1
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Prenzler S, Rudrawar S, Waespy M, Kelm S, Anoopkumar-Dukie S, Haselhorst T. The role of sialic acid-binding immunoglobulin-like-lectin-1 (siglec-1) in immunology and infectious disease. Int Rev Immunol 2023; 42:113-138. [PMID: 34494938 DOI: 10.1080/08830185.2021.1931171] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Siglec-1, also known as Sialoadhesin (Sn) and CD169 is highly conserved among vertebrates and with 17 immunoglobulin-like domains is Siglec-1 the largest member of the Siglec family. Expression of Siglec-1 is found primarily on dendritic cells (DCs), macrophages and interferon induced monocyte. The structure of Siglec-1 is unique among siglecs and its function as a receptor is also different compared to other receptors in this class as it contains the most extracellular domains out of all the siglecs. However, the ability of Siglec-1 to internalize antigens and to pass them on to lymphocytes by allowing dendritic cells and macrophages to act as antigen presenting cells, is the main reason that has granted Siglec-1's key role in multiple human disease states including atherosclerosis, coronary artery disease, autoimmune diseases, cell-cell signaling, immunology, and more importantly bacterial and viral infections. Enveloped viruses for example have been shown to manipulate Siglec-1 to increase their virulence by binding to sialic acids present on the virus glycoproteins allowing them to spread or evade immune response. Siglec-1 mediates dissemination of HIV-1 in activated tissues enhancing viral spread via infection of DC/T-cell synapses. Overall, the ability of Siglec-1 to bind a variety of target cells within the immune system such as erythrocytes, B-cells, CD8+ granulocytes and NK cells, highlights that Siglec-1 is a unique player in these essential processes.
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Affiliation(s)
- Shane Prenzler
- School of Pharmacy and Medical Sciences, Griffith University, Gold Coast, Queensland, Australia.,Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia
| | - Santosh Rudrawar
- School of Pharmacy and Medical Sciences, Griffith University, Gold Coast, Queensland, Australia.,Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia
| | - Mario Waespy
- Centre for Biomolecular Interactions Bremen, Department of Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Sørge Kelm
- Centre for Biomolecular Interactions Bremen, Department of Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Shailendra Anoopkumar-Dukie
- School of Pharmacy and Medical Sciences, Griffith University, Gold Coast, Queensland, Australia.,Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia
| | - Thomas Haselhorst
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
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2
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Klamer Z, Haab B. Combined Analysis of Multiple Glycan-Array Datasets: New Explorations of Protein-Glycan Interactions. Anal Chem 2021; 93:10925-10933. [PMID: 34319080 DOI: 10.1021/acs.analchem.1c01739] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Glycan arrays are indispensable for learning about the specificities of glycan-binding proteins. Despite the abundance of available data, the current analysis methods do not have the ability to interpret and use the variety of data types and to integrate information across datasets. Here, we evaluated whether a novel, automated algorithm for glycan-array analysis could meet that need. We developed a regression-tree algorithm with simultaneous motif optimization and packaged it in software called MotifFinder. We applied the software to analyze data from eight different glycan-array platforms with widely divergent characteristics and observed an accurate analysis of each dataset. We then evaluated the feasibility and value of the combined analyses of multiple datasets. In an integrated analysis of datasets covering multiple lectin concentrations, the software determined approximate binding constants for distinct motifs and identified major differences between the motifs that were not apparent from single-concentration analyses. Furthermore, an integrated analysis of data sources with complementary sets of glycans produced broader views of lectin specificity than produced by the analysis of just one data source. MotifFinder, therefore, enables the optimal use of the expanding resource of the glycan-array data and promises to advance the studies of protein-glycan interactions.
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Affiliation(s)
- Zachary Klamer
- Van Andel Institute, 333 Bostwick NE, Grand Rapids, Michigan 49503, United States
| | - Brian Haab
- Van Andel Institute, 333 Bostwick NE, Grand Rapids, Michigan 49503, United States
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3
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Song N, Chen L, Ren X, Waterfield NR, Yang J, Yang G. N-Glycans and sulfated glycosaminoglycans contribute to the action of diverse Tc toxins on mammalian cells. PLoS Pathog 2021; 17:e1009244. [PMID: 33539469 PMCID: PMC7861375 DOI: 10.1371/journal.ppat.1009244] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 12/18/2020] [Indexed: 01/11/2023] Open
Abstract
Tc toxin is an exotoxin composed of three subunits named TcA, TcB and TcC. Structural analysis revealed that TcA can form homopentamer that mediates the cellular recognition and delivery processes, thus contributing to the host tropism of Tc toxin. N-glycans and heparan sulfates have been shown to act as receptors for several Tc toxins. Here, we performed two independent genome-wide CRISPR-Cas9 screens, and have validated glycans and sulfated glycosaminoglycans (sGAGs) as Tc toxin receptors also for previously uncharacterized Tc toxins. We found that TcdA1 form Photorhabdus luminescens W14 (TcdA1W14) can recognize N-glycans via the RBD-D domain, corroborating previous findings. Knockout of N-glycan processing enzymes specifically blocks the intoxication of TcdA1W14-assembled Tc toxin. On the other hand, our results showed that sGAG biosynthesis pathway is involved in the cell surface binding of TcdA2TT01 (TcdA2 from P. luminescens TT01). Competition assays and biolayer interferometry demonstrated that the sulfation group in sGAGs is required for the binding of TcdA2TT01. Finally, based on the conserved domains of representative TcA proteins, we have identified 1,189 putative TcAs from 1,039 bacterial genomes. These TcAs are categorized into five subfamilies. Each subfamily shows a good correlation with both genetic organization of the TcA protein(s) and taxonomic origin of the genomes, suggesting these subfamilies may utilize different mechanisms for cellular recognition. Taken together, our results support the previously described two different binding modalities of Tc toxins, leading to unique host targeting properties. We also present the bioinformatics data and receptor screening strategies for TcA proteins, provide new insights into understanding host specificity and biomedical applications of Tc toxins. The Toxin complexes, also referred to as Tc toxins, are a family of A5BC exotoxins widely distributed among Gram-negative and positive bacteria. First identified in Entomopathogenic bacteria as key virulence factors to combat insect hosts, putative Tc toxin loci are also encoded by a range of human pathogens such as Salmonella and Yersinia. Previous studies indicated that several Tc toxins can target invertebrate and vertebrate cells via binding with N-glycans and heparan sulfates. Here our genome-wide CRISPR-Cas9 screens validated that different Tc toxins utilized distinct receptors for the adhesion to their targets, which is determined by TcA homopentamer. For example, TcdA1 from Photorhabdus luminescens W14 (TcdA1W14) relies on N-glycan binding to exert its toxic effects, while sulfate groups of sulfated glycosaminoglycans are critical for the cell targeting of other TcAs such as TcdA2TT01 (TcdA2 from P. luminescens TT01). Consistent with the previously described different binding modalities of Tc toxins, our results confirm that the receptor selectivity of TcAs contribute to the cellular tropism of Tc toxins. Furthermore we has also identified 1,189 TcA homologues and categorized them into five subfamilies. Each TcA subfamily shows a good correlation with the taxonomic origin of the genomes, suggesting these subfamilies are linked to diverse host tropisms via different binding modalities. Together, our findings provide mechanistic insights into understanding host specificity of distinct Tc toxins and the development of therapeutics for Tc toxin-related infections, as well as the adaptation of Tc-injectisomes as potential biotechnology tools and pest-control weapons.
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Affiliation(s)
- Nan Song
- Beijing Institute of Tropical Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, China
- Emergency and Critical Care Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Lihong Chen
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xingmei Ren
- Beijing Institute of Tropical Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, China
- Emergency and Critical Care Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | | | - Jian Yang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Guowei Yang
- Beijing Institute of Tropical Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, China
- Emergency and Critical Care Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China
- * E-mail:
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4
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Abstract
The importance of post-translational glycosylation in protein structure and function has gained significant clinical relevance recently. The latest developments in glycobiology, glycochemistry, and glycoproteomics have made the field more manageable and relevant to disease progression and immune-response signaling. Here, we summarize the current progress in glycoscience, including the new methodologies that have led to the introduction of programmable and automatic as well as large-scale enzymatic synthesis, and the development of glycan array, glycosylation probes, and inhibitors of carbohydrate-associated enzymes or receptors. These novel methodologies and tools have facilitated our understanding of the significance of glycosylation and development of carbohydrate-derived medicines that bring the field to the next level of scientific and medical significance.
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Affiliation(s)
- Sachin S Shivatare
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California 92037, USA
| | - Chi-Huey Wong
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California 92037, USA
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
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5
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Li L, Guan W, Zhang G, Wu Z, Yu H, Chen X, Wang PG. Microarray analyses of closely related glycoforms reveal different accessibilities of glycan determinants on N-glycan branches. Glycobiology 2020; 30:334-345. [PMID: 32026940 PMCID: PMC7175966 DOI: 10.1093/glycob/cwz100] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 11/27/2019] [Accepted: 12/02/2019] [Indexed: 01/03/2023] Open
Abstract
Glycans mediate a wide variety of biological roles via recognition by glycan-binding proteins (GBPs). Comprehensive knowledge of such interaction is thus fundamental to glycobiology. While the primary binding feature of GBPs can be easily uncovered by using a simple glycan microarray harboring limited numbers of glycan motifs, their fine specificities are harder to interpret. In this study, we prepared 98 closely related N-glycoforms that contain 5 common glycan epitopes which allowed the determination of the fine binding specificities of several plant lectins and anti-glycan antibodies. These N-glycoforms differ from each other at the monosaccharide level and were presented in an identical format to ensure comparability. With the analysis platform we used, it was found that most tested GBPs have preferences toward only one branch of the complex N-glycans, and their binding toward the epitope-presenting branch can be significantly affected by structures on the other branch. Fine specificities described here are valuable for a comprehensive understanding and applications of GBPs.
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Affiliation(s)
- Lei Li
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Wanyi Guan
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Gaolan Zhang
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Zhigang Wu
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Hai Yu
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Xi Chen
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Peng G Wang
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
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6
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Haab BB, Klamer Z. Advances in Tools to Determine the Glycan-Binding Specificities of Lectins and Antibodies. Mol Cell Proteomics 2020; 19:224-232. [PMID: 31848260 PMCID: PMC7000120 DOI: 10.1074/mcp.r119.001836] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/13/2019] [Indexed: 01/17/2023] Open
Abstract
Proteins that bind carbohydrate structures can serve as tools to quantify or localize specific glycans in biological specimens. Such proteins, including lectins and glycan-binding antibodies, are particularly valuable if accurate information is available about the glycans that a protein binds. Glycan arrays have been transformational for uncovering rich information about the nuances and complexities of glycan-binding specificity. A challenge, however, has been the analysis of the data. Because protein-glycan interactions are so complex, simplistic modes of analyzing the data and describing glycan-binding specificities have proven inadequate in many cases. This review surveys the methods for handling high-content data on protein-glycan interactions. We contrast the approaches that have been demonstrated and provide an overview of the resources that are available. We also give an outlook on the promising experimental technologies for generating new insights into protein-glycan interactions, as well as a perspective on the limitations that currently face the field.
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7
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Comparative binding and uptake of liposomes decorated with mannose oligosaccharides by cells expressing the mannose receptor or DC-SIGN. Carbohydr Res 2020; 487:107877. [DOI: 10.1016/j.carres.2019.107877] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 11/08/2019] [Accepted: 11/11/2019] [Indexed: 02/06/2023]
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8
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Burnett DL, Reed JH, Christ D, Goodnow CC. Clonal redemption and clonal anergy as mechanisms to balance B cell tolerance and immunity. Immunol Rev 2019; 292:61-75. [DOI: 10.1111/imr.12808] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/10/2019] [Accepted: 09/13/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Deborah L. Burnett
- Garvan Institute of Medical Research Darlinghurst NSW Australia
- St Vincent's Clinical School UNSW Sydney Darlinghurst NSW Australia
| | - Joanne H. Reed
- Garvan Institute of Medical Research Darlinghurst NSW Australia
- St Vincent's Clinical School UNSW Sydney Darlinghurst NSW Australia
| | - Daniel Christ
- Garvan Institute of Medical Research Darlinghurst NSW Australia
- St Vincent's Clinical School UNSW Sydney Darlinghurst NSW Australia
| | - Christopher C. Goodnow
- Garvan Institute of Medical Research Darlinghurst NSW Australia
- St Vincent's Clinical School UNSW Sydney Darlinghurst NSW Australia
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9
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Taylor ME, Drickamer K. Mammalian sugar-binding receptors: known functions and unexplored roles. FEBS J 2019; 286:1800-1814. [PMID: 30657247 PMCID: PMC6563452 DOI: 10.1111/febs.14759] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 12/11/2018] [Accepted: 01/15/2019] [Indexed: 12/13/2022]
Abstract
Mammalian glycan-binding receptors, sometimes known as lectins, interact with glycans, the oligosaccharide portions of endogenous mammalian glycoproteins and glycolipids as well as sugars on the surfaces of microbes. These receptors guide glycoproteins out of and back into cells, facilitate communication between cells through both adhesion and signaling, and allow the innate immune system to respond quickly to viral, fungal, bacterial, and parasitic pathogens. For many of the roughly 100 glycan-binding receptors that are known in humans, there are good descriptions of what types of glycans they bind and how selectivity for these ligands is achieved at the molecular level. In some cases, there is also comprehensive evidence for the roles that the receptors play at the cellular and organismal levels. In addition to highlighting these well-understood paradigms for glycan-binding receptors, this review will suggest where gaps remain in our understanding of the physiological functions that they can serve.
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10
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Martini F, Eckmair B, Štefanić S, Jin C, Garg M, Yan S, Jiménez-Castells C, Hykollari A, Neupert C, Venco L, Varón Silva D, Wilson IBH, Paschinger K. Highly modified and immunoactive N-glycans of the canine heartworm. Nat Commun 2019; 10:75. [PMID: 30622255 PMCID: PMC6325117 DOI: 10.1038/s41467-018-07948-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 12/06/2018] [Indexed: 01/05/2023] Open
Abstract
The canine heartworm (Dirofilaria immitis) is a mosquito-borne parasitic nematode whose range is extending due to climate change. In a four-dimensional analysis involving HPLC, MALDI-TOF–MS and MS/MS in combination with chemical and enzymatic digestions, we here reveal an N-glycome of unprecedented complexity. We detect N-glycans of up to 7000 Da, which contain long fucosylated HexNAc-based repeats, as well as glucuronylated structures. While some modifications including LacdiNAc, chitobiose, α1,3-fucose and phosphorylcholine are familiar, anionic N-glycans have previously not been reported in nematodes. Glycan array data show that the neutral glycans are preferentially recognised by IgM in dog sera or by mannose binding lectin when antennal fucose and phosphorylcholine residues are removed; this pattern of reactivity is reversed for mammalian C-reactive protein, which can in turn be bound by the complement component C1q. Thereby, the N-glycans of D. immitis contain features which may either mediate immunomodulation of the host or confer the ability to avoid immune surveillance. The glycome of parasites can have immunomodulatory properties or help to avoid immune surveillance, but details are unknown. Here, Martini et al. characterize the N-glycome of the canine heartworm, reveal an unprecedented complexity, particularly in anionic N-glycans, and determine recognition by components of the immune system.
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Affiliation(s)
| | - Barbara Eckmair
- Department für Chemie, Universität für Bodenkultur, Muthgasse 18, 1190, Wien, Austria
| | - Saša Štefanić
- Institute of Parasitology, Universität Zürich, Winterthurerstraße 266a, 8057, Zürich, Switzerland
| | - Chunsheng Jin
- Institutionen för Biomedicin, Göteborgs Universitet, 405 30, Göteborg, Sweden
| | - Monika Garg
- Max-Planck-Institut für Kolloid- und Grenzflächenforschung, Biomolekulare Systeme, 14424, Potsdam, Germany
| | - Shi Yan
- Department für Chemie, Universität für Bodenkultur, Muthgasse 18, 1190, Wien, Austria.,Institut für Parasitologie, Veterinärmedizinische Universität, 1210, Wien, Austria
| | | | - Alba Hykollari
- Department für Chemie, Universität für Bodenkultur, Muthgasse 18, 1190, Wien, Austria
| | | | - Luigi Venco
- Clinica Veterinaria Lago Maggiore, Arona, 28040, Italy
| | - Daniel Varón Silva
- Max-Planck-Institut für Kolloid- und Grenzflächenforschung, Biomolekulare Systeme, 14424, Potsdam, Germany
| | - Iain B H Wilson
- Department für Chemie, Universität für Bodenkultur, Muthgasse 18, 1190, Wien, Austria.
| | - Katharina Paschinger
- Department für Chemie, Universität für Bodenkultur, Muthgasse 18, 1190, Wien, Austria
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11
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Echeverria B, Serna S, Achilli S, Vivès C, Pham J, Thépaut M, Hokke CH, Fieschi F, Reichardt NC. Chemoenzymatic Synthesis of N-glycan Positional Isomers and Evidence for Branch Selective Binding by Monoclonal Antibodies and Human C-type Lectin Receptors. ACS Chem Biol 2018; 13:2269-2279. [PMID: 29894153 DOI: 10.1021/acschembio.8b00431] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Here, we describe a strategy for the rapid preparation of pure positional isomers of complex N-glycans to complement an existing array comprising a larger number of N-glycans and smaller glycan structures. The expanded array was then employed to study context-dependent binding of structural glycan fragments by monoclonal antibodies and C-type lectins. A partial enzymatic elongation of semiprotected core structures was combined with the protecting-group-aided separation of positional isomers by preparative HPLC. This methodology, which avoids the laborious chemical differentiation of antennae, was employed for the preparation of eight biantennary N-glycans with Galβ1,4GlcNAc (LN), GalNAcβ1,4GlcNAc (LDN), and GalNAcβ1,4[Fucα1,3]GlcNAc (LDNF) motifs presented on either one or both antennae. Screening of the binding specificities of three anti-LeX monoclonal IgM antibodies raised against S. mansoni glycans and three C-type lectin receptors of the innate immune system, namely DC-SIGN, DC-SIGNR, and LSECtin, revealed a surprising context-dependent fine specificity for the recognition of the glycan motifs. Moreover, we observed a striking selection of one individual positional isomer over the other by the C-type lectins tested, underscoring the biological relevance of the structural context of glycan elements in molecular recognition.
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Affiliation(s)
- Begoña Echeverria
- CIC biomaGUNE, Glycotechnology Laboratory, Paseo Miramón 182, 20014 San Sebastian, Spain
| | - Sonia Serna
- CIC biomaGUNE, Glycotechnology Laboratory, Paseo Miramón 182, 20014 San Sebastian, Spain
| | - Silvia Achilli
- Université Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Corinne Vivès
- Université Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Julie Pham
- CIC biomaGUNE, Glycotechnology Laboratory, Paseo Miramón 182, 20014 San Sebastian, Spain
| | - Michel Thépaut
- Université Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Cornelis H. Hokke
- Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - Franck Fieschi
- Université Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Niels-Christian Reichardt
- CIC biomaGUNE, Glycotechnology Laboratory, Paseo Miramón 182, 20014 San Sebastian, Spain
- CIBER-BBN, Paseo Miramón 182, 20014 San Sebastian, Spain
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12
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Zheng RB, Jégouzo SAF, Joe M, Bai Y, Tran HA, Shen K, Saupe J, Xia L, Ahmed MF, Liu YH, Patil PS, Tripathi A, Hung SC, Taylor ME, Lowary TL, Drickamer K. Insights into Interactions of Mycobacteria with the Host Innate Immune System from a Novel Array of Synthetic Mycobacterial Glycans. ACS Chem Biol 2017; 12:2990-3002. [PMID: 29048873 PMCID: PMC5735379 DOI: 10.1021/acschembio.7b00797] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
An
array of homogeneous glycans representing all the major carbohydrate
structures present in the cell wall of the human pathogen Mycobacterium tuberculosis and other mycobacteria has been
probed with a panel of glycan-binding receptors expressed on cells
of the mammalian innate immune system. The results provide an overview
of interactions between mycobacterial glycans and receptors that mediate
uptake and survival in macrophages, dendritic cells, and sinusoidal
endothelial cells. A subset of the wide variety of glycan structures
present on mycobacterial surfaces interact with cells of the innate
immune system through the receptors tested. Endocytic receptors, including
the mannose receptor, DC-SIGN, langerin, and DC-SIGNR (L-SIGN), interact
predominantly with mannose-containing caps found on the mycobacterial
polysaccharide lipoarabinomannan. Some of these receptors also interact
with phosphatidyl-myo-inositol mannosides and mannose-containing
phenolic glycolipids. Many glycans are ligands for overlapping sets
of receptors, suggesting multiple, redundant routes by which mycobacteria
can enter cells. Receptors with signaling capability interact with
two distinct sets of mycobacterial glycans: targets for dectin-2 overlap
with ligands for the mannose-binding endocytic receptors, while mincle
binds exclusively to trehalose-containing structures such as trehalose
dimycolate. None of the receptors surveyed bind furanose residues,
which often form part of the epitopes recognized by antibodies to
mycobacteria. Thus, the innate and adaptive immune systems can target
different sets of mycobacterial glycans. This array, the first of
its kind, represents an important new tool for probing, at a molecular
level, biological roles of a broad range of mycobacterial glycans,
a task that has not previously been possible.
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Affiliation(s)
- Ruixiang Blake Zheng
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | | | - Maju Joe
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Yu Bai
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Huu-Anh Tran
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Ke Shen
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Jörn Saupe
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Li Xia
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Md. Faiaz Ahmed
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Yu-Hsuan Liu
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | | | - Ashish Tripathi
- Genomics
Research Centre, Academia Sinica, Nangang, Taipei 11529, Taiwan
| | - Shang-Cheng Hung
- Genomics
Research Centre, Academia Sinica, Nangang, Taipei 11529, Taiwan
| | - Maureen E. Taylor
- Department
of Life Sciences, Imperial College, London SW7 2AZ, United Kingdom
| | - Todd L. Lowary
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Kurt Drickamer
- Department
of Life Sciences, Imperial College, London SW7 2AZ, United Kingdom
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13
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Klamer Z, Staal B, Prudden AR, Liu L, Smith DF, Boons GJ, Haab B. Mining High-Complexity Motifs in Glycans: A New Language To Uncover the Fine Specificities of Lectins and Glycosidases. Anal Chem 2017; 89:12342-12350. [PMID: 29058413 PMCID: PMC5700451 DOI: 10.1021/acs.analchem.7b04293] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Knowledge of lectin
and glycosidase specificities is fundamental
to the study of glycobiology. The primary specificities of such molecules
can be uncovered using well-established tools, but the complex details
of their specificities are difficult to determine and describe. Here
we present a language and algorithm for the analysis and description
of glycan motifs with high complexity. The language uses human-readable
notation and wildcards, modifiers, and logical operators to define
motifs of nearly any complexity. By applying the syntax to the analysis
of glycan-array data, we found that the lectin AAL had higher binding
where fucose groups are displayed on separate branches. The lectin
SNA showed gradations in binding based on the length of the extension
displaying sialic acid and on characteristics of the opposing branches.
A new algorithm to evaluate changes in lectin binding upon treatment
with exoglycosidases identified the primary specificities and potential
fine specificities of an α1–2-fucosidase and an α2–3,6,8-neuraminidase.
The fucosidase had significantly lower action where sialic acid neighbors
the fucose, and the neuraminidase showed statistically lower action
where α1–2 fucose neighbors the sialic acid or is on
the opposing branch. The complex features identified here would have
been inaccessible to analysis using previous methods. The new language
and algorithms promise to facilitate the precise determination and
description of lectin and glycosidase specificities.
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Affiliation(s)
- Zachary Klamer
- Van Andel Research Institute , 333 Bostwick NE, Grand Rapids, Michigan 49503, United States
| | - Ben Staal
- Van Andel Research Institute , 333 Bostwick NE, Grand Rapids, Michigan 49503, United States
| | - Anthony R Prudden
- Complex Carbohydrate Research Center, University of Georgia , 315 Riverbend Road, Athens, Georgia 30602, United States
| | - Lin Liu
- Complex Carbohydrate Research Center, University of Georgia , 315 Riverbend Road, Athens, Georgia 30602, United States
| | - David F Smith
- Emory Comprehensive Glycomics Core, Emory University School of Medicine , Atlanta, Georgia 30322, United States
| | - Geert-Jan Boons
- Complex Carbohydrate Research Center, University of Georgia , 315 Riverbend Road, Athens, Georgia 30602, United States
| | - Brian Haab
- Van Andel Research Institute , 333 Bostwick NE, Grand Rapids, Michigan 49503, United States
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14
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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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15
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Abstract
Despite mammalian glycans typically having highly complex asymmetrical multiantennary architectures, chemical and chemoenzymatic synthesis has almost exclusively focused on the preparation of simpler symmetrical structures. This deficiency hampers investigations into the biology of glycan-binding proteins, which in turn complicates the biomedical use of this class of biomolecules. Herein, we describe an enzymatic strategy, using a limited number of human glycosyltransferases, to access a collection of 60 asymmetric, multiantennary human milk oligosaccharides (HMOs), which were used to develop a glycan microarray. Probing the array with several glycan-binding proteins uncovered that not only terminal glycoepitopes but also complex architectures of glycans can influence binding selectivity in unanticipated manners. N- and O-linked glycans express structural elements of HMOs, and thus, the reported synthetic principles will find broad applicability.
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16
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Abstract
Simple and complex carbohydrates (glycans) have long been known to play major metabolic, structural and physical roles in biological systems. Targeted microbial binding to host glycans has also been studied for decades. But such biological roles can only explain some of the remarkable complexity and organismal diversity of glycans in nature. Reviewing the subject about two decades ago, one could find very few clear-cut instances of glycan-recognition-specific biological roles of glycans that were of intrinsic value to the organism expressing them. In striking contrast there is now a profusion of examples, such that this updated review cannot be comprehensive. Instead, a historical overview is presented, broad principles outlined and a few examples cited, representing diverse types of roles, mediated by various glycan classes, in different evolutionary lineages. What remains unchanged is the fact that while all theories regarding biological roles of glycans are supported by compelling evidence, exceptions to each can be found. In retrospect, this is not surprising. Complex and diverse glycans appear to be ubiquitous to all cells in nature, and essential to all life forms. Thus, >3 billion years of evolution consistently generated organisms that use these molecules for many key biological roles, even while sometimes coopting them for minor functions. In this respect, glycans are no different from other major macromolecular building blocks of life (nucleic acids, proteins and lipids), simply more rapidly evolving and complex. It is time for the diverse functional roles of glycans to be fully incorporated into the mainstream of biological sciences.
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Affiliation(s)
- Ajit Varki
- Departments of Medicine and Cellular & Molecular Medicine, Glycobiology Research and Training Center, University of California at San Diego, La Jolla, CA 92093-0687, USA
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17
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Reatini BS, Ensink E, Liau B, Sinha JY, Powers TW, Partyka K, Bern M, Brand RE, Rudd PM, Kletter D, Drake R, Haab BB. Characterizing Protein Glycosylation through On-Chip Glycan Modification and Probing. Anal Chem 2016; 88:11584-11592. [PMID: 27809484 PMCID: PMC5290727 DOI: 10.1021/acs.analchem.6b02998] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Glycans are critical to protein biology and are useful as disease biomarkers. Many studies of glycans rely on clinical specimens, but the low amount of sample available for some specimens limits the experimental options. Here we present a method to obtain information about protein glycosylation using a minimal amount of protein. We treat proteins that were captured or directly spotted in small microarrays (2.2 mm × 2.2 mm) with exoglycosidases to successively expose underlying features, and then we probe the native or exposed features using a panel of lectins or glycan-binding reagents. We developed an algorithm to interpret the data and provide predictions about the glycan motifs that are present in the sample. We demonstrated the efficacy of the method to characterize differences between glycoproteins in their sialic acid linkages and N-linked glycan branching, and we validated the assignments by comparing results from mass spectrometry and chromatography. The amount of protein used on-chip was about 11 ng. The method also proved effective for analyzing the glycosylation of a cancer biomarker in human plasma, MUC5AC, using only 20 μL of the plasma. A glycan on MUC5AC that is associated with cancer had mostly 2,3-linked sialic acid, whereas other glycans on MUC5AC had a 2,6 linkage of sialic acid. The on-chip glycan modification and probing (on-chip GMAP) method provides a platform for analyzing protein glycosylation in clinical specimens and could complement the existing toolkit for studying glycosylation in disease.
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Affiliation(s)
| | - Elliot Ensink
- Van Andel Research Institute, Grand Rapids, Michigan
| | - Brian Liau
- Bioprocessing Technology Institute, Singapore
| | | | - Thomas W. Powers
- Medical University of South Carolina, Charleston, South Carolina
| | - Katie Partyka
- Van Andel Research Institute, Grand Rapids, Michigan
| | | | - Randall E. Brand
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Pauline M. Rudd
- Bioprocessing Technology Institute, Singapore
- National Institute for Bioprocessing Research and Training, Dublin, Ireland
| | | | | | - Brian B. Haab
- Van Andel Research Institute, Grand Rapids, Michigan
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18
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Grant OC, Tessier MB, Meche L, Mahal LK, Foley BL, Woods RJ. Combining 3D structure with glycan array data provides insight into the origin of glycan specificity. Glycobiology 2016; 26:772-783. [PMID: 26911287 PMCID: PMC4976521 DOI: 10.1093/glycob/cww020] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 02/17/2016] [Accepted: 02/17/2016] [Indexed: 12/30/2022] Open
Abstract
Defining how a glycan-binding protein (GBP) specifically selects its cognate glycan from among the ensemble of glycans within the cellular glycome is an area of intense study. Powerful insight into recognition mechanisms can be gained from 3D structures of GBPs complexed to glycans; however, such structures remain difficult to obtain experimentally. Here an automated 3D structure generation technique, called computational carbohydrate grafting, is combined with the wealth of specificity information available from glycan array screening. Integration of the array data with modeling and crystallography allows generation of putative co-complex structures that can be objectively assessed and iteratively altered until a high level of agreement with experiment is achieved. Given an accurate model of the co-complexes, grafting is also able to discern which binding determinants are active when multiple potential determinants are present within a glycan. In some cases, induced fit in the protein or glycan was necessary to explain the observed specificity, while in other examples a revised definition of the minimal binding determinants was required. When applied to a collection of 10 GBP-glycan complexes, for which crystallographic and array data have been reported, grafting provided a structural rationalization for the binding specificity of >90% of 1223 arrayed glycans. A webtool that enables researchers to perform computational carbohydrate grafting is available at www.glycam.org/gr (accessed 03 March 2016).
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Affiliation(s)
- Oliver C Grant
- Complex Carbohydrate Research Center and Department of Biochemistry, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Matthew B Tessier
- Complex Carbohydrate Research Center and Department of Biochemistry, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Lawrence Meche
- New York University Department of Chemistry, Biomedical Chemistry Institute, 100 Washington Square East, Room 1001, New York, NY 10003, USA
| | - Lara K Mahal
- New York University Department of Chemistry, Biomedical Chemistry Institute, 100 Washington Square East, Room 1001, New York, NY 10003, USA
| | - Bethany L Foley
- New York University Department of Chemistry, Biomedical Chemistry Institute, 100 Washington Square East, Room 1001, New York, NY 10003, USA
| | - Robert J Woods
- Complex Carbohydrate Research Center and Department of Biochemistry, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
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19
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Structural basis for sulfation-dependent self-glycan recognition by the human immune-inhibitory receptor Siglec-8. Proc Natl Acad Sci U S A 2016; 113:E4170-9. [PMID: 27357658 DOI: 10.1073/pnas.1602214113] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Siglec-8 is a human immune-inhibitory receptor that, when engaged by specific self-glycans, triggers eosinophil apoptosis and inhibits mast cell degranulation, providing an endogenous mechanism to down-regulate immune responses of these central inflammatory effector cells. Here we used solution NMR spectroscopy to dissect the fine specificity of Siglec-8 toward different sialylated and sulfated carbohydrate ligands and determined the structure of the Siglec-8 lectin domain in complex with its prime glycan target 6'-sulfo sialyl Lewis(x) A canonical motif for sialic acid recognition, extended by a secondary motif formed by unique loop regions, recognizing 6-O-sulfated galactose dictates tight specificity distinct from other Siglec family members and any other endogenous glycan recognition receptors. Structure-guided mutagenesis revealed key contacts of both interfaces to be equally essential for binding. Our work provides critical structural and mechanistic insights into how Siglec-8 selectively recognizes its glycan target, rationalizes the functional impact of site-specific glycan sulfation in modulating this lectin-glycan interaction, and will enable the rational design of Siglec-8-targeted agonists to treat eosinophil- and mast cell-related allergic and inflammatory diseases, such as asthma.
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20
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Jiménez-Castells C, Stanton R, Yan S, Kosma P, Wilson IB. Development of a multifunctional aminoxy-based fluorescent linker for glycan immobilization and analysis. Glycobiology 2016; 26:1297-1307. [PMID: 27222531 DOI: 10.1093/glycob/cww051] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 04/20/2016] [Accepted: 04/20/2016] [Indexed: 12/17/2022] Open
Abstract
Glycan arrays have become a technique of choice to screen glycan-protein interactions in a high-throughput manner with high sensitivity and low sample consumption. Here, the synthesis of a new multifunctional fluorescent linker for glycan labeling via aminoxy ligation and immobilization is described; the linker features a fluorescent naphthalene group suitable for highly sensitive high-performance liquid chromatography-based purification and an azido- or amino-modified pentanoyl moiety for the immobilization onto solid supports. Several glycoconjugates displaying small sugar epitopes via chemical or chemoenzymatic synthesis were covalently attached onto a microarray support and tested with lectins of known carbohydrate binding specificity. The glycan library was extended using glycosyltransferases (e.g. galactosyl-, sialyl- and fucosyltransferases); the resulting neoglycoconjugates, which are easily detected by mass spectrometry, mimic antennal elements of N- and O-glycans, including ABH blood group epitopes and sialylated structures. Furthermore, an example natural plant N-glycan containing core α1,3-fucose and β1,2-xylose was also successfully conjugated to the fluorescent linker, immobilized and probed with lectins as well as antihorseradish peroxidase. These experiments validate our linker as being a potentially valuable tool to study glycozyme and lectin specificities, sensitive enough to allow purification of natural glycans.
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Affiliation(s)
| | - Rhiannon Stanton
- Department für Chemie, Universität für Bodenkultur, 1190 Wien, Austria
| | - Shi Yan
- Department für Chemie, Universität für Bodenkultur, 1190 Wien, Austria
| | - Paul Kosma
- Department für Chemie, Universität für Bodenkultur, 1190 Wien, Austria
| | - Iain Bh Wilson
- Department für Chemie, Universität für Bodenkultur, 1190 Wien, Austria
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21
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Nivedha AK, Thieker DF, Makeneni S, Hu H, Woods RJ. Vina-Carb: Improving Glycosidic Angles during Carbohydrate Docking. J Chem Theory Comput 2016; 12:892-901. [PMID: 26744922 DOI: 10.1021/acs.jctc.5b00834] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Molecular docking programs are primarily designed to align rigid, drug-like fragments into the binding sites of macromolecules and frequently display poor performance when applied to flexible carbohydrate molecules. A critical source of flexibility within an oligosaccharide is the glycosidic linkages. Recently, Carbohydrate Intrinsic (CHI) energy functions were reported that attempt to quantify the glycosidic torsion angle preferences. In the present work, the CHI-energy functions have been incorporated into the AutoDock Vina (ADV) scoring function, subsequently termed Vina-Carb (VC). Two user-adjustable parameters have been introduced, namely, a CHI- energy weight term (chi_coeff) that affects the magnitude of the CHI-energy penalty and a CHI-cutoff term (chi_cutoff) that negates CHI-energy penalties below a specified value. A data set consisting of 101 protein-carbohydrate complexes and 29 apoprotein structures was used in the development and testing of VC, including antibodies, lectins, and carbohydrate binding modules. Accounting for the intramolecular energies of the glycosidic linkages in the oligosaccharides during docking led VC to produce acceptable structures within the top five ranked poses in 74% of the systems tested, compared to a success rate of 55% for ADV. An enzyme system was employed in order to illustrate the potential application of VC to proteins that may distort glycosidic linkages of carbohydrate ligands upon binding. VC represents a significant step toward accurately predicting the structures of protein-carbohydrate complexes. Furthermore, the described approach is conceptually applicable to any class of ligands that populate well-defined conformational states.
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Affiliation(s)
- Anita K Nivedha
- Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States
| | - David F Thieker
- Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States
| | - Spandana Makeneni
- Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States
| | - Huimin Hu
- Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States
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22
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Sleiman MH, Csonka R, Arbez-Gindre C, Heropoulos GA, Calogeropoulou T, Signorelli M, Schiraldi A, Steele BR, Fessas D, Micha-Screttas M. Binding and stabilisation effects of glycodendritic compounds with peanut agglutinin. Int J Biol Macromol 2015. [DOI: 10.1016/j.ijbiomac.2015.07.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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23
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Abstract
C-type lectin-like receptor 2 (CLEC-2) is a member of the C-type lectin (like) receptor (CLR) family that uses a Ca(2+) binding domain to bind specific glycans. However, in this issue of Structure, Nagae and colleagues report on how the structures of CLEC-2 in complex with a glycopeptide podoplanin and a snake venom protein, rhodocytin, show a different mode of binding.
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Affiliation(s)
- Hideo Fukuhara
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Atsushi Furukawa
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Katsumi Maenaka
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan; Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan; CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan.
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24
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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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25
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Grant OC, Woods RJ. Recent advances in employing molecular modelling to determine the specificity of glycan-binding proteins. Curr Opin Struct Biol 2014; 28:47-55. [PMID: 25108191 DOI: 10.1016/j.sbi.2014.07.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 07/09/2014] [Accepted: 07/10/2014] [Indexed: 01/11/2023]
Abstract
Impressive improvements in docking performance can be achieved by applying energy bonuses to poses in which glycan hydroxyl groups occupy positions otherwise preferred by bound waters. In addition, inclusion of glycosidic conformational energies allows unlikely glycan conformations to be appropriately penalized. A method for predicting the binding specificity of glycan-binding proteins has been developed, which is based on grafting glycan branches onto a minimal binding determinant in the binding site. Grafting can be used either to screen virtual libraries of glycans, such as the known glycome, or to identify docked poses of minimal binding determinants that are consistent with specificity data. The reviewed advances allow accurate modelling of carbohydrate-protein 3D co-complexes, but challenges remain in ranking the affinity of congeners.
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Affiliation(s)
- Oliver C Grant
- Complex Carbohydrate Research Center, 315 Riverbend Road, University of Georgia, Athens, GA 30602, United States
| | - Robert J Woods
- Complex Carbohydrate Research Center, 315 Riverbend Road, University of Georgia, Athens, GA 30602, United States; School of Chemistry, University Road, National University of Ireland, Galway, Ireland.
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26
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Silva E, Kadirvel G, Jiang R, Bovin N, Miller D. Multiple proteins from ejaculated and epididymal porcine spermatozoa bind glycan motifs found in the oviduct. Andrology 2014; 2:763-71. [DOI: 10.1111/j.2047-2927.2014.00249.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 06/03/2014] [Accepted: 06/20/2014] [Indexed: 02/03/2023]
Affiliation(s)
- E. Silva
- Department of Animal Sciences; University of Illinois; Urbana IL USA
| | - G. Kadirvel
- Department of Animal Sciences; University of Illinois; Urbana IL USA
| | - R. Jiang
- College of Life Sciences; Zhejiang University; Hangzhou China
| | - N. Bovin
- Shemyakin Institute of Bioorganic Chemistry RAS; Moscow Russia
| | - D. Miller
- Department of Animal Sciences; University of Illinois; Urbana IL USA
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27
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Hotaling NA, Cummings RD, Ratner DM, Babensee JE. Molecular factors in dendritic cell responses to adsorbed glycoconjugates. Biomaterials 2014; 35:5862-74. [PMID: 24746228 PMCID: PMC4127877 DOI: 10.1016/j.biomaterials.2014.03.048] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 03/18/2014] [Indexed: 11/23/2022]
Abstract
Carbohydrates and glycoconjugates have been shown to exert pro-inflammatory effects on the dendritic cells (DCs), supporting pathogen-induced innate immunity and antigen processing, as well as immunosuppressive effects in the tolerance to self-proteins. Additionally, the innate inflammatory response to implanted biomaterials has been hypothesized to be mediated by inflammatory cells interacting with adsorbed proteins, many of which are glycosylated. However, the molecular factors relevant for surface displayed glycoconjugate modulation of dendritic cell (DC) phenotype are unknown. Thus, in this study, a model system was developed to establish the role of glycan composition, density, and carrier cationization state on DC response. Thiol modified glycans were covalently bound to a model protein carrier, maleimide functionalized bovine serum albumin (BSA), and the number of glycans per BSA modulated. Additionally, the carrier isoelectric point was scaled from a pI of ∼4.0 to ∼10.0 using ethylenediamine (EDA). The DC response to the neoglycoconjugates adsorbed to wells of a 384-well plate was determined via a high throughput assay. The underlying trends in DC phenotype in relation to conjugate properties were elucidated via multivariate general linear models. It was found that glycoconjugates with more than 20 glycans per carrier had the greatest impact on the pro-inflammatory response from DCs, followed by conjugates having an isoelectric point above 9.5. Surfaces displaying terminal α1-2 linked mannose structures were able to increase the inflammatory DC response to a greater extent than did any other terminal glycan structure. The results herein can be applied to inform the design of the next generation of combination products and biomaterials for use in future vaccines and implanted materials.
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Affiliation(s)
- Nathan A Hotaling
- Wallace H. Coulter Dept. of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | | | - Daniel M Ratner
- Dept. of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Julia E Babensee
- Wallace H. Coulter Dept. of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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28
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Redemption of autoantibodies on anergic B cells by variable-region glycosylation and mutation away from self-reactivity. Proc Natl Acad Sci U S A 2014; 111:E2567-75. [PMID: 24821781 DOI: 10.1073/pnas.1406974111] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The best-understood mechanisms for achieving antibody self/non-self discrimination discard self-reactive antibodies before they can be tested for binding microbial antigens, potentially creating holes in the repertoire. Here we provide evidence for a complementary mechanism: retaining autoantibodies in the repertoire displayed as low levels of IgM and high IgD on anergic B cells, masking a varying proportion of autoantibody-binding sites with carbohydrates, and removing their self-reactivity by somatic hypermutation and selection in germinal centers (GCs). Analysis of human antibody sequences by deep sequencing of isotype-switched memory B cells or in IgG antibodies elicited against allogeneic RhD+ erythrocytes, vaccinia virus, rotavirus, or tetanus toxoid provides evidence for reactivation of anergic IgM(low) IgD+ IGHV4-34+ B cells and removal of cold agglutinin self-reactivity by hypermutation, often accompanied by mutations that inactivated an N-linked glycosylation sequon in complementarity-determining region 2 (CDR2). In a Hy10 antibody transgenic model where anergic B cells respond to a biophysically defined lysozyme epitope displayed on both foreign and self-antigens, cell transfers revealed that anergic IgM(low) IgD+ B cells form twice as many GC progeny as naïve IgM(hi) IgD+ counterparts. Their GC progeny were rapidly selected for CDR2 mutations that blocked 72% of antigen-binding sites with N-linked glycan, decreased affinity 100-fold, and then cleared the binding sites of blocking glycan. These results provide evidence for a mechanism to acquire self/non-self discrimination by somatic mutation away from self-reactivity, and reveal how varying the efficiency of N-glycosylation provides a mechanism to modulate antibody avidity.
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29
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Bini D, Russo L, Battocchio C, Natalello A, Polzonetti G, Doglia SM, Nicotra F, Cipolla L. Dendron Synthesis and Carbohydrate Immobilization on a Biomaterial Surface by a Double-Click Reaction. Org Lett 2014; 16:1298-301. [DOI: 10.1021/ol403476z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Davide Bini
- Department
of Biotechnology and Biosciences, University of Milan—Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Laura Russo
- Department
of Biotechnology and Biosciences, University of Milan—Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Chiara Battocchio
- Department
of Sciences, INSTM, CNISM and CISDiC, University Roma Tre, Via della Vasca
Navale 84, 00146 Rome, Italy
| | - Antonino Natalello
- Department
of Biotechnology and Biosciences, University of Milan—Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Giovanni Polzonetti
- Department
of Sciences, INSTM, CNISM and CISDiC, University Roma Tre, Via della Vasca
Navale 84, 00146 Rome, Italy
| | - Silvia Maria Doglia
- Department
of Biotechnology and Biosciences, University of Milan—Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Francesco Nicotra
- Department
of Biotechnology and Biosciences, University of Milan—Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Laura Cipolla
- Department
of Biotechnology and Biosciences, University of Milan—Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
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30
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Yaniv O, Fichman G, Borovok I, Shoham Y, Bayer EA, Lamed R, Shimon LJW, Frolow F. Fine-structural variance of family 3 carbohydrate-binding modules as extracellular biomass-sensing components of Clostridium thermocellum anti-σI factors. ACTA ACUST UNITED AC 2014; 70:522-34. [PMID: 24531486 DOI: 10.1107/s139900471302926x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 10/23/2013] [Indexed: 11/11/2022]
Abstract
The anaerobic, thermophilic, cellulosome-producing bacterium Clostridium thermocellum relies on a variety of carbohydrate-active enzymes in order to efficiently break down complex carbohydrates into utilizable simple sugars. The regulation mechanism of the cellulosomal genes was unknown until recently, when genomic analysis revealed a set of putative operons in C. thermocellum that encode σI factors (i.e. alternative σ factors that control specialized regulon activation) and their cognate anti-σI factor (RsgI). These putative anti-σI-factor proteins have modules that are believed to be carbohydrate sensors. Three of these modules were crystallized and their three-dimensional structures were solved. The structures show a high overall degree of sequence and structural similarity to the cellulosomal family 3 carbohydrate-binding modules (CBM3s). The structures of the three carbohydrate sensors (RsgI-CBM3s) and a reference CBM3 are compared in the context of the structural determinants for the specificity of cellulose and complex carbohydrate binding. Fine structural variations among the RsgI-CBM3s appear to result in alternative substrate preferences for each of the sensors.
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Affiliation(s)
- Oren Yaniv
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Galit Fichman
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Ilya Borovok
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Yuval Shoham
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Edward A Bayer
- Department of Biological Chemistry, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Linda J W Shimon
- Department of Chemical Research Support, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Felix Frolow
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 69978 Tel Aviv, Israel
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Donczo B, Kerekgyarto J, Szurmai Z, Guttman A. Glycan microarrays: new angles and new strategies. Analyst 2014; 139:2650-7. [DOI: 10.1039/c3an02289g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Cohen M, Varki A. Modulation of glycan recognition by clustered saccharide patches. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 308:75-125. [PMID: 24411170 DOI: 10.1016/b978-0-12-800097-7.00003-8] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
All cells in nature are covered with a dense and complex array of glycan chains. Specific recognition and binding of glycans is a critical aspect of cellular interactions, both within and between species. Glycan-protein interactions tend to be of low affinity but high specificity, typically utilizing multivalency to generate the affinity required for biologically relevant binding. This review focuses on a higher level of glycan organization, the formation of clustered saccharide patches (CSPs), which can constitute unique ligands for highly specific interactions. Due to technical challenges, this aspect of glycan recognition remains poorly understood. We present a wealth of evidence for CSPs-mediated interactions, and discuss recent advances in experimental tools that are beginning to provide new insights into the composition and organization of CSPs. The examples presented here are likely the tip of the iceberg, and much further work is needed to elucidate fully this higher level of glycan organization.
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Affiliation(s)
- Miriam Cohen
- Department Cellular and Molecular Medicine, Glycobiology Research and Training Center, University of California, San Diego, California, USA.
| | - Ajit Varki
- Department of Medicine, University of California, San Diego, California, USA; Department Cellular and Molecular Medicine, Glycobiology Research and Training Center, University of California, San Diego, California, USA.
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33
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Deng L, Chen X, Varki A. Exploration of sialic acid diversity and biology using sialoglycan microarrays. Biopolymers 2013; 99:650-65. [PMID: 23765393 PMCID: PMC7161822 DOI: 10.1002/bip.22314] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Accepted: 06/04/2013] [Indexed: 12/13/2022]
Abstract
Sialic acids (Sias) are a group of α-keto acids with a nine-carbon backbone, which display many types of modifications in nature. The diversity of natural Sia presentations is magnified by a variety of glycosidic linkages to underlying glycans, the sequences and classes of such glycans, as well as the spatial organization of Sias with their surroundings. This diversity is closely linked to the numerous and varied biological functions of Sias. Relatively large libraries of natural and unnatural Sias have recently been chemically/chemoenzymatically synthesized and/or isolated from natural sources. The resulting sialoglycan microarrays have proved to be valuable tools for the exploration of diversity and biology of Sias. Here we provide an overview of Sia diversity in nature, the approaches used to generate sialoglycan microarrays, and the achievements and challenges arising.
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Affiliation(s)
- Lingquan Deng
- Departments of Medicine and Cellular & Molecular MedicineGlycobiology Research and Training Center, University of CaliforniaSan Diego, La JollaCA92093‐0687
| | - Xi Chen
- Department of ChemistryUniversity of CaliforniaDavisCA95616
| | - Ajit Varki
- Departments of Medicine and Cellular & Molecular MedicineGlycobiology Research and Training Center, University of CaliforniaSan Diego, La JollaCA92093‐0687
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Jégouzo SAF, Quintero-Martínez A, Ouyang X, dos Santos Á, Taylor ME, Drickamer K. Organization of the extracellular portion of the macrophage galactose receptor: a trimeric cluster of simple binding sites for N-acetylgalactosamine. Glycobiology 2013; 23:853-64. [PMID: 23507965 PMCID: PMC3671775 DOI: 10.1093/glycob/cwt022] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The properties of the human macrophage galactose receptor have been investigated. Specificity for N-acetylgalactosamine (GalNAc) residues with exposed 3- and 4-hydroxyl groups explains virtually all of the results obtained from a recently expanded array of synthetic glycans and is consistent with a model for the structure of the binding site. This simple interaction is sufficient to explain the ability of the receptor to bind to tumor-cell glycans bearing Tn and sialyl-Tn antigens, but not to more elaborate O-linked glycans that predominate on normal cells. This specificity also allows for binding of parasite glycans and screening of an array of bacterial outer membrane oligosaccharides confirms that the receptor binds to a subset of these structures with appropriately exposed GalNAc residues. A key feature of the receptor is the clustering of binding sites in the extracellular portion of the protein, which retains the trimeric structure observed in the cell membrane. Chemical crosslinking, gel filtration, circular dichroism analysis and differential scanning calorimetry demonstrate that this trimeric structure of the receptor is stabilized by an α-helical coiled coil that extends from the surface of the membrane to the globular carbohydrate-recognition domains. The helical neck domains form independent trimerization domains. Taken together, these results indicate that the macrophage galactose receptor shares many of the features of serum mannose-binding protein, in which clusters of monosaccharide-binding sites serve as detectors for a simple epitope that is not common on endogenous cell surface glycans but that is abundant on the surfaces of tumor cells and certain pathogens.
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Affiliation(s)
- Sabine A F Jégouzo
- Department of Life Sciences, Imperial College, Sir Ernst Chain Building, London SW7 2AZ, UK
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35
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Tessier MB, Grant OC, Heimburg-Molinaro J, Smith D, Jadey S, Gulick AM, Glushka J, Deutscher SL, Rittenhouse-Olson K, Woods RJ. Computational screening of the human TF-glycome provides a structural definition for the specificity of anti-tumor antibody JAA-F11. PLoS One 2013; 8:e54874. [PMID: 23365681 PMCID: PMC3554700 DOI: 10.1371/journal.pone.0054874] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 12/17/2012] [Indexed: 11/19/2022] Open
Abstract
Recombinant antibodies are of profound clinical significance; yet, anti-carbohydrate antibodies are prone to undesirable cross-reactivity with structurally related-glycans. Here we introduce a new technology called Computational Carbohydrate Grafting (CCG), which enables a virtual library of glycans to be assessed for protein binding specificity, and employ it to define the scope and structural origin of the binding specificity of antibody JAA-F11 for glycans containing the Thomsen-Friedenreich (TF) human tumor antigen. A virtual library of the entire human glycome (GLibrary-3D) was constructed, from which 1,182 TF-containing human glycans were identified and assessed for their ability to fit into the antibody combining site. The glycans were categorized into putative binders, or non-binders, on the basis of steric clashes with the antibody surface. The analysis employed a structure of the immune complex, generated by docking the TF-disaccharide (Galβ1-3GalNAcα) into a crystal structure of the JAA-F11 antigen binding fragment, which was shown to be consistent with saturation transfer difference (STD) NMR data. The specificities predicted by CCG were fully consistent with data from experimental glycan array screening, and confirmed that the antibody is selective for the TF-antigen and certain extended core-2 type mucins. Additionally, the CCG analysis identified a limited number of related putative binding motifs, and provided a structural basis for interpreting the specificity. CCG can be utilized to facilitate clinical applications through the determination of the three-dimensional interaction of glycans with proteins, thus augmenting drug and vaccine development techniques that seek to optimize the specificity and affinity of neutralizing proteins, which target glycans associated with diseases including cancer and HIV.
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Affiliation(s)
- Matthew B. Tessier
- Complex Carbohydrate Research Center and Department of Chemistry, University of Georgia, Athens, Georgia, United States of America
| | - Oliver C. Grant
- School of Chemistry, National University of Ireland, Galway, University Road, Galway, Ireland
| | - Jamie Heimburg-Molinaro
- Department of Biotechnical and Clinical Laboratory Sciences, State University of New York, Buffalo, New York, United States of America
| | - David Smith
- Department of Biochemistry, Emory University, Atlanta, Georgia, United States of America
| | - Snehal Jadey
- Department of Biotechnical and Clinical Laboratory Sciences, State University of New York, Buffalo, New York, United States of America
| | - Andrew M. Gulick
- Hauptman-Woodward Institute, Department of Structural Biology, State University of New York, Buffalo, New York, United States of America
| | - John Glushka
- Complex Carbohydrate Research Center and Department of Chemistry, University of Georgia, Athens, Georgia, United States of America
| | - Susan L. Deutscher
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
| | - Kate Rittenhouse-Olson
- Department of Biotechnical and Clinical Laboratory Sciences, State University of New York, Buffalo, New York, United States of America
- * E-mail: (KRO); (RJW)
| | - Robert J. Woods
- Complex Carbohydrate Research Center and Department of Chemistry, University of Georgia, Athens, Georgia, United States of America
- School of Chemistry, National University of Ireland, Galway, University Road, Galway, Ireland
- * E-mail: (KRO); (RJW)
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36
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Ligand and pathogen specificity of the Atlantic salmon serum C-type lectin. Biochim Biophys Acta Gen Subj 2013; 1830:2129-38. [DOI: 10.1016/j.bbagen.2012.09.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Revised: 09/11/2012] [Accepted: 09/21/2012] [Indexed: 11/20/2022]
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Photocrosslinking approaches to interactome mapping. Curr Opin Chem Biol 2012; 17:90-101. [PMID: 23149092 DOI: 10.1016/j.cbpa.2012.10.034] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 10/22/2012] [Indexed: 11/21/2022]
Abstract
Photocrosslinking approaches can be used to map interactome networks within the context of living cells. Photocrosslinking methods rely on use of metabolic engineering or genetic code expansion to incorporate photocrosslinking analogs of amino acids or sugars into cellular biomolecules. Immunological and mass spectrometry techniques are used to analyze crosslinked complexes, thereby defining specific interactomes. Because photocrosslinking can be conducted in native, cellular settings, it can be used to define context-dependent interactions. Photocrosslinking methods are also ideally suited for determining interactome dynamics, mapping interaction interfaces, and identifying transient interactions in which intrinsically disordered proteins and glycoproteins engage. Here we discuss the application of cell-based photocrosslinking to the study of specific problems in immune cell signaling, transcription, membrane protein dynamics, nucleocytoplasmic transport, and chaperone-assisted protein folding.
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Gauto DF, Petruk AA, Modenutti CP, Blanco JI, Di Lella S, Martí MA. Solvent structure improves docking prediction in lectin-carbohydrate complexes. Glycobiology 2012; 23:241-58. [PMID: 23089616 DOI: 10.1093/glycob/cws147] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Recognition and complex formation between proteins and carbohydrates is a key issue in many important biological processes. Determination of the three-dimensional structure of such complexes is thus most relevant, but particularly challenging because of their usually low binding affinity. In silico docking methods have a long-standing tradition in predicting protein-ligand complexes, and allow a potentially fast exploration of a number of possible protein-carbohydrate complex structures. However, determining which of these predicted complexes represents the correct structure is not always straightforward. In this work, we present a modification of the scoring function provided by AutoDock4, a widely used docking software, on the basis of analysis of the solvent structure adjacent to the protein surface, as derived from molecular dynamics simulations, that allows the definition and characterization of regions with higher water occupancy than the bulk solvent, called water sites. They mimic the interaction held between the carbohydrate -OH groups and the protein. We used this information for an improved docking method in relation to its capacity to correctly predict the protein-carbohydrate complexes for a number of tested proteins, whose ligands range in size from mono- to tetrasaccharide. Our results show that the presented method significantly improves the docking predictions. The resulting solvent-structure-biased docking protocol, therefore, appears as a powerful tool for the design and optimization of development of glycomimetic drugs, while providing new insights into protein-carbohydrate interactions. Moreover, the achieved improvement also underscores the relevance of the solvent structure to the protein carbohydrate recognition process.
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Affiliation(s)
- Diego F Gauto
- Departamento de Química Inorgánica, Analítica y Química Física, CONICET, Ciudad Universitaria, Buenos Aires, Argentina
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Etxebarria J, Calvo J, Martin-Lomas M, Reichardt NC. Lectin-array blotting: profiling protein glycosylation in complex mixtures. ACS Chem Biol 2012; 7:1729-37. [PMID: 22871985 DOI: 10.1021/cb300262x] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
By combining electrophoretic protein separation with lectin-array-based glycan profiling into a single experiment, we have developed a high-throughput method for the rapid analysis of protein glycosylation in biofluids. Fluorescently tagged proteins are separated by SDS-PAGE and transferred by diffusion to a microscope slide covered with multiple copies of 20 different lectins, where they are trapped by specific carbohydrate protein interactions while retaining their relative locations on the gel. A fluorescence scan of the slide then provides an affinity profile with each of the 20 lectins containing a wealth of structural information regarding the present glycans. The affinity of the employed lectins toward N-glycans was verified on a glycan array of 76 structures. While current lectin-based methods for glycan analysis provide only a picture of the bulk glycosylation in complex protein mixtures or are focused on a few specific known biomarkers, our array-based glycoproteomics method can be used as a biomarker discovery tool for the qualitative exploration of protein glycosylation in an unbiased fashion.
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Affiliation(s)
- Juan Etxebarria
- Biofunctional Nanomaterials
Unit and ‡Mass Spectrometry Platform, CIC biomaGUNE, and §CIBER-BBN, Paseo Miramon
182, 20009 San Sebastian, Spain
| | - Javier Calvo
- Biofunctional Nanomaterials
Unit and ‡Mass Spectrometry Platform, CIC biomaGUNE, and §CIBER-BBN, Paseo Miramon
182, 20009 San Sebastian, Spain
| | - Manuel Martin-Lomas
- Biofunctional Nanomaterials
Unit and ‡Mass Spectrometry Platform, CIC biomaGUNE, and §CIBER-BBN, Paseo Miramon
182, 20009 San Sebastian, Spain
| | - Niels-Christian Reichardt
- Biofunctional Nanomaterials
Unit and ‡Mass Spectrometry Platform, CIC biomaGUNE, and §CIBER-BBN, Paseo Miramon
182, 20009 San Sebastian, Spain
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40
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Nairn AV, Aoki K, dela Rosa M, Porterfield M, Lim JM, Kulik M, Pierce JM, Wells L, Dalton S, Tiemeyer M, Moremen KW. Regulation of glycan structures in murine embryonic stem cells: combined transcript profiling of glycan-related genes and glycan structural analysis. J Biol Chem 2012; 287:37835-56. [PMID: 22988249 DOI: 10.1074/jbc.m112.405233] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The abundance and structural diversity of glycans on glycoproteins and glycolipids are highly regulated and play important roles during vertebrate development. Because of the challenges associated with studying glycan regulation in vertebrate embryos, we have chosen to study mouse embryonic stem (ES) cells as they differentiate into embryoid bodies (EBs) or into extraembryonic endodermal (ExE) cells as a model for cellular differentiation. We profiled N- and O-glycan structures isolated from these cell populations and examined transcripts encoding the corresponding enzymatic machinery for glycan biosynthesis in an effort to probe the mechanisms that drive the regulation of glycan diversity. During differentiation from mouse ES cells to either EBs or ExE cells, general trends were detected. The predominance of high mannose N-glycans in ES cells shifted to an equal abundance of complex and high mannose structures, increased sialylation, and increased α-Gal termination in the differentiated cell populations. Whereas core 1 O-glycan structures predominated in all three cell populations, increased sialylation and increased core diversity characterized the O-glycans of both differentiated cell types. Increased polysialylation was also found in both differentiated cell types. Differences between the two differentiated cell types included greater sialylation of N-glycans in EBs, whereas α-Gal-capped structures were more prevalent in ExE cells. Changes in glycan structures generally, but not uniformly, correlated with alterations in transcript abundance for the corresponding biosynthetic enzymes, suggesting that transcriptional regulation contributes significantly to the regulation of glycan expression. Knowledge of glycan structural diversity and transcript regulation should provide greater understanding of the roles of protein glycosylation in vertebrate development.
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Affiliation(s)
- Alison V Nairn
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, USA
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Chen WC, Kawasaki N, Nycholat CM, Han S, Pilotte J, Crocker PR, Paulson JC. Antigen delivery to macrophages using liposomal nanoparticles targeting sialoadhesin/CD169. PLoS One 2012; 7:e39039. [PMID: 22723922 PMCID: PMC3378521 DOI: 10.1371/journal.pone.0039039] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 05/15/2012] [Indexed: 01/15/2023] Open
Abstract
Sialoadhesin (Sn, Siglec-1, CD169) is a member of the sialic acid binding Ig-like lectin (siglec) family expressed on macrophages. Its macrophage specific expression makes it an attractive target for delivering antigens to tissue macrophages via Sn-mediated endocytosis. Here we describe a novel approach for delivering antigens to macrophages using liposomal nanoparticles displaying high affinity glycan ligands of Sn. The Sn-targeted liposomes selectively bind to and are internalized by Sn-expressing cells, and accumulate intracellularly over time. Our results show that ligand decorated liposomes are specific for Sn, since they are taken up by bone marrow derived macrophages that are derived from wild type but not Sn(-/-) mice. Importantly, the Sn-targeted liposomes dramatically enhance the delivery of antigens to macrophages for presentation to and proliferation of antigen-specific T cells. Together, these data provide insights into the potential of cell-specific targeting and delivery of antigens to intracellular organelles of macrophages using Sn-ligand decorated liposomal nanoparticles.
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Affiliation(s)
- Weihsu C. Chen
- Departments of Chemical Physiology and Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Norihito Kawasaki
- Departments of Chemical Physiology and Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Corwin M. Nycholat
- Departments of Chemical Physiology and Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Shoufa Han
- Departments of Chemical Physiology and Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Julie Pilotte
- Departments of Chemical Physiology and Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Paul R. Crocker
- Wellcome Trust Biocentre, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - James C. Paulson
- Departments of Chemical Physiology and Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail:
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Abstract
The C-type lectin dendritic cell-specific intercellular adhesion molecule 3-grabbing nonintegrin (DC-SIGN) can serve as a docking site for pathogens on the surface of dendritic cells. Pathogen binding to DC-SIGN can have diverse consequences for the host. DC-SIGN can facilitate HIV-1 dissemination, but the interaction of Mycobacterium tuberculosis with DC-SIGN is important for host immunity. The ability of pathogens to target DC-SIGN provides impetus to identify ligands that can perturb these interactions. Here, we describe the first stable small molecule inhibitors of DC-SIGN. These inhibitors were derived from a collection of quinoxalinones, which were assembled using a tandem cross metathesis-hydrogenation sequence. To assess the ability of these small molecules to block DC-SIGN-mediated glycan adhesion and internalization, we developed a sensitive flow cytometry assay. Our results reveal that the quinoxalinones are effective inhibitors of DC-SIGN-glycan interactions. These compounds block both glycan binding to cells and glycan internalization. We anticipate that these non-carbohydrate inhibitors can be used to elucidate the role of DC-SIGN in pathogenesis and immune function.
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Affiliation(s)
- Shane L. Mangold
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Lynne R. Prost
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Laura L. Kiessling
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
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Robinson LN, Artpradit C, Raman R, Shriver ZH, Ruchirawat M, Sasisekharan R. Harnessing glycomics technologies: integrating structure with function for glycan characterization. Electrophoresis 2012; 33:797-814. [PMID: 22522536 PMCID: PMC3743516 DOI: 10.1002/elps.201100231] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Glycans, or complex carbohydrates, are a ubiquitous class of biological molecule which impinge on a variety of physiological processes ranging from signal transduction to tissue development and microbial pathogenesis. In comparison to DNA and proteins, glycans present unique challenges to the study of their structure and function owing to their complex and heterogeneous structures and the dominant role played by multivalency in their sequence-specific biological interactions. Arising from these challenges, there is a need to integrate information from multiple complementary methods to decode structure-function relationships. Focusing on acidic glycans, we describe here key glycomics technologies for characterizing their structural attributes, including linkage, modifications, and topology, as well as for elucidating their role in biological processes. Two cases studies, one involving sialylated branched glycans and the other sulfated glycosaminoglycans, are used to highlight how integration of orthogonal information from diverse datasets enables rapid convergence of glycan characterization for development of robust structure-function relationships.
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Affiliation(s)
- Luke N. Robinson
- Department of Biological Engineering, Harvard-MIT Division of Health Sciences & Technology and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA
| | - Charlermchai Artpradit
- Program in Applied Biological Sciences: Environmental Health, Chulabhorn Graduate Institute, Bangkok, Thailand
| | - Rahul Raman
- Department of Biological Engineering, Harvard-MIT Division of Health Sciences & Technology and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA
| | - Zachary H. Shriver
- Department of Biological Engineering, Harvard-MIT Division of Health Sciences & Technology and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA
| | - Mathuros Ruchirawat
- Program in Applied Biological Sciences: Environmental Health, Chulabhorn Graduate Institute, Bangkok, Thailand
- Laboratory of Environmental Toxicology, Chulabhorn Research Institute, Bangkok, Thailand
| | - Ram Sasisekharan
- Department of Biological Engineering, Harvard-MIT Division of Health Sciences & Technology and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA
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Safina G. Application of surface plasmon resonance for the detection of carbohydrates, glycoconjugates, and measurement of the carbohydrate-specific interactions: A comparison with conventional analytical techniques. A critical review. Anal Chim Acta 2012; 712:9-29. [DOI: 10.1016/j.aca.2011.11.016] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 10/07/2011] [Accepted: 11/04/2011] [Indexed: 12/16/2022]
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45
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Koh G, Low A, Poh D, Yao Y, Ng SK, Wong VVT, Vagenende V, Lam KP, Lee DY. Integrative analysis workflow for the structural and functional classification of C-type lectins. BMC Bioinformatics 2011; 12 Suppl 14:S5. [PMID: 22372988 PMCID: PMC3287470 DOI: 10.1186/1471-2105-12-s14-s5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background It is important to understand the roles of C-type lectins in the immune system due to their ubiquity and diverse range of functions in animal cells. It has been observed that currently confirmed C-type lectins share a highly conserved domain known as the C-type carbohydrate recognition domain (CRD). Using the sequence profile of the CRD, an increasing number of putative C-type lectins have been identified. Hence, it is highly needed to develop a systematic framework that enables us to elucidate their carbohydrate (glycan) recognition function, and discover their physiological and pathological roles. Results Presented herein is an integrated workflow for characterizing the sequence and structural features of novel C-type lectins. Our workflow utilizes web-based queries and available software suites to annotate features that can be found on the C-type lectin, given its amino acid sequence. At the same time, it incorporates modeling and analysis of glycans - a major class of ligands that interact with C-type lectins. Thereafter, the results are analyzed together with context-specific knowledge to filter off unlikely predictions. This allows researchers to design their subsequent experiments to confirm the functions of the C-type lectins in a systematic manner. Conclusions The efficacy and usefulness of our proposed immunoinformatics workflow was demonstrated by applying our integrated workflow to a novel C-type lectin -CLEC17A - and we report some of its possible functions that warrants further validation through wet-lab experiments.
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Affiliation(s)
- Geoffrey Koh
- Bioprocessing Technology Institute, Agency for Science, Technology and Research, 20 Biopolis Way, #06-01, Centros, 138668, Singapore
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Xuan P, Zhang Y, Tzeng TRJ, Wan XF, Luo F. A quantitative structure-activity relationship (QSAR) study on glycan array data to determine the specificities of glycan-binding proteins. Glycobiology 2011; 22:552-60. [PMID: 22156918 DOI: 10.1093/glycob/cwr163] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Advances in glycan array technology have provided opportunities to automatically and systematically characterize the binding specificities of glycan-binding proteins. However, there is still a lack of robust methods for such analyses. In this study, we developed a novel quantitative structure-activity relationship (QSAR) method to analyze glycan array data. We first decomposed glycan chains into mono-, di-, tri- or tetrasaccharide subtrees. The bond information was incorporated into subtrees to help distinguish glycan chain structures. Then, we performed partial least-squares (PLS) regression on glycan array data using the subtrees as features. The application of QSAR to the glycan array data of different glycan-binding proteins demonstrated that PLS regression using subtree features can obtain higher R(2) values and a higher percentage of variance explained in glycan array intensities. Based on the regression coefficients of PLS, we were able to effectively identify subtrees that indicate the binding specificities of a glycan-binding protein. Our approach will facilitate the glycan-binding specificity analysis using the glycan array. A user-friendly web tool of the QSAR method is available at http://bci.clemson.edu/tools/glycan_array.
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Affiliation(s)
- Pengfei Xuan
- School of Computing, Clemson University, Clemson, SC 29634, USA
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Lakhtin V, Lakhtin M, Alyoshkin V. Lectins of living organisms. The overview. Anaerobe 2011; 17:452-5. [DOI: 10.1016/j.anaerobe.2011.06.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Accepted: 06/09/2011] [Indexed: 10/18/2022]
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Abstract
In the last decade, glycan microarrays have revolutionized the analysis of the specificity of glycan-binding proteins (GBPs), providing information that simultaneously illuminates the biology mediated by them and decodes the informational content of the glycome. Numerous methods have emerged for arraying glycans in a "chip" format, and glycan libraries have been assembled that address the diversity of the human glycome. Such arrays have been successfully used for analysis of GBPs, which mediate mammalian biology, host-pathogen interactions, and immune recognition of glycans relevant to vaccine production and cancer antigens. This review covers the development of glycan microarrays and applications that have provided insights into the roles of mammalian and microbial GBPs.
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Affiliation(s)
- Cory D Rillahan
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA.
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Vandenborre G, Smagghe G, Van Damme EJM. Plant lectins as defense proteins against phytophagous insects. PHYTOCHEMISTRY 2011; 72:1538-50. [PMID: 21429537 DOI: 10.1016/j.phytochem.2011.02.024] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Revised: 02/21/2011] [Accepted: 02/22/2011] [Indexed: 05/19/2023]
Abstract
One of the most important direct defense responses in plants against the attack by phytophagous insects is the production of insecticidal peptides or proteins. One particular class of entomotoxic proteins present in many plant species is the group of carbohydrate-binding proteins or lectins. During the last decade a lot of progress was made in the study of a few lectins that are expressed in response to herbivory by phytophagous insects and the insecticidal properties of plant lectins in general. This review gives an overview of lectins with high potential for the use in pest control strategies based on their activity towards pest insects. In addition, potential target sites for lectins inside the insect and the mode of action are discussed. In addition, the effect of plant lectins on non-target organisms such as beneficial insects as well as on human/animal consumers is discussed. It can be concluded that some insecticidal lectins are useful tools that can contribute to the development of integrated pest management strategies with minimal effect(s) on non-target organisms.
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Affiliation(s)
- Gianni Vandenborre
- Laboratory of Biochemistry and Glycobiology, Department of Molecular Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
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Joshi MD, Unger WW, van Beelen AJ, Bruijns SC, Litjens M, van Bloois L, Kalay H, van Kooyk Y, Storm G. DC-SIGN mediated antigen-targeting using glycan-modified liposomes: Formulation considerations. Int J Pharm 2011; 416:426-32. [DOI: 10.1016/j.ijpharm.2011.02.055] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Revised: 02/19/2011] [Accepted: 02/21/2011] [Indexed: 10/18/2022]
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