effects observed upon mammalian envenomation. Glycosylation is a major protein post-translational modification in venoms and contributes to the diversification of proteomes. We have shown that Bothrops venoms are markedly defined by their content of glycoproteins, and that most N-glycan structures of eight Bothrops venoms contain sialic acid, while bisected N-acetylglucosamine was identified in Bothrops cotiara venom. To further investigate the mechanisms involved in the generation of different venoms by related snakes, here the glycoproteomes of nine Bothrops venoms (Bothrops atrox, B. cotiara, Bothrops erythromelas, Bothrops fonsecai, B. insularis, Bothrops jararaca, Bothrops jararacussu, Bothrops moojeni and Bothrops neuwiedi) were comparatively analyzed by enrichment with three lectins of different specificities, recognizing bisecting N-acetylglucosamine- and sialic acid-containing glycoproteins, and mass spectrometry. The lectin capture strategy generated venom fractions enriched with several glycoproteins, including metalloprotease, serine protease, and L- amino acid oxidase, in addition to various types of low abundant enzymes. The different contents of lectin-enriched proteins underscore novel aspects of the variability of the glycoprotein subproteomes of Bothrops venoms and point to the role of distinct types of glycan chains in generating different venoms by closely related snake species.
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Affiliation(s)
- Carolina Brás-Costa
- Laboratory of Applied Toxinology, Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Alison Felipe Alencar Chaves
- Laboratory of Applied Toxinology, Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Daniela Cajado-Carvalho
- Laboratory of Applied Toxinology, Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - David da Silva Pires
- Laboratory of Cell Cycle, Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Débora Andrade-Silva
- Laboratory of Applied Toxinology, Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Solange M T Serrano
- Laboratory of Applied Toxinology, Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil.
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9
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Cao X, Wang S, Gadi MR, Liu D, Wang PG, Wan XF, Zhang J, Chen X, Pepi LE, Azadi P, Li L. Systematic synthesis of bisected N-glycans and unique recognitions by glycan-binding proteins. Chem Sci 2022; 13:7644-7656. [PMID: 35872821 PMCID: PMC9241959 DOI: 10.1039/d1sc05435j] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 05/29/2022] [Indexed: 12/13/2022] Open
Abstract
Bisected N-glycans represent a unique class of protein N-glycans that play critical roles in many biological processes. Herein, we describe the systematic synthesis of these structures. A bisected N-glycan hexasaccharide was chemically assembled with two orthogonal protecting groups attached at the C2 of the branching mannose residues, followed by sequential installation of GlcNAc and LacNAc building blocks to afford two asymmetric bisecting "cores". Subsequent enzymatic modular extension of the "cores" yielded a comprehensive library of biantennary N-glycans containing the bisecting GlcNAc and presenting 6 common glycan determinants in a combinatorial fashion. These bisected N-glycans and their non-bisected counterparts were used to construct a distinctive glycan microarray to study their recognition by a wide variety of glycan-binding proteins (GBPs), including plant lectins, animal lectins, and influenza A virus hemagglutinins. Significantly, the bisecting GlcNAc could bestow (PHA-L, rDCIR2), enhance (PHA-E), or abolish (ConA, GNL, anti-CD15s antibody, etc.) N-glycan recognition of specific GBPs, and is tolerated by many others. In summary, synthesized compounds and the unique glycan microarray provide ideal standards and tools for glycoanalysis and functional glycomic studies. The microarray data provide new information regarding the fine details of N-glycan recognition by GBPs, and in turn improve their applications.
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Affiliation(s)
- Xuefeng Cao
- Department of Chemistry, Georgia State UniversityAtlantaGAUSA
| | - Shuaishuai Wang
- Department of Chemistry, Georgia State UniversityAtlantaGAUSA
| | | | - Ding Liu
- Department of Chemistry, Georgia State UniversityAtlantaGAUSA
| | - Peng G. Wang
- Department of Chemistry, Georgia State UniversityAtlantaGAUSA
| | - Xiu-Feng Wan
- MU Center for Research on Influenza Systems Biology (CRISB), University of MissouriColumbiaMOUSA,Department of Molecular Microbiology and Immunology, School of Medicine, University of MissouriColumbiaMOUSA,Bond Life Sciences Center, University of MissouriColumbiaMOUSA,Department of Electrical Engineering & Computer Science, College of Engineering, University of MissouriColumbiaMOUSA
| | | | - Xi Chen
- Department of Chemistry, University of CaliforniaOne Shields AvenueDavisCAUSA
| | - Lauren E. Pepi
- Complex Carbohydrate Research Center, University of GeorgiaAthensGAUSA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of GeorgiaAthensGAUSA
| | - Lei Li
- Department of Chemistry, Georgia State UniversityAtlantaGAUSA
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10
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Wang WL, Kasamatsu J, Joshita S, Gilfillan S, Di Luccia B, Panda SK, Kim DH, Desai P, Bando JK, Huang SCC, Yomogida K, Hoshino H, Fukushima M, Jacobsen EA, Van Dyken SJ, Ruedl C, Cella M, Colonna M. The aryl hydrocarbon receptor instructs the immunomodulatory profile of a subset of Clec4a4 + eosinophils unique to the small intestine. Proc Natl Acad Sci U S A 2022; 119:e2204557119. [PMID: 35653568 PMCID: PMC9191779 DOI: 10.1073/pnas.2204557119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 04/10/2022] [Indexed: 11/18/2022] Open
Abstract
C-type lectin domain family 4, member a4 (Clec4a4) is a C-type lectin inhibitory receptor specific for glycans thought to be exclusively expressed on murine CD8α− conventional dendritic cells. Using newly generated Clec4a4-mCherry knock-in mice, we identify a subset of Clec4a4-expressing eosinophils uniquely localized in the small intestine lamina propria. Clec4a4+ eosinophils evinced an immunomodulatory signature, whereas Clec4a4− eosinophils manifested a proinflammatory profile. Clec4a4+ eosinophils expressed high levels of aryl hydrocarbon receptor (Ahr), which drove the expression of Clec4a4 as well as other immunomodulatory features, such as PD-L1. The abundance of Clec4a4+ eosinophils was dependent on dietary AHR ligands, increased with aging, and declined in inflammatory conditions. Mice lacking AHR in eosinophils expanded innate lymphoid cells of type 2 and cleared Nippostrongylus brasiliensis infection more effectively than did wild-type mice. These results highlight the heterogeneity of eosinophils in response to tissue cues and identify a unique AHR-dependent subset of eosinophils in the small intestine with an immunomodulatory profile.
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Affiliation(s)
- Wei-Le Wang
- Department of Pathology and Immunology, Washington University School of Medicine in Saint Louis, St. Louis, MO 63110
| | - Jun Kasamatsu
- Department of Pathology and Immunology, Washington University School of Medicine in Saint Louis, St. Louis, MO 63110
- Department of Intelligent Network for Infection Control, Tohoku University Graduate School of Medicine, 980-8575 Sendai, Japan
| | - Satoru Joshita
- Department of Pathology and Immunology, Washington University School of Medicine in Saint Louis, St. Louis, MO 63110
- Department of Medicine, Division of Gastroenterology and Hepatology, Shinshu University School of Medicine, 390-8621 Matsumoto, Japan
| | - Susan Gilfillan
- Department of Pathology and Immunology, Washington University School of Medicine in Saint Louis, St. Louis, MO 63110
| | - Blanda Di Luccia
- Department of Pathology and Immunology, Washington University School of Medicine in Saint Louis, St. Louis, MO 63110
| | - Santosh K. Panda
- Department of Pathology and Immunology, Washington University School of Medicine in Saint Louis, St. Louis, MO 63110
| | - Do-Hyun Kim
- Department of Pathology and Immunology, Washington University School of Medicine in Saint Louis, St. Louis, MO 63110
| | - Pritesh Desai
- Department of Medicine, Washington University School of Medicine in Saint Louis, St. Louis, MO 63110
| | - Jennifer K. Bando
- Department of Pathology and Immunology, Washington University School of Medicine in Saint Louis, St. Louis, MO 63110
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Stanley Ching-Cheng Huang
- Department of Pathology and Immunology, Washington University School of Medicine in Saint Louis, St. Louis, MO 63110
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106
| | - Kentaro Yomogida
- Department of Pathology and Immunology, Washington University School of Medicine in Saint Louis, St. Louis, MO 63110
| | - Hitomi Hoshino
- Department of Tumor Pathology, Faculty of Medical Sciences, University of Fukui, 910-1193 Eiheiji, Japan
| | - Mana Fukushima
- Department of Tumor Pathology, Faculty of Medical Sciences, University of Fukui, 910-1193 Eiheiji, Japan
| | - Elizabeth A. Jacobsen
- Division of Allergy, Asthma and Clinical Immunology, Mayo Clinic Arizona, Scottsdale, AZ 85259
| | - Steven J. Van Dyken
- Department of Pathology and Immunology, Washington University School of Medicine in Saint Louis, St. Louis, MO 63110
| | - Christiane Ruedl
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Marina Cella
- Department of Pathology and Immunology, Washington University School of Medicine in Saint Louis, St. Louis, MO 63110
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine in Saint Louis, St. Louis, MO 63110
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11
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Willment JA. Fc-conjugated C-type lectin receptors: Tools for understanding host-pathogen interactions. Mol Microbiol 2021; 117:632-660. [PMID: 34709692 DOI: 10.1111/mmi.14837] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 10/25/2021] [Indexed: 12/24/2022]
Abstract
The use of soluble fusion proteins of pattern recognition receptors (PRRs) used in the detection of exogenous and endogenous ligands has helped resolve the roles of PRRs in the innate immune response to pathogens, how they shape the adaptive immune response, and function in maintaining homeostasis. Using the immunoglobulin (Ig) crystallizable fragment (Fc) domain as a fusion partner, the PRR fusion proteins are soluble, stable, easily purified, have increased affinity due to the Fc homodimerization properties, and consequently have been used in a wide range of applications such as flow cytometry, screening of protein and glycan arrays, and immunofluorescent microscopy. This review will predominantly focus on the recognition of pathogens by the cell membrane-expressed glycan-binding proteins of the C-type lectin receptor (CLR) subgroup of PRRs. PRRs bind to conserved pathogen-associated molecular patterns (PAMPs), such as glycans, usually located within or on the outer surface of the pathogen. Significantly, many glycans structures are identical on both host and pathogen (e.g. the Lewis (Le) X glycan), allowing the use of Fc CLR fusion proteins with known endogenous and/or exogenous ligands as tools to identify pathogen structures that are able to interact with the immune system. Screens of highly purified pathogen-derived cell wall components have enabled identification of many unique PAMP structures recognized by CLRs. This review highlights studies using Fc CLR fusion proteins, with emphasis on the PAMPs found in fungi, bacteria, viruses, and parasites. The structure and unique features of the different CLR families is presented using examples from a broad range of microbes whenever possible.
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Affiliation(s)
- Janet A Willment
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
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12
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Warkentin R, Kwan DH. Resources and Methods for Engineering "Designer" Glycan-Binding Proteins. Molecules 2021; 26:E380. [PMID: 33450899 PMCID: PMC7828330 DOI: 10.3390/molecules26020380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/04/2021] [Accepted: 01/10/2021] [Indexed: 12/11/2022] Open
Abstract
This review provides information on available methods for engineering glycan-binding proteins (GBP). Glycans are involved in a variety of physiological functions and are found in all domains of life and viruses. Due to their wide range of functions, GBPs have been developed with diagnostic, therapeutic, and biotechnological applications. The development of GBPs has traditionally been hindered by a lack of available glycan targets and sensitive and selective protein scaffolds; however, recent advances in glycobiology have largely overcome these challenges. Here we provide information on how to approach the design of novel "designer" GBPs, starting from the protein scaffold to the mutagenesis methods, selection, and characterization of the GBPs.
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Affiliation(s)
- Ruben Warkentin
- Department of Biology, Centre for Applied Synthetic Biology, and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6, Canada;
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec City, QC G1V 0A6, Canada
| | - David H. Kwan
- Department of Biology, Centre for Applied Synthetic Biology, and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6, Canada;
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec City, QC G1V 0A6, Canada
- Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6, Canada
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13
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Chen Q, Tan Z, Guan F, Ren Y. The Essential Functions and Detection of Bisecting GlcNAc in Cell Biology. Front Chem 2020; 8:511. [PMID: 32719771 PMCID: PMC7350706 DOI: 10.3389/fchem.2020.00511] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 05/18/2020] [Indexed: 12/11/2022] Open
Abstract
The N-glycans of mammalian glycoproteins vary greatly in structure, and the biological importance of these variations is mostly unknown. It is widely acknowledged that the bisecting N-acetylglucosamine (GlcNAc) structure, a β1,4-linked GlcNAc attached to the core β-mannose residue, represents a special type of N-glycosylated modification, and it has been reported to be involved in various biological processes, such as cell adhesion, fertilization and fetal development, neuritogenesis, and tumor development. In particular, the occurrence of N-glycans with a bisecting GlcNAc modification on proteins has been proven, with many implications for immune biology. Due to the essential functions of bisecting GlcNAc structures, analytical approaches to this modification are highly required. The traditional approach that has been used for bisecting GlcNAc determinations is based on the lectin recognition of Phaseolus vulgaris erythroagglutinin (PHA-E); however, poor binding specificity hinders the application of this method. With the development of mass spectrometry (MS) with high resolution and improved sensitivity and accuracy, MS-based glycomic analysis has provided precise characterization and quantification for glycosylation modification. In this review, we first provide an overview of the bisecting GlcNAc structure and its biological importance in neurological systems, immune tolerance, immunoglobulin G (IgG), and tumor metastasis and development and then summarize approaches to its determination by MS for performing precise functional studies. This review is valuable for those readers who are interested in the importance of bisecting GlcNAc in cell biology.
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Affiliation(s)
- Qiushi Chen
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
| | - Zengqi Tan
- Joint International Research Laboratory of Glycobiology and Medical Chemistry, College of Life Sciences, Northwest University, Xi'an, China
| | - Feng Guan
- Joint International Research Laboratory of Glycobiology and Medical Chemistry, College of Life Sciences, Northwest University, Xi'an, China
| | - Yan Ren
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China.,Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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14
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Shajahan A, Supekar NT, Chapla D, Heiss C, Moremen KW, Azadi P. Simplifying Glycan Profiling through a High-Throughput Micropermethylation Strategy. SLAS Technol 2020; 25:367-379. [PMID: 32364434 DOI: 10.1177/2472630320912929] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Glycoproteins play key roles in various molecular and cellular functions and are among the most difficult to analyze biomolecules on account of their microheterogeneity, non-template-driven synthesis, and low abundances. The stability, serum half-life, immunogenicity, and biological activity of therapeutic glycoproteins, including antibodies, vaccines, and biomarkers, are regulated by their glycosylation profile. Thus, there is increasing demand for the qualitative and quantitative characterization and validation of glycosylation on glycoproteins. One of the most important derivatization processes for the structural characterization of released glycans by mass spectrometry (MS) is permethylation. We have recently developed a permethylation strategy in microscale that allows facile permethylation of glycans and permits the processing of large sample sets in nanogram amounts through high-throughput sample handling. Here, we are reporting the wide potential of micropermethylation-based high-throughput structural analysis of glycans from various sources, including human plasma, mammalian cells, and purified glycoproteins, through an automated tandem electrospray ionization-mass spectrometry (ESI-MSn) platform. The glycans released from the plasma, cells, and glycoproteins are permethylated in microscale in a 96-well plate or microcentrifuge tube and isolated by a C18 tip-based cleanup through a shorter and simple process. We have developed a workflow to accomplish an in-depth automated structural characterization MS program for permethylated N/O-glycans through an automated high-throughput multistage tandem MS acquisition. We have demonstrated the utility of this workflow using the examples of sialic acid linkages and bisecting GlcNAc (N-acetylglucosamine) on the glycans. This approach can automate the high-throughput screening of glycosylation on large sample sets of glycoproteins, including clinical glycan biomarkers and glycoprotein therapeutics.
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Affiliation(s)
- Asif Shajahan
- Complex Carbohydrate Research Center, The University of Georgia, Athens, GA, USA
| | - Nitin T Supekar
- Complex Carbohydrate Research Center, The University of Georgia, Athens, GA, USA
| | - Digantkumar Chapla
- Complex Carbohydrate Research Center, The University of Georgia, Athens, GA, USA
| | - Christian Heiss
- Complex Carbohydrate Research Center, The University of Georgia, Athens, GA, USA
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, The University of Georgia, Athens, GA, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, The University of Georgia, Athens, GA, USA
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15
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Omahdi Z, Horikawa Y, Nagae M, Toyonaga K, Imamura A, Takato K, Teramoto T, Ishida H, Kakuta Y, Yamasaki S. Structural insight into the recognition of pathogen-derived phosphoglycolipids by C-type lectin receptor DCAR. J Biol Chem 2020; 295:5807-5817. [PMID: 32139512 PMCID: PMC7186165 DOI: 10.1074/jbc.ra120.012491] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/02/2020] [Indexed: 01/08/2023] Open
Abstract
The C-type lectin receptors (CLRs) form a family of pattern recognition receptors that recognize numerous pathogens, such as bacteria and fungi, and trigger innate immune responses. The extracellular carbohydrate-recognition domain (CRD) of CLRs forms a globular structure that can coordinate a Ca2+ ion, allowing receptor interactions with sugar-containing ligands. Although well-conserved, the CRD fold can also display differences that directly affect the specificity of the receptors for their ligands. Here, we report crystal structures at 1.8-2.3 Å resolutions of the CRD of murine dendritic cell-immunoactivating receptor (DCAR, or Clec4b1), the CLR that binds phosphoglycolipids such as acylated phosphatidyl-myo-inositol mannosides (AcPIMs) of mycobacteria. Using mutagenesis analysis, we identified critical residues, Ala136 and Gln198, on the surface surrounding the ligand-binding site of DCAR, as well as an atypical Ca2+-binding motif (Glu-Pro-Ser/EPS168-170). By chemically synthesizing a water-soluble ligand analog, inositol-monophosphate dimannose (IPM2), we confirmed the direct interaction of DCAR with the polar moiety of AcPIMs by biolayer interferometry and co-crystallization approaches. We also observed a hydrophobic groove extending from the ligand-binding site that is in a suitable position to interact with the lipid portion of whole AcPIMs. These results suggest that the hydroxyl group-binding ability and hydrophobic groove of DCAR mediate its specific binding to pathogen-derived phosphoglycolipids such as mycobacterial AcPIMs.
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Affiliation(s)
- Zakaria Omahdi
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita 565-0871, Japan; Laboratory of Molecular Immunology, Immunology Frontier Research Center (IFReC), Osaka University, Suita 565-0871, Japan; Division of Molecular Immunology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Yuto Horikawa
- Laboratory of Structural Biology, Graduate School of System Life Sciences, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Masamichi Nagae
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita 565-0871, Japan; Laboratory of Molecular Immunology, Immunology Frontier Research Center (IFReC), Osaka University, Suita 565-0871, Japan; Department of Pharmaceutical Sciences, University of Tokyo, Bunkyo-Ku, Tokyo 113-0033, Japan
| | - Kenji Toyonaga
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita 565-0871, Japan; Laboratory of Molecular Immunology, Immunology Frontier Research Center (IFReC), Osaka University, Suita 565-0871, Japan
| | - Akihiro Imamura
- Department of Applied Bioorganic Chemistry, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan; United Graduate School of Agricultural Science, Gifu University, Gifu 501-1193, Japan
| | - Koichi Takato
- Department of Applied Bioorganic Chemistry, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan
| | - Takamasa Teramoto
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Hideharu Ishida
- Department of Applied Bioorganic Chemistry, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan; United Graduate School of Agricultural Science, Gifu University, Gifu 501-1193, Japan; Center for Highly Advanced Integration of Nano and Life Sciences, Gifu University, Gifu 501-1193, Japan
| | - Yoshimitsu Kakuta
- Laboratory of Structural Biology, Graduate School of System Life Sciences, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan; Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Sho Yamasaki
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita 565-0871, Japan; Laboratory of Molecular Immunology, Immunology Frontier Research Center (IFReC), Osaka University, Suita 565-0871, Japan; Division of Molecular Immunology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan; Division of Molecular Design, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan; Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, Chiba 260-8673, Japan.
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16
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Zhang W, Meredith RJ, Oliver AG, Carmichael I, Serianni AS. Glycosidic linkage, N-acetyl side-chain, and other structural properties of methyl 2-acetamido-2-deoxy-β-D-glucopyranosyl-(1→4)-β-D-mannopyranoside monohydrate and related compounds. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2020; 76:287-297. [PMID: 32132287 DOI: 10.1107/s2053229620001515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 02/03/2020] [Indexed: 11/10/2022]
Abstract
The crystal structure of methyl 2-acetamido-2-deoxy-β-D-glycopyranosyl-(1→4)-β-D-mannopyranoside monohydrate, C15H27NO11·H2O, was determined and its structural properties compared to those in a set of mono- and disaccharides bearing N-acetyl side-chains in βGlcNAc aldohexopyranosyl rings. Valence bond angles and torsion angles in these side chains are relatively uniform, but C-N (amide) and C-O (carbonyl) bond lengths depend on the state of hydrogen bonding to the carbonyl O atom and N-H hydrogen. Relative to N-acetyl side chains devoid of hydrogen bonding, those in which the carbonyl O atom serves as a hydrogen-bond acceptor display elongated C-O and shortened C-N bonds. This behavior is reproduced by density functional theory (DFT) calculations, indicating that the relative contributions of amide resonance forms to experimental C-N and C-O bond lengths depend on the solvation state, leading to expectations that activation barriers to amide cis-trans isomerization will depend on the polarity of the environment. DFT calculations also revealed useful predictive information on the dependencies of inter-residue hydrogen bonding and some bond angles in or proximal to β-(1→4) O-glycosidic linkages on linkage torsion angles φ and ψ. Hypersurfaces correlating φ and ψ with the linkage C-O-C bond angle and total energy are sufficiently similar to render the former a proxy of the latter.
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Affiliation(s)
- Wenhui Zhang
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN 46556-5670, USA
| | - Reagan J Meredith
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN 46556-5670, USA
| | - Allen G Oliver
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN 46556-5670, USA
| | - Ian Carmichael
- Radiation Laboratory, University of Notre Dame, Notre Dame, IN 46556-5670, USA
| | - Anthony S Serianni
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN 46556-5670, USA
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17
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Keller BG, Rademacher C. Allostery in C-type lectins. Curr Opin Struct Biol 2019; 62:31-38. [PMID: 31838280 DOI: 10.1016/j.sbi.2019.11.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/30/2019] [Accepted: 11/04/2019] [Indexed: 10/25/2022]
Abstract
C-type lectins are the largest and most diverse family of mammalian carbohydrate-binding proteins. They share a common protein fold, which provides the unifying basis for calcium-mediated carbohydrate recognition. Their involvement in a multitude of biological functions is remarkable. Here, we review the variety of tasks these lectins are involved in alongside with the structural demands on the overall protein architecture. Subtle changes of the protein structure are implemented to cope with such diverse functional requirements. The presence of a high level of structural dynamics over a broad palette of time scales is paired with the presence of secondary binding sites and allosteric coordination of remote sites and renders this lectin fold a highly adaptable scaffold.
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Affiliation(s)
- Bettina G Keller
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
| | - Christoph Rademacher
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany; Max Planck Institute of Colloids and Interfaces, Department of Biomolecular Systems, 14424 Potsdam, Germany.
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18
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Ouyang Z, Felix J, Zhou J, Pei Y, Ma B, Hwang PM, Lemieux MJ, Gutsche I, Zheng F, Wen Y. Trimeric structure of the mouse Kupffer cell C-type lectin receptor Clec4f. FEBS Lett 2019; 594:189-198. [PMID: 31369681 DOI: 10.1002/1873-3468.13565] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/13/2019] [Accepted: 07/30/2019] [Indexed: 11/09/2022]
Abstract
The C-type lectin receptor Clec4f has been identified as a specific surface marker for Kupffer cells, although its ortholog is absent in humans and its biological function remains elusive. Here, we report the crystal structure of a truncated mouse trimeric Clec4f. The orientation between the carbohydrate-recognition domain of Clec4f and its neck region differs from other C-type lectins, resulting in an observed distance of 45 Å between the glycan-binding sites within the Clec4f trimer. Interestingly, the trimeric coiled-coil interface within its heptad neck region contains multiple polyglutamine interactions instead of the predominantly hydrophobic leucine zipper found in other C-type lectin receptors. The Clec4f trimeric structure displays unique features regarding its assembly and ligand recognition, shedding light on the evolution and diversity of the C-type lectin family.
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Affiliation(s)
- Zhenlin Ouyang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, China.,Department of Biochemistry and Molecular Biology, The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, Health Science Center, Xi'an Jiaotong University, China
| | - Jan Felix
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Jinhong Zhou
- Department of Biochemistry and Molecular Biology, The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, Health Science Center, Xi'an Jiaotong University, China
| | - Yingmei Pei
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, China
| | - Bohan Ma
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, China
| | - Peter M Hwang
- Department of Biochemistry, Faculty of Medicine & Dentistry, Edmonton, Canada
| | - M Joanne Lemieux
- Department of Biochemistry, Faculty of Medicine & Dentistry, Edmonton, Canada.,Membrane Protein Disease Research Group, University of Alberta, Edmonton, Canada
| | - Irina Gutsche
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Fang Zheng
- Department of Biochemistry and Molecular Biology, The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, Health Science Center, Xi'an Jiaotong University, China
| | - Yurong Wen
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, China.,Department of Biochemistry and Molecular Biology, The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, Health Science Center, Xi'an Jiaotong University, China.,Department of Biochemistry, Faculty of Medicine & Dentistry, Edmonton, Canada.,Membrane Protein Disease Research Group, University of Alberta, Edmonton, Canada
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19
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Dang L, Shen J, Zhao T, Zhao F, Jia L, Zhu B, Ma C, Chen D, Zhao Y, Sun S. Recognition of Bisecting N-Glycans on Intact Glycopeptides by Two Characteristic Ions in Tandem Mass Spectra. Anal Chem 2019; 91:5478-5482. [PMID: 30973713 DOI: 10.1021/acs.analchem.8b05639] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Bisecting N-glycan represents one of the most important modifications to the N-glycan core, and it is involved in various biological processes. Despite many studies on the biological roles of bisecting N-glycans, current approaches for bisecting N-glycan analysis mainly rely on the use of the lectin PHA-E, which are of low specificity and sensitivity. Here, we describe a straightforward method for the recognition of bisecting N-glycans on intact glycopeptides using two characteristic Y ions [peptide+HexNAc3Hex1] and [peptide+HexNAc3Hex1Fuc1] in low energy fragmented MS/MS spectra under higher energy collisional dissociation (HCD) mode. The critical aspect of the method is the combination use of low energy HCD fragmentation and intact glycopeptide analysis. With samples from rat renal tissues, we determined the optimal fragmentation energies and analyzed the influence of core fucosylation on the intensity of the [peptide+HexNAc3Hex1] ion. Using the method, we identified 183 intact glycopeptides with bisecting N-glycans and investigated the primary bisecting N-glycan structures and the possible biological roles of these identified proteins.
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Affiliation(s)
- Liuyi Dang
- College of Life Sciences , Northwest University , Xi'an 710069 , China
| | - Jiechen Shen
- College of Life Sciences , Northwest University , Xi'an 710069 , China
| | - Ting Zhao
- College of Life Sciences , Northwest University , Xi'an 710069 , China
| | - Fei Zhao
- College of Basic Medical Sciences , Shaanxi University of Chinese Medicine , Xianyang 712046 , China
| | - Li Jia
- College of Life Sciences , Northwest University , Xi'an 710069 , China
| | - Bojing Zhu
- College of Life Sciences , Northwest University , Xi'an 710069 , China
| | - Chen Ma
- College of Life Sciences , Northwest University , Xi'an 710069 , China
| | - Danqian Chen
- College of Life Sciences , Northwest University , Xi'an 710069 , China
| | - Yingyong Zhao
- College of Life Sciences , Northwest University , Xi'an 710069 , China
| | - Shisheng Sun
- College of Life Sciences , Northwest University , Xi'an 710069 , China
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20
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Harada Y, Kizuka Y, Tokoro Y, Kondo K, Yagi H, Kato K, Inoue H, Taniguchi N, Maruyama I. N-glycome inheritance from cells to extracellular vesicles in B16 melanomas. FEBS Lett 2019; 593:942-951. [PMID: 30943309 PMCID: PMC6594130 DOI: 10.1002/1873-3468.13377] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/20/2019] [Accepted: 04/01/2019] [Indexed: 01/09/2023]
Abstract
We investigated the correlation between metastatic behaviors of tumor cells and asparagine‐linked glycosylation (N‐glycosylation) of tumor‐derived extracellular vesicles (EVs). Three mouse melanoma B16 variants with distinct metastatic potentials show similar gene expression levels and enzymatic activities of glycosyltransferases involved in N‐glycosylation. All melanoma variants and EVs have nearly identical profiles of de‐sialylated N‐glycans. The major de‐sialylated N‐glycan structures of cells and EVs are core‐fucosylated, tetra‐antennary N‐glycans with β1,6‐N‐acetylglucosamine branches. A few N‐glycans are extended by N‐acetyllactosamine repeats. Sialylation of these N‐glycans may generate cell‐type‐specific N‐glycomes on EVs. Taken together, melanoma‐derived EVs show high expression of tumor‐associated N‐glycans, and the core structure profile is inherited during multiple selection cycles of B16 melanomas and from tumor cells to EVs.
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Affiliation(s)
- Yoichiro Harada
- Department of Systems Biology in Thromboregulation, Kagoshima University Graduate School of Medical and Dental Sciences, Japan
| | - Yasuhiko Kizuka
- Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN), Gifu University, Japan
| | - Yuko Tokoro
- Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN), Gifu University, Japan
| | - Kiyotaka Kondo
- Department of Pulmonary Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, Japan
| | - Hirokazu Yagi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Japan
| | - Koichi Kato
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Japan.,Exploratory Research Center on Life and Living Systems (ExCELLS), Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Okazaki, Japan
| | - Hiromasa Inoue
- Department of Pulmonary Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, Japan
| | - Naoyuki Taniguchi
- Department of Glyco-Oncology, Osaka International Cancer Institute, Japan
| | - Ikuro Maruyama
- Department of Systems Biology in Thromboregulation, Kagoshima University Graduate School of Medical and Dental Sciences, Japan
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21
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Nagae M, Yamaguchi Y. Structural Aspects of Carbohydrate Recognition Mechanisms of C-Type Lectins. Curr Top Microbiol Immunol 2019; 429:147-176. [PMID: 31781867 DOI: 10.1007/82_2019_181] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Carbohydrate recognition is an essential function occurring in all living organisms. Lectins are carbohydrate-binding proteins and are classified into several families. In mammals, Ca2+-dependent C-type lectins, such as β-galactoside-binding galectin and sialic acid-binding siglec, play crucial roles in the immune response and homeostasis. C-type lectins are abundant and diverse in animals. Their immunological activities include lymphocyte homing, pathogen recognition, and clearance of apoptotic bodies. C-type lectin domains are composed of 110-130 amino acid residues with highly conserved structural folds. Remarkably, individual lectins can accept a wide variety of sugar ligands and can distinguish subtle structural differences in closely related ligands. In addition, several C-type lectin-like proteins specifically bind to carbohydrate ligands in Ca2+-independent ways. The accumulated 3D structural evidence clarifies the unexpected structural versatility of C-type lectins underlying the variety of ligand binding modes. In this issue, we focus on the structural aspects of carbohydrate recognition mechanisms of C-type lectins and C-type lectin-like proteins.
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Affiliation(s)
- Masamichi Nagae
- Department 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.
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22
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Biophysical Analyses for Probing Glycan-Protein Interactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1104:119-147. [PMID: 30484247 PMCID: PMC7153041 DOI: 10.1007/978-981-13-2158-0_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Glycan-protein interactions occur at many physiological events, and the analyses are of considerable importance for understanding glycan-dependent mechanisms. Biophysical approaches including 3D structural analysis are essential for revealing glycan-protein interactions at the atomic level. The inherent diversity of glycans suits them to function as identification tags, e.g., distinguish self from the nonself components of pathogens. However, the complexity of glycans and poor affinities for interaction partners limit the usefulness of conventional analyses. To cope with such troublesome glycans, a logical sequence of biophysical analyses need to be developed. In this chapter, we introduce a workflow of glycan-protein interaction analysis consisting of six steps: preparation of lectin and glycan, screening of glycan ligand, determination of binding epitope, quantitative interaction analysis, 3D structural analysis, and molecular dynamics simulation. Our increasing knowledge and understanding of lectin-glycan interactions will hopefully lead to the design of glyco-based medicines and vaccines.
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23
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Yang W, Ramadan S, Orwenyo J, Kakeshpour T, Diaz T, Eken Y, Sanda M, Jackson JE, Wilson AK, Huang X. Chemoenzymatic synthesis of glycopeptides bearing rare N-glycan sequences with or without bisecting GlcNAc. Chem Sci 2018; 9:8194-8206. [PMID: 30542567 PMCID: PMC6240809 DOI: 10.1039/c8sc02457j] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 08/31/2018] [Indexed: 01/24/2023] Open
Abstract
A glycopeptide bearing a bisecting glucosamine, a rare N-glycan branch, and two LewisX trisaccharides was synthesized for the first time.
N-Linked glycopeptides have highly diverse structures in nature. Herein, we describe the first synthesis of rare multi-antennary N-glycan bearing glycan chains on 6-OH of both α1,6- and α1,3-linked mannose arms. To expedite divergent generation of N-glycan structures, four orthogonal protective groups were installed at the branching points on the core tetrasaccharide, which could be removed individually without affecting one another. In addition, the synthetic route is flexible, allowing a bisecting glucosamine moiety to be introduced at a late stage of the synthesis, further expanding the diversity of sequences that could be achieved. The bisecting glucosamine unit significantly reduced the glycosylation yields of adjacent mannoses, which was attributed to steric hindrance imposed by the glucosamine based on molecular modelling analysis. The N-glycans were then transformed to oxazoline donors and ligated with a glycopeptide acceptor from haptoglobin promoted by the wild type Arthrobacter endo-β-N-acetylglucosaminidase (Endo-A). Endo-A exhibited interesting substrate preferences depending on donor sizes, which was rationalized through molecular dynamics studies. This is the first time that a glycopeptide bearing a bisecting N-acetyl glucosamine (GlcNAc), the rare N-glycan branch, and two LewisX trisaccharide antennae was synthesized, enabling access to this class of complex glycopeptide structures.
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Affiliation(s)
- Weizhun Yang
- Department of Chemistry , Michigan State University , 578 South Shaw Lane , East Lansing , MI 48824 , USA . ; ;
| | - Sherif Ramadan
- Department of Chemistry , Michigan State University , 578 South Shaw Lane , East Lansing , MI 48824 , USA . ; ; .,Chemistry Department , Faculty of Science , Benha University , Benha , Qaliobiya 13518 , Egypt
| | - Jared Orwenyo
- Department of Chemistry and Biochemistry , University of Maryland , College Park , MD 20742 , USA
| | - Tayeb Kakeshpour
- Department of Chemistry , Michigan State University , 578 South Shaw Lane , East Lansing , MI 48824 , USA . ; ;
| | - Thomas Diaz
- Department of Chemistry , Michigan State University , 578 South Shaw Lane , East Lansing , MI 48824 , USA . ; ;
| | - Yigitcan Eken
- Department of Chemistry , Michigan State University , 578 South Shaw Lane , East Lansing , MI 48824 , USA . ; ;
| | - Miloslav Sanda
- Department of Oncology , Georgetown University , Washington DC 20057 , USA
| | - James E Jackson
- Department of Chemistry , Michigan State University , 578 South Shaw Lane , East Lansing , MI 48824 , USA . ; ;
| | - Angela K Wilson
- Department of Chemistry , Michigan State University , 578 South Shaw Lane , East Lansing , MI 48824 , USA . ; ;
| | - Xuefei Huang
- Department of Chemistry , Michigan State University , 578 South Shaw Lane , East Lansing , MI 48824 , USA . ; ; .,Department of Biomedical Engineering , Michigan State University , East Lansing , MI 48824 , USA.,Institute for Quantitative Health Science and Engineering , Michigan State University , East Lansing , MI 48824 , USA
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24
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Tabansky I, Keskin DB, Watts D, Petzold C, Funaro M, Sands W, Wright P, Yunis EJ, Najjar S, Diamond B, Cao Y, Mooney D, Kretschmer K, Stern JNH. Targeting DEC-205 -DCIR2 + dendritic cells promotes immunological tolerance in proteolipid protein-induced experimental autoimmune encephalomyelitis. Mol Med 2018; 24:17. [PMID: 30134798 PMCID: PMC6016871 DOI: 10.1186/s10020-018-0017-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 03/19/2018] [Indexed: 12/16/2022] Open
Abstract
Background Dendritic cells (DC) induce adaptive responses against foreign antigens, and play an essential role in maintaining peripheral tolerance to self-antigens. Therefore they are involved in preventing fatal autoimmunity. Selective delivery of antigens to immature DC via the endocytic DEC-205 receptor on their surface promotes antigen-specific T cell tolerance, both by recessive and dominant mechanisms. We provide evidence that the induction of antigen-specific T cell tolerance is not a unique property of CD11c+CD8+DEC-205+ DCs. Methods We employed a fusion between αDCIR2 antibodies and the highly encephalitogenic peptide 139–151 of myelin-derived proteolipid protein (PLP139–151), to target CD11c +CD8- DCs with a DEC-205−DCIR2+ phenotype in vivo, and to substantially improve clinical symptoms in the PLP139–151-induced model of experimental autoimmune encephalomyelitis (EAE). Results Consistent with previous studies targeting other cell surface receptors, EAE protection mediated by αDCIR2-PLP139–151 fusion antibody (Ab) depended on an immature state of targeted DCIR2+ DCs. The mechanism of αDCIR2-PLP139–151 mAb function included the deletion of IL-17- and IFN-γ-producing pathogenic T cells, as well as the enhancement of regulatory T (Treg) cell activity. In contrast to the effect of αDEC-205+ fusion antibodies, which involves extrathymic induction of a Foxp3+ Treg cell phenotype in naïve CD4+Foxp3- T cells, treatment of animals with DCIR2+ fusion antibodies resulted in antigen-specific activation and proliferative expansion of natural Foxp3+ Treg cells. Conclusions These results suggest that multiple mechanisms can lead to the expansion of the Treg population, depending on the DC subset and receptor targeted. Electronic supplementary material The online version of this article (10.1186/s10020-018-0017-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Inna Tabansky
- Department of Neurobiology and Behavior, The Rockefeller University, New York, NY, USA
| | - Derin B Keskin
- Department of Medical Oncology, Dana Farber-Harvard Cancer Institute, Boston, MA, USA.,Departments of Neurology, Surgery, Molecular Medicine, and Science Education, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Deepika Watts
- Molecular and Cellular Immunology/Immune Regulation, CRTD/DFG-Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany.,Paul Langerhans Institute Dresden, German Center for Diabetes Research (DZD), Dresden, Germany
| | - Cathleen Petzold
- Molecular and Cellular Immunology/Immune Regulation, CRTD/DFG-Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Michael Funaro
- Departments of Neurology, Surgery, Molecular Medicine, and Science Education, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA.,Department of Autoimmunity, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Warren Sands
- Department of Engineering, School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Paul Wright
- Department of Neurology, Lenox Hill Hospital, Northwell Health, New York, NY, USA
| | - Edmond J Yunis
- Department of Medical Oncology, Dana Farber-Harvard Cancer Institute, Boston, MA, USA
| | - Souhel Najjar
- Department of Neurology, Lenox Hill Hospital, Northwell Health, New York, NY, USA
| | - Betty Diamond
- Department of Autoimmunity, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Yonghao Cao
- Departments of Neurology, Surgery, Molecular Medicine, and Science Education, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA.,Department of Autoimmunity, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, USA
| | - David Mooney
- Department of Engineering, School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Karsten Kretschmer
- Molecular and Cellular Immunology/Immune Regulation, CRTD/DFG-Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany. .,Paul Langerhans Institute Dresden, German Center for Diabetes Research (DZD), Dresden, Germany.
| | - Joel N H Stern
- Department of Neurobiology and Behavior, The Rockefeller University, New York, NY, USA. .,Departments of Neurology, Surgery, Molecular Medicine, and Science Education, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA. .,Department of Autoimmunity, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, USA.
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25
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Andrade-Silva D, Ashline D, Tran T, Lopes AS, Travaglia Cardoso SR, Reis MDS, Zelanis A, Serrano SMT, Reinhold V. Structures of N-Glycans of Bothrops Venoms Revealed as Molecular Signatures that Contribute to Venom Phenotype in Viperid Snakes. Mol Cell Proteomics 2018; 17:1261-1284. [PMID: 29716988 DOI: 10.1074/mcp.ra118.000748] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 04/26/2018] [Indexed: 11/06/2022] Open
Abstract
The complexity of snake venoms has long been investigated to explore a myriad of biologically active proteins and peptides that are used for immobilizing or killing prey, and are responsible for the pathological effects observed on envenomation. Glycosylation is the main post-translational modification (PTM) of viperid venoms but currently there is little understanding of how protein glycosylation impacts the variation of venom proteomes. We have previously reported that Bothrops venom glycoproteomes contain a core of components that markedly define their composition and parallel their phylogenetic classification. Here we extend those observations to eight Bothrops species evaluating the N-glycomes by LC-MS as assigned cartoon structures and detailing those structures separately as methylated analogs using ion-trap mass spectrometry (MSn). Following ion disassembly through multiple steps provided sequence and linkage isomeric details that characterized 52 unique compositions in Bothrops venoms. These occurred as 60 structures, of which 26 were identified in the venoms of the Jararaca Complex (B. alcatraz, B. insularis, and B. jararaca), 20 in B. erythromelas, B. jararacussu, B. moojeni and B. neuwiedi venoms, and 22 in B. cotiara venom. Further, quantitative analysis of these N-glycans showed variable relative abundances in the venoms. For the first time a comprehensive set of N-glycan structures present in snake venoms are defined. Despite the fact that glycosylation is not template-defined, the N-glycomes of these venoms mirror the phylogeny cladograms of South American bothropoid snakes reported in studies on morphological, molecular data and feeding habits, exhibiting distinct molecular signatures for each venom. Considering the complexity of N-glycan moieties generally found in glycoproteins, characterized by different degrees of branching, isomer structures, and variable abundances, our findings point to these factors as another level of complexity in Bothrops venoms, features that could dramatically contribute to their distinct biological activities.
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Affiliation(s)
| | - David Ashline
- §The Glycomics Center, University of New Hampshire, Durham, NH 03824
| | - Thuy Tran
- §The Glycomics Center, University of New Hampshire, Durham, NH 03824
| | - Aline Soriano Lopes
- ‖Departamento de Química, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Diadema, 09913-030 Brazil
| | | | - Marcelo da Silva Reis
- ¶Laboratório Especial de Ciclo Celular, Center of Toxins, Immune-Response, and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, 05503-900, Brazil
| | - André Zelanis
- ‡‡Instituto de Ciência e Tecnologia, Universidade Federal de São Paulo (ICT-UNIFESP), São José dos Campos, 12231-280, Brazil
| | | | - Vernon Reinhold
- §The Glycomics Center, University of New Hampshire, Durham, NH 03824;
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26
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High affinity sugar ligands of C-type lectin receptor langerin. Biochim Biophys Acta Gen Subj 2018; 1862:1592-1601. [PMID: 29631057 DOI: 10.1016/j.bbagen.2018.04.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 04/04/2018] [Accepted: 04/05/2018] [Indexed: 12/21/2022]
Abstract
BACKGROUND Langerin, a C-type lectin receptor (CLR) expressed in a subset of dendritic cells (DCs), binds to glycan ligands for pathogen capture and clearance. Previous studies revealed that langerin has an unusual binding affinity toward 6-sulfated galactose (Gal), a structure primarily found in keratan sulfate (KS). However, details and biological outcomes of this interaction have not been characterized. Based on a recent discovery that the disaccharide L4, a KS component that contains 6-sulfo-Gal, exhibits anti-inflammatory activity in mouse lung, we hypothesized that L4-related compounds are useful tools for characterizing the langerin-ligand interactions and their therapeutic application. METHODS We performed binding analysis between purified long and short forms of langerin and a series of KS disaccharide components. We also chemically synthesized oligomeric derivatives of L4 to develop a new high-affinity ligand of langerin. RESULTS We show that the binding critically requires the 6-sulfation of Gal and that the long form of langerin displays higher affinity than the short form. The synthesized trimeric (also designated as triangle or Tri) and polymeric (pendant) L4 derivatives displayed over 1000-fold higher affinity toward langerin than monomeric L4. The pendant L4, but not the L4 monomer, was found to effectively transduce langerin signaling in a model cell system. CONCLUSIONS L4 is a specific ligand for langerin. Oligomerization of L4 unit increased the affinity toward langerin. GENERAL SIGNIFICANCE These results suggest that oligomeric L4 derivatives will be useful for clarifying the langerin functions and for the development of new glycan-based anti-inflammatory drugs.
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27
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Link-Lenczowski P, Bubka M, Balog CIA, Koeleman CAM, Butters TD, Wuhrer M, Lityńska A. The glycomic effect of N-acetylglucosaminyltransferase III overexpression in metastatic melanoma cells. GnT-III modifies highly branched N-glycans. Glycoconj J 2018; 35:217-231. [PMID: 29502191 PMCID: PMC5916991 DOI: 10.1007/s10719-018-9814-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 01/15/2018] [Accepted: 01/30/2018] [Indexed: 11/28/2022]
Abstract
N-acetylglucosaminyltransferase III (GnT-III) is known to catalyze N-glycan "bisection" and thereby modulate the formation of highly branched complex structures within the Golgi apparatus. While active, it inhibits the action of other GlcNAc transferases such as GnT-IV and GnT-V. Moreover, GnT-III is considered as an inhibitor of the metastatic potential of cancer cells both in vitro and in vivo. However, the effects of GnT-III may be more diverse and depend on the cellular context. We describe the detailed glycomic analysis of the effect of GnT-III overexpression in WM266-4-GnT-III metastatic melanoma cells. We used MALDI-TOF and ESI-ion-trap-MS/MS together with HILIC-HPLC of 2-AA labeled N-glycans to study the N-glycome of membrane-attached and secreted proteins. We found that the overexpression of GnT-III in melanoma leads to the modification of a broad range of N-glycan types by the introduction of the "bisecting" GlcNAc residue with highly branched complex structures among them. The presence of these unusual complex N-glycans resulted in stronger interactions of cellular glycoproteins with the PHA-L. Based on the data presented here we conclude that elevated activity of GnT-III in cancer cells does not necessarily lead to a total abrogation of the formation of highly branched glycans. In addition, the modification of pre-existing N-glycans by the introduction of "bisecting" GlcNAc can modulate their capacity to interact with carbohydrate-binding proteins such as plant lectins. Our results suggest further studies on the biological function of "bisected" oligosaccharides in cancer cell biology and their interactions with carbohydrate-binding proteins.
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Affiliation(s)
- Paweł Link-Lenczowski
- Department of Medical Physiology, Faculty of Health Sciences, Jagiellonian University Medical College, Michałowskiego 12, 31-126, Kraków, Poland.
- Department of Glycoconjugate Biochemistry, Institute of Zoology and Biomedical Research, Jagiellonian University, Kraków, Poland.
| | - Monika Bubka
- Department of Glycoconjugate Biochemistry, Institute of Zoology and Biomedical Research, Jagiellonian University, Kraków, Poland
| | - Crina I A Balog
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Carolien A M Koeleman
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Anna Lityńska
- Department of Glycoconjugate Biochemistry, Institute of Zoology and Biomedical Research, Jagiellonian University, Kraków, Poland
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28
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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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29
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Hsu Y, Okada R, Nishimura T, Kawasaki N, Yamamoto K, Matsumoto N. DCIR3 and DCIR4 are co-expressed on inflammatory and patrolling monocytes. Biochem Biophys Res Commun 2017; 494:440-445. [DOI: 10.1016/j.bbrc.2017.10.067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 10/13/2017] [Indexed: 12/17/2022]
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30
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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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31
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Feinberg H, Jégouzo SAF, Rex MJ, Drickamer K, Weis WI, Taylor ME. Mechanism of pathogen recognition by human dectin-2. J Biol Chem 2017; 292:13402-13414. [PMID: 28652405 PMCID: PMC5555199 DOI: 10.1074/jbc.m117.799080] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 06/23/2017] [Indexed: 11/17/2022] Open
Abstract
Dectin-2, a C-type lectin on macrophages and other cells of the innate immune system, functions in response to pathogens, particularly fungi. The carbohydrate-recognition domain (CRD) in dectin-2 is linked to a transmembrane sequence that interacts with the common Fc receptor γ subunit to initiate immune signaling. The molecular mechanism by which dectin-2 selectively binds to pathogens has been investigated by characterizing the CRD expressed in a bacterial system. Competition binding studies indicated that the CRD binds to monosaccharides with modest affinity and that affinity was greatly enhanced for mannose-linked α1–2 or α1–4 to a second mannose residue. Glycan array analysis confirmed selective binding of the CRD to glycans that contain Manα1–2Man epitopes. Crystals of the CRD in complex with a mammalian-type high-mannose Man9GlcNAc2 oligosaccharide exhibited interaction with Manα1–2Man on two different termini of the glycan, with the reducing-end mannose residue ligated to Ca2+ in a primary binding site and the nonreducing terminal mannose residue occupying an adjacent secondary site. Comparison of the binding sites in DC-SIGN and langerin, two other pathogen-binding receptors of the innate immune system, revealed why these two binding sites accommodate only terminal Manα1–2Man structures, whereas dectin-2 can bind Manα1–2Man in internal positions in mannans and other polysaccharides. The specificity and geometry of the dectin-2-binding site provide the molecular mechanism for binding of dectin-2 to fungal mannans and also to bacterial lipopolysaccharides, capsular polysaccharides, and lipoarabinomannans that contain the Manα1–2Man disaccharide unit.
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Affiliation(s)
- Hadar Feinberg
- From the Departments of Structural Biology and Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305 and
| | - Sabine A F Jégouzo
- the Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Maximus J Rex
- the Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Kurt Drickamer
- the Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - William I Weis
- From the Departments of Structural Biology and Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305 and
| | - Maureen E Taylor
- the Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
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Dendritic cell inhibitory receptor 4 (DCIR4) is preferentially expressed on inflammatory and patrolling monocytes. Biochem Biophys Res Commun 2016; 480:215-221. [DOI: 10.1016/j.bbrc.2016.10.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 10/13/2016] [Indexed: 11/19/2022]
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33
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Tabansky I, Messina MD, Bangeranye C, Goldstein J, Blitz-Shabbir KM, Machado S, Jeganathan V, Wright P, Najjar S, Cao Y, Sands W, Keskin DB, Stern JNH. Advancing drug delivery systems for the treatment of multiple sclerosis. Immunol Res 2016; 63:58-69. [PMID: 26475738 DOI: 10.1007/s12026-015-8719-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Multiple sclerosis (MS) is a chronic inflammatory autoimmune disease of the central nervous system. It is characterized by demyelination of neurons and loss of neuronal axons and oligodendrocytes. In MS, auto-reactive T cells and B cells cross the blood-brain barrier (BBB), causing perivenous demyelinating lesions that form multiple discrete inflammatory demyelinated plaques located primarily in the white matter. In chronic MS, cortical demyelination and progressive axonal transections develop. Treatment for MS can be stratified into disease-modifying therapies (DMTs) and symptomatic therapy. DMTs aim to decrease circulating immune cells or to prevent these cells from crossing the BBB and reduce the inflammatory response. There are currently 10 DMTs approved for the relapsing forms of MS; these vary with regard to their efficacy, route and frequency of administration, adverse effects, and toxicity profile. Better drug delivery systems are being developed in order to decrease adverse effects, increase drug efficacy, and increase patient compliance through the direct targeting of pathologic cells. Here, we address the uses and benefits of advanced drug delivery systems, including nanoparticles, microparticles, fusion antibodies, and liposomal formulations. By altering the properties of therapeutic particles and enhancing targeting, breakthrough drug delivery technologies potentially applicable to multiple disease treatments may rapidly emerge.
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Affiliation(s)
- Inna Tabansky
- Department of Neurobiology and Behavior, The Rockefeller University, New York, NY, USA
| | - Mark D Messina
- Department of Neurology, Hofstra North Shore-LIJ School of Medicine, Hempstead, NY, USA.,Department of Science Education, Hofstra North Shore-LIJ School of Medicine, Hempstead, NY, USA
| | - Catherine Bangeranye
- Department of Science Education, Hofstra North Shore-LIJ School of Medicine, Hempstead, NY, USA
| | - Jeffrey Goldstein
- Department of Neurology, Hofstra North Shore-LIJ School of Medicine, Hempstead, NY, USA.,Department of Science Education, Hofstra North Shore-LIJ School of Medicine, Hempstead, NY, USA
| | - Karen M Blitz-Shabbir
- Department of Neurology, Hofstra North Shore-LIJ School of Medicine, Hempstead, NY, USA
| | - Suly Machado
- Department of Neurology, Hofstra North Shore-LIJ School of Medicine, Hempstead, NY, USA.,Department of Science Education, Hofstra North Shore-LIJ School of Medicine, Hempstead, NY, USA
| | - Venkatesh Jeganathan
- Department of Autoimmunity, The Feinstein Institute for Medical Research, North Shore-LIJ Health System, Manhasset, NY, USA
| | - Paul Wright
- Department of Neurology, Hofstra North Shore-LIJ School of Medicine, Hempstead, NY, USA
| | - Souhel Najjar
- Department of Neurology, Hofstra North Shore-LIJ School of Medicine, Hempstead, NY, USA
| | - Yonghao Cao
- Department of Autoimmunity, The Feinstein Institute for Medical Research, North Shore-LIJ Health System, Manhasset, NY, USA
| | - Warren Sands
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA.,Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Derin B Keskin
- Department of Cancer Immunology and AIDS, Dana Farber-Harvard Cancer Institute, Boston, MA, USA
| | - Joel N H Stern
- Department of Neurobiology and Behavior, The Rockefeller University, New York, NY, USA. .,Department of Neurology, Hofstra North Shore-LIJ School of Medicine, Hempstead, NY, USA. .,Department of Science Education, Hofstra North Shore-LIJ School of Medicine, Hempstead, NY, USA. .,Department of Autoimmunity, The Feinstein Institute for Medical Research, North Shore-LIJ Health System, Manhasset, NY, USA.
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34
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Feinberg H, Rambaruth NDS, Jégouzo SAF, Jacobsen KM, Djurhuus R, Poulsen TB, Weis WI, Taylor ME, Drickamer K. Binding Sites for Acylated Trehalose Analogs of Glycolipid Ligands on an Extended Carbohydrate Recognition Domain of the Macrophage Receptor Mincle. J Biol Chem 2016; 291:21222-21233. [PMID: 27542410 PMCID: PMC5076529 DOI: 10.1074/jbc.m116.749515] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Indexed: 11/29/2022] Open
Abstract
The macrophage receptor mincle binds to trehalose dimycolate on the surface of Mycobacterium tuberculosis. Signaling initiated by this interaction leads to cytokine production, which underlies the ability of mycobacteria to evade the immune system and also to function as adjuvants. In previous work the mechanism for binding of the sugar headgroup of trehalose dimycolate to mincle has been elucidated, but the basis for enhanced binding to glycolipid ligands, in which hydrophobic substituents are attached to the 6-hydroxyl groups, has been the subject of speculation. In the work reported here, the interaction of trehalose derivatives with bovine mincle has been probed with a series of synthetic mimics of trehalose dimycolate in binding assays, in structural studies by x-ray crystallography, and by site-directed mutagenesis. Binding studies reveal that, rather than reflecting specific structural preference, the apparent affinity of mincle for ligands with hydrophobic substituents correlates with their overall size. Structural and mutagenesis analysis provides evidence for interaction of the hydrophobic substituents with multiple different portions of the surface of mincle and confirms the presence of three Ca2+-binding sites. The structure of an extended portion of the extracellular domain of mincle, beyond the minimal C-type carbohydrate recognition domain, also constrains the way the binding domains may interact on the surface of macrophages.
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Affiliation(s)
- Hadar Feinberg
- From the Departments of Structural Biology and Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305
| | - Neela D S Rambaruth
- the Department of Life Sciences, Imperial College, London SW7 2AZ, United Kingdom, and
| | - Sabine A F Jégouzo
- the Department of Life Sciences, Imperial College, London SW7 2AZ, United Kingdom, and
| | - Kristian M Jacobsen
- Chemical Biology Laboratory, Department of Chemistry, Aarhus University, DK-8000 Aarhus, Denmark
| | - Rasmus Djurhuus
- Chemical Biology Laboratory, Department of Chemistry, Aarhus University, DK-8000 Aarhus, Denmark
| | - Thomas B Poulsen
- Chemical Biology Laboratory, Department of Chemistry, Aarhus University, DK-8000 Aarhus, Denmark
| | - William I Weis
- From the Departments of Structural Biology and Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305
| | - Maureen E Taylor
- the Department of Life Sciences, Imperial College, London SW7 2AZ, United Kingdom, and
| | - Kurt Drickamer
- the Department of Life Sciences, Imperial College, London SW7 2AZ, United Kingdom, and
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35
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Clec4A4 is a regulatory receptor for dendritic cells that impairs inflammation and T-cell immunity. Nat Commun 2016; 7:11273. [PMID: 27068492 PMCID: PMC4832068 DOI: 10.1038/ncomms11273] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 03/08/2016] [Indexed: 01/13/2023] Open
Abstract
Dendritic cells (DCs) comprise several subsets that are critically involved in the initiation and regulation of immunity. Clec4A4/DC immunoreceptor 2 (DCIR2) is a C-type lectin receptor (CLR) exclusively expressed on CD8α− conventional DCs (cDCs). However, how Clec4A4 controls immune responses through regulation of the function of CD8α− cDCs remains unclear. Here we show that Clec4A4 is a regulatory receptor for the activation of CD8α− cDCs that impairs inflammation and T-cell immunity. Clec4a4−/−CD8α− cDCs show enhanced cytokine production and T-cell priming following Toll-like receptor (TLR)-mediated activation. Furthermore, Clec4a4−/− mice exhibit TLR-mediated hyperinflammation. On antigenic immunization, Clec4a4−/− mice show not only augmented T-cell responses but also progressive autoimmune pathogenesis. Conversely, Clec4a4−/− mice exhibit resistance to microbial infection, accompanied by enhanced T-cell responses against microbes. Thus, our findings highlight roles of Clec4A4 in regulation of the function of CD8α− cDCs for control of the magnitude and quality of immune response. Clec4A4 is a C-type lectin receptor highly expressed by CD8α− dendritic cells. Here the authors show that its loss of function results in enhanced T cell responses and exacerbated autoimmunity, implicating Clec4A4 in limiting activation of the CD8α− dendritic cells.
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36
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Nagae M, Ikeda A, Hanashima S, Kojima T, Matsumoto N, Yamamoto K, Yamaguchi Y. Crystal structure of human dendritic cell inhibitory receptor C-type lectin domain reveals the binding mode with N-glycan. FEBS Lett 2016; 590:1280-8. [PMID: 27015765 DOI: 10.1002/1873-3468.12162] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 02/19/2016] [Accepted: 03/24/2016] [Indexed: 01/09/2023]
Abstract
Human dendritic cell inhibitory receptor (DCIR) is a C-type lectin receptor expressed in classical dendritic cells and accepts several oligosaccharide ligands including N-glycans. Here, we report the crystal structures of human DCIR C-type lectin domains in the absence and presence of a branched N-glycan unit. The domain has a typical C-type lectin fold and two bound calcium ions. In the ligand-bound form, the disaccharide unit (GlcNAcβ1-2Man) acceptably fits the electron density map, indicating that it forms the main epitope. The recognition of the nonterminal N-glycan unit explains the relatively broad specificity of this lectin.
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Affiliation(s)
- Masamichi Nagae
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, RIKEN Global Research Cluster, Wako, Saitama, Japan
| | - Akemi Ikeda
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, RIKEN Global Research Cluster, Wako, Saitama, Japan
| | - Shinya Hanashima
- Department of Chemistry, Osaka University, Machikaneyama, Toyonaka, Osaka, Japan
| | - Takumi Kojima
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Naoki Matsumoto
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Kazuo Yamamoto
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Yoshiki Yamaguchi
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, RIKEN Global Research Cluster, Wako, Saitama, Japan
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37
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Abstract
In this chapter, a comprehensive overview of the known ligands for the C-type lectins (CTLs) is provided. Emphasis has been placed on the chemical structure of the glycans that bind to the different CTLs and the amount of structural variation (or overlap) that each CTL can tolerate. In this way, both the synthetic carbohydrate chemist and the immunologist can more readily gain insight into the existing structure-activity space for the CTL ligands and, ideally, see areas of synergy that will help identify and refine the ligands for these receptors.
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Affiliation(s)
- Sho Yamasaki
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
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38
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Nagae M, Kanagawa M, Morita-Matsumoto K, Hanashima S, Kizuka Y, Taniguchi N, Yamaguchi Y. Atomic visualization of a flipped-back conformation of bisected glycans bound to specific lectins. Sci Rep 2016; 6:22973. [PMID: 26971576 PMCID: PMC4789653 DOI: 10.1038/srep22973] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 02/23/2016] [Indexed: 11/09/2022] Open
Abstract
Glycans normally exist as a dynamic equilibrium of several conformations. A fundamental question concerns how such molecules bind lectins despite disadvantageous entropic loss upon binding. Bisected glycan, a glycan possessing bisecting N-acetylglucosamine (GlcNAc), is potentially a good model for investigating conformational dynamics and glycan-lectin interactions, owing to the unique ability of this sugar residue to alter conformer populations and thus modulate the biological activities. Here we analyzed bisected glycan in complex with two unrelated lectins, Calsepa and PHA-E. The crystal structures of the two complexes show a conspicuous flipped back glycan structure (designated 'back-fold' conformation), and solution NMR analysis also provides evidence of 'back-fold' glycan structure. Indeed, statistical conformational analysis of available bisected and non-bisected glycan structures suggests that bisecting GlcNAc restricts the conformations of branched structures. Restriction of glycan flexibility by certain sugar residues may be more common than previously thought and impinges on the mechanism of glycoform-dependent biological functions.
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Affiliation(s)
- Masamichi Nagae
- Structural Glycobiology Team, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Mayumi Kanagawa
- Structural Glycobiology Team, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | | | - Shinya Hanashima
- Department of Chemistry, Osaka University, Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yasuhiko Kizuka
- Disease Glycomics Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, RIKEN Global Research Cluster, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Naoyuki Taniguchi
- Disease Glycomics Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, RIKEN Global Research Cluster, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yoshiki Yamaguchi
- Structural Glycobiology Team, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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39
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Nagae M, Yamaguchi Y. Sugar recognition and protein-protein interaction of mammalian lectins conferring diverse functions. Curr Opin Struct Biol 2015; 34:108-15. [PMID: 26418728 DOI: 10.1016/j.sbi.2015.08.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 08/06/2015] [Accepted: 08/10/2015] [Indexed: 11/24/2022]
Abstract
Recent advances in structural analyses of mammalian lectins reveal atomic-level details of their fine specificities toward diverse endogenous and exogenous glycans. Local variations on a common scaffold can enable certain lectins to recognize complex carbohydrate ligands including branched glycans and O-glycosylated peptides. Simultaneous recognition of both glycan and the aglycon moieties enhances the affinity and specificity of lectins such as CLEC-2 and PILRα. Attention has been paid to the roles of galectin and RegIII family of proteins in protein-protein interactions involved in critical biological functions including signal transduction and bactericidal pore formation.
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Affiliation(s)
- Masamichi Nagae
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, RIKEN Global Research Cluster, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yoshiki Yamaguchi
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, RIKEN Global Research Cluster, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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40
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Guan X, Chaffey PK, Zeng C, Greene ER, Chen L, Drake MR, Chen C, Groobman A, Resch MG, Himmel ME, Beckham GT, Tan Z. Molecular-scale features that govern the effects of O-glycosylation on a carbohydrate-binding module. Chem Sci 2015; 6:7185-7189. [PMID: 28966766 PMCID: PMC5580309 DOI: 10.1039/c5sc02636a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 09/16/2015] [Indexed: 12/15/2022] Open
Abstract
Protein glycosylation is a ubiquitous post-translational modification in all kingdoms of life. Despite its importance in molecular and cellular biology, the molecular-level ramifications of O-glycosylation on biomolecular structure and function remain elusive. Here, we took a small model glycoprotein and changed the glycan structure and size, amino acid residues near the glycosylation site, and glycosidic linkage while monitoring any corresponding changes to physical stability and cellulose binding affinity. The results of this study reveal the collective importance of all the studied features in controlling the most pronounced effects of O-glycosylation in this system. Going forward, this study suggests the possibility of designing proteins with multiple improved properties by simultaneously varying the structures of O-glycans and amino acids local to the glycosylation site.
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Affiliation(s)
- Xiaoyang Guan
- Department of Chemistry and Biochemistry , BioFrontiers Institute , University of Colorado , Boulder , CO 80303 , USA .
| | - Patrick K Chaffey
- Department of Chemistry and Biochemistry , BioFrontiers Institute , University of Colorado , Boulder , CO 80303 , USA .
| | - Chen Zeng
- Department of Chemistry and Biochemistry , BioFrontiers Institute , University of Colorado , Boulder , CO 80303 , USA .
| | - Eric R Greene
- Department of Chemistry and Biochemistry , BioFrontiers Institute , University of Colorado , Boulder , CO 80303 , USA .
| | - Liqun Chen
- Department of Chemistry and Biochemistry , BioFrontiers Institute , University of Colorado , Boulder , CO 80303 , USA .
| | - Matthew R Drake
- Department of Chemistry and Biochemistry , BioFrontiers Institute , University of Colorado , Boulder , CO 80303 , USA .
| | - Claire Chen
- Department of Chemistry and Biochemistry , BioFrontiers Institute , University of Colorado , Boulder , CO 80303 , USA .
| | - Ari Groobman
- Department of Chemistry and Biochemistry , BioFrontiers Institute , University of Colorado , Boulder , CO 80303 , USA .
| | - Michael G Resch
- National Bioenergy Center , National Renewable Energy Laboratory , Golden , CO 80401 , USA .
| | - Michael E Himmel
- Biosciences Center , National Renewable Energy Laboratory , Golden , CO 80401 , USA
| | - Gregg T Beckham
- National Bioenergy Center , National Renewable Energy Laboratory , Golden , CO 80401 , USA .
| | - Zhongping Tan
- Department of Chemistry and Biochemistry , BioFrontiers Institute , University of Colorado , Boulder , CO 80303 , USA .
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41
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Drickamer K, Taylor ME. Recent insights into structures and functions of C-type lectins in the immune system. Curr Opin Struct Biol 2015; 34:26-34. [PMID: 26163333 PMCID: PMC4681411 DOI: 10.1016/j.sbi.2015.06.003] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 05/22/2015] [Accepted: 06/19/2015] [Indexed: 12/05/2022]
Abstract
Sugar-binding C-type carbohydrate-recognition domains fall in five structural groups. Structures for many of these domains, covering all of the groups, have been obtained. Not all human C-type lectins have clear orthologues in other mammals such as mice. Different mechanisms by which C-type lectins initiate signalling remain to be defined. Hetero-oligomeric receptors add to the complexity of overlapping specificities.
The majority of the C-type lectin-like domains in the human genome likely to bind sugars have been investigated structurally, although novel mechanisms of sugar binding are still being discovered. In the immune system, adhesion and endocytic receptors that bind endogenous mammalian glycans are often conserved, while pathogen-binding C-type lectins on cells of the innate immune system are more divergent. Lack of orthology between some human and mouse receptors, as well as overlapping specificities of many receptors and formation of receptor hetero-oligomers, can make it difficult to define the roles of individual receptors. There is good evidence that C-type lectins initiate signalling pathways in several different ways, but this function remains the least well understood from a mechanistic perspective.
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Affiliation(s)
- Kurt Drickamer
- Department of Life Sciences, Imperial College, London SW7 2AZ, United Kingdom
| | - Maureen E Taylor
- Department of Life Sciences, Imperial College, London SW7 2AZ, United Kingdom.
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42
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Jégouzo SAF, Feinberg H, Dungarwalla T, Drickamer K, Weis WI, Taylor ME. A Novel Mechanism for Binding of Galactose-terminated Glycans by the C-type Carbohydrate Recognition Domain in Blood Dendritic Cell Antigen 2. J Biol Chem 2015; 290:16759-71. [PMID: 25995448 PMCID: PMC4505424 DOI: 10.1074/jbc.m115.660613] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Indexed: 11/06/2022] Open
Abstract
Blood dendritic cell antigen 2 (BDCA-2; also designated CLEC4C or CD303) is uniquely expressed on plasmacytoid dendritic cells. Stimulation of BDCA-2 with antibodies leads to an anti-inflammatory response in these cells, but the natural ligands for the receptor are not known. The C-type carbohydrate recognition domain in the extracellular portion of BDCA-2 contains a signature motif typical of C-type animal lectins that bind mannose, glucose, or GlcNAc, yet it has been reported that BDCA-2 binds selectively to galactose-terminated, biantennary N-linked glycans. A combination of glycan array analysis and binding competition studies with monosaccharides and natural and synthetic oligosaccharides have been used to define the binding epitope for BDCA-2 as the trisaccharide Galβ1-3/4GlcNAcβ1-2Man. X-ray crystallography and mutagenesis studies show that mannose is ligated to the conserved Ca(2+) in the primary binding site that is characteristic of C-type carbohydrate recognition domains, and the GlcNAc and galactose residues make additional interactions in a wide, shallow groove adjacent to the primary binding site. As predicted from these studies, BDCA-2 binds to IgG, which bears galactose-terminated glycans that are not commonly found attached to other serum glycoproteins. Thus, BDCA-2 has the potential to serve as a previously unrecognized immunoglobulin Fc receptor.
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Affiliation(s)
- Sabine A F Jégouzo
- the Department of Life Sciences, Imperial College, London SW7 2AZ, United Kingdom
| | - Hadar Feinberg
- From the Departments of Structural Biology and Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305 and
| | - Tabassum Dungarwalla
- the Department of Life Sciences, Imperial College, London SW7 2AZ, United Kingdom
| | - Kurt Drickamer
- the Department of Life Sciences, Imperial College, London SW7 2AZ, United Kingdom
| | - William I Weis
- From the Departments of Structural Biology and Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305 and
| | - Maureen E Taylor
- the Department of Life Sciences, Imperial College, London SW7 2AZ, United Kingdom
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43
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Hanashima S, Korekane H, Taniguchi N, Yamaguchi Y. Synthesis of N-glycan units for assessment of substrate structural requirements of N-acetylglucosaminyltransferase III. Bioorg Med Chem Lett 2014; 24:4533-4537. [PMID: 25139566 DOI: 10.1016/j.bmcl.2014.07.074] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/22/2014] [Accepted: 07/29/2014] [Indexed: 12/27/2022]
Abstract
N-Acetylglucosaminyltransferase (GnT) III is a glycosyltransferase which produces bisected N-glycans by transferring GlcNAc to the 4-position of core mannose. Bisected N-glycans are involved in physiological and pathological processes through the functional regulation of their carrier proteins. An understanding of the biological functions of bisected glycans will be greatly accelerated by use of specific inhibitors of GnT-III. Thus far, however, such inhibitors have not been developed and even the substrate-binding mode of GnT-III is not fully understood. To gain insight into structural features required of the substrate, we systematically synthesized four N-glycan units, the branching parts of the bisected and non-bisected N-glycans. The series of syntheses were achieved from a common core trimannose, giving bisected tetra- and hexasaccharides as well as non-bisected tri- and pentasaccharides. A competitive GnT-III inhibition assay using the synthetic substrates revealed a vital role for the Manβ(1-4)GlcNAc moiety. In keeping with previous reports, GlcNAc at the α1,3-branch is also involved in the interaction. The structural requirements of GnT-III elucidated in this study will provide a basis for rational inhibitor design.
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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
| | - Hiroaki Korekane
- Disease Glycomics Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center for Systems Chemical Biology, RIKEN Global Research Cluster, Wako, Saitama 351-0198, Japan
| | - Naoyuki Taniguchi
- Disease Glycomics 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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44
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Nagae M, Soga K, Morita-Matsumoto K, Hanashima S, Ikeda A, Yamamoto K, Yamaguchi Y. Phytohemagglutinin from Phaseolus vulgaris (PHA-E) displays a novel glycan recognition mode using a common legume lectin fold. Glycobiology 2014; 24:368-78. [DOI: 10.1093/glycob/cwu004] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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45
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Nagae M, Ikeda A, Kitago Y, Matsumoto N, Yamamoto K, Yamaguchi Y. Crystal structures of carbohydrate recognition domain of blood dendritic cell antigen-2 (BDCA2) reveal a common domain-swapped dimer. Proteins 2014; 82:1512-8. [PMID: 24425442 DOI: 10.1002/prot.24504] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 11/22/2013] [Accepted: 12/12/2013] [Indexed: 11/11/2022]
Abstract
We report on crystal structures of a carbohydrate recognition domain (CRD) of human C-type lectin receptor blood dendritic cell antigen-2 (BDCA2). Three different crystal forms were obtained at 1.8-2.3 Å resolution. In all three, the CRD has a basic C-type lectin fold, but a long loop extends away from the core domain to form a domain-swapped dimer. The structures of the dimers from the three different crystal forms superimpose well, indicating that domain swapping and dimer formation are energetically stable. The structure of the dimer is compared with other domain-swapped proteins, and a possible regulation mechanism of BDCA2 is discussed.
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Affiliation(s)
- Masamichi Nagae
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, RIKEN Global Research Cluster, Wako, Saitama, 351-0198, Japan
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