201
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Huang ML, Fisher CJ, Godula K. Glycomaterials for probing host-pathogen interactions and the immune response. Exp Biol Med (Maywood) 2016; 241:1042-53. [PMID: 27190259 DOI: 10.1177/1535370216647811] [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] [Indexed: 01/21/2023] Open
Abstract
The initial engagement of host cells by pathogens is often mediated by glycan structures presented on the cell surface. Various components of the glycocalyx can be targeted by pathogens for adhesion to facilitate infection. Glycans also play integral roles in the modulation of the host immune response to infection. Therefore, understanding the parameters that define glycan interactions with both pathogens and the various components of the host immune system can aid in the development of strategies to prevent, interrupt, or manage infection. Glycomaterials provide a unique and powerful tool with which to interrogate the compositional and functional complexity of the glycocalyx. The objective of this review is to highlight some key contributions from this area of research in deciphering the mechanisms of pathogenesis and the associated host response.
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Affiliation(s)
- Mia L Huang
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA 92093, USA
| | - Christopher J Fisher
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA 92093, USA
| | - Kamil Godula
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA 92093, USA
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202
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Accogli G, Desantis S, Martino NA, Dell'Aquila ME, Gemeiner P, Katrlík J. A lectin-based cell microarray approach to analyze the mammalian granulosa cell surface glycosylation profile. Glycoconj J 2016; 33:717-24. [PMID: 27085877 DOI: 10.1007/s10719-016-9666-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 03/07/2016] [Accepted: 04/01/2016] [Indexed: 10/21/2022]
Abstract
The high complexity of glycome, the repertoire of glycans expressed in a cell or in an organism, is difficult to analyze and the use of new technologies has accelerated the progress of glycomics analysis. In the last decade, the microarray approaches, and in particular glycan and lectin microarrays, have provided new insights into evaluation of cell glycosylation status. Here we present a cell microarray method based on cell printing on microarray slides for the analysis of the glycosylation pattern of the cell glycocalyx. In order to demonstrate the reliability of the developed method, the glycome profiles of equine native uncultured mural granulosa cells (uGCs) and in vitro cultured mural granulosa cells (cGCs) were determined and compared. The method consists in the isolation of GCs, cell printing into arrays on microarray slide, incubation with a panel of biotinylated lectins, reaction with fluorescent streptavidin and signal intensity detection by a microarray scanner. Cell microarray technology revealed that glycocalyx of both uGCs and cGCs contains N-glycans, sialic acid terminating glycans, N-acetylglucosamine and O-glycans. The comparison of uGCs and cGCs glycan signals indicated an increase in the expression of sialic acids, N-acetylglucosamine, and N-glycans in cGCs. Glycan profiles determined by cell microarray agreed with those revealed by lectin histochemistry. The described cell microarray method represents a simple and sensitive procedure to analyze cell surface glycome in mammalian cells.
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Affiliation(s)
- Gianluca Accogli
- Department of Emergency and Organ Transplantation (DETO), Veterinary Clinics and Animal Productions Unit, University of Bari Aldo Moro, SP Casamassima, km 3, 70010, Valenzano, Bari, Italy
| | - Salvatore Desantis
- Department of Emergency and Organ Transplantation (DETO), Veterinary Clinics and Animal Productions Unit, University of Bari Aldo Moro, SP Casamassima, km 3, 70010, Valenzano, Bari, Italy
| | - Nicola Antonio Martino
- Department of Biosciences, Biotechnologies and Biopharmaceutics (DBBB), University of Bari Aldo Moro, SP Casamassima, km 3, 70010, Valenzano, Bari, Italy.,Experimental Zooprophylactic Institute of Puglia and Basilicata, Via Manfredonia 20, 71121, Foggia, Italy
| | - Maria Elena Dell'Aquila
- Department of Biosciences, Biotechnologies and Biopharmaceutics (DBBB), University of Bari Aldo Moro, SP Casamassima, km 3, 70010, Valenzano, Bari, Italy
| | - Peter Gemeiner
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, SK-84538, Bratislava, Slovakia
| | - Jaroslav Katrlík
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, SK-84538, Bratislava, Slovakia.
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203
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Zhang H, Palma AS, Zhang Y, Childs RA, Liu Y, Mitchell DA, Guidolin LS, Weigel W, Mulloy B, Ciocchini AE, Feizi T, Chai W. Generation and characterization of β1,2-gluco-oligosaccharide probes from Brucella abortus cyclic β-glucan and their recognition by C-type lectins of the immune system. Glycobiology 2016; 26:1086-1096. [PMID: 27053576 PMCID: PMC5072146 DOI: 10.1093/glycob/cww041] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 03/17/2016] [Accepted: 03/24/2016] [Indexed: 12/16/2022] Open
Abstract
The β1,2-glucans produced by bacteria are important in invasion, survival and immunomodulation in infected hosts be they mammals or plants. However, there has been a lack of information on proteins which recognize these molecules. This is partly due to the extremely limited availability of the sequence-defined oligosaccharides and derived probes for use in the study of their interactions. Here we have used the cyclic β1,2-glucan (CβG) of the bacterial pathogen Brucella abortus, after removal of succinyl side chains, to prepare linearized oligosaccharides which were used to generate microarrays. We describe optimized conditions for partial depolymerization of the cyclic glucan by acid hydrolysis and conversion of the β1,2-gluco-oligosaccharides, with degrees of polymerization 2-13, to neoglycolipids for the purpose of generating microarrays. By microarray analyses, we show that the C-type lectin receptor DC-SIGNR, like the closely related DC-SIGN we investigated earlier, binds to the β1,2-gluco-oligosaccharides, as does the soluble immune effector serum mannose-binding protein. Exploratory studies with DC-SIGN are suggestive of the recognition also of the intact CβG by this receptor. These findings open the way to unravelling mechanisms of immunomodulation mediated by β1,2-glucans in mammalian systems.
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Affiliation(s)
- Hongtao Zhang
- Glycosciences Laboratory, Department of Medicine, Imperial College London, London W12 0NN, UK.,Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Angelina S Palma
- Glycosciences Laboratory, Department of Medicine, Imperial College London, London W12 0NN, UK .,UCIBIO-REQUIMTE, Department of Chemistry, Faculty of Science and Technology, NOVA Universidade de Lisboa, Caparica 2829-516, Portugal
| | - Yibing Zhang
- Glycosciences Laboratory, Department of Medicine, Imperial College London, London W12 0NN, UK
| | - Robert A Childs
- Glycosciences Laboratory, Department of Medicine, Imperial College London, London W12 0NN, UK
| | - Yan Liu
- Glycosciences Laboratory, Department of Medicine, Imperial College London, London W12 0NN, UK
| | - Daniel A Mitchell
- CSRI-UHCW, Walsgrave Campus, University of Warwick, Coventry CV2 2DX, UK
| | - Leticia S Guidolin
- Instituto de Investigaciones Biotecnológicas "Dr. Rodolfo A. Ugalde", Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín, San Martín, Buenos Aires 1650, Argentina
| | | | - Barbara Mulloy
- Glycosciences Laboratory, Department of Medicine, Imperial College London, London W12 0NN, UK
| | - Andrés E Ciocchini
- Instituto de Investigaciones Biotecnológicas "Dr. Rodolfo A. Ugalde", Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín, San Martín, Buenos Aires 1650, Argentina
| | - Ten Feizi
- Glycosciences Laboratory, Department of Medicine, Imperial College London, London W12 0NN, UK
| | - Wengang Chai
- Glycosciences Laboratory, Department of Medicine, Imperial College London, London W12 0NN, UK
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204
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Schnaar RL. Glycobiology simplified: diverse roles of glycan recognition in inflammation. J Leukoc Biol 2016; 99:825-38. [PMID: 27004978 DOI: 10.1189/jlb.3ri0116-021r] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 02/18/2016] [Indexed: 12/30/2022] Open
Abstract
Glycans and complementary glycan-binding proteins are essential components in the language of cell-cell interactions in immunity. The study of glycan function is the purview of glycobiology, which has often been presented as an unusually complex discipline. In fact, the human glycome, composed of all of its glycans, is built primarily from only 9 building blocks that are combined by enzymes (writers) with specific and limited biosynthetic capabilities into a tractable and increasingly accessible number of potential glycan patterns that are functionally read by several dozen human glycan-binding proteins (readers). Nowhere is the importance of glycan recognition better understood than in infection and immunity, and knowledge in this area has already led to glycan mimetic anti-infective and anti-inflammatory drugs. This review includes a brief tutorial on human glycobiology and a limited number of specific examples of glycan-binding protein-glycan interactions that initiate and regulate inflammation. Examples include representatives from different glycan-binding protein families, including the C-type lectins (E-selectin, P-selectin, dectin-1, and dectin-2), sialic acid-binding immunoglobulin-like lectins (sialic acid-binding immunoglobulin-like lectins 8 and 9), galectins (galectin-1, galectin-3, and galectin-9), as well as hyaluronic acid-binding proteins. As glycoscience technologies advance, opportunities for enhanced understanding of glycans and their roles in leukocyte cell biology provide increasing opportunities for discovery and therapeutic intervention.
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Affiliation(s)
- Ronald L Schnaar
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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205
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Shivatare SS, Chang SH, Tsai TI, Tseng SY, Shivatare VS, Lin YS, Cheng YY, Ren CT, Lee CCD, Pawar S, Tsai CS, Shih HW, Zeng YF, Liang CH, Kwong PD, Burton DR, Wu CY, Wong CH. Modular synthesis of N-glycans and arrays for the hetero-ligand binding analysis of HIV antibodies. Nat Chem 2016; 8:338-46. [PMID: 27001729 DOI: 10.1038/nchem.2463] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 01/20/2016] [Indexed: 01/22/2023]
Abstract
A new class of broadly neutralizing antibodies (bNAbs) from HIV donors has been reported to target the glycans on gp120--a glycoprotein found on the surface of the virus envelope--thus renewing hope of developing carbohydrate-based HIV vaccines. However, the version of gp120 used in previous studies was not from human T cells and so the glycosylation pattern could be somewhat different to that found in the native system. Moreover, some antibodies recognized two different glycans simultaneously and this cannot be detected with the commonly used glycan microarrays on glass slides. Here, we have developed a glycan microarray on an aluminium-oxide-coated glass slide containing a diverse set of glycans, including homo- and mixed N-glycans (high-mannose, hybrid and complex types) that were prepared by modular chemo-enzymatic methods to detect the presence of hetero-glycan binding behaviours. This new approach allows rapid screening and identification of optimal glycans recognized by neutralizing antibodies, and could speed up the development of HIV-1 vaccines targeting cell surface glycans.
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Affiliation(s)
- Sachin S Shivatare
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan.,Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, 1 Roosevelt Road, Section 4, Taipei, 106, Taiwan.,CHO Pharma Inc., Park Street, Nangang District, Taipei 11503, Taiwan
| | - Shih-Huang Chang
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, 1 Roosevelt Road, Section 4, Taipei, 106, Taiwan
| | - Tsung-I Tsai
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Susan Yu Tseng
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan
| | - Vidya S Shivatare
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan
| | - Yih-Shyan Lin
- CHO Pharma Inc., Park Street, Nangang District, Taipei 11503, Taiwan
| | - Yang-Yu Cheng
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan
| | - Chien-Tai Ren
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan
| | - Chang-Chun David Lee
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan
| | - Sujeet Pawar
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan.,Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taiwan
| | - Charng-Sheng Tsai
- CHO Pharma Inc., Park Street, Nangang District, Taipei 11503, Taiwan
| | - Hao-Wei Shih
- CHO Pharma Inc., Park Street, Nangang District, Taipei 11503, Taiwan
| | - Yi-Fang Zeng
- CHO Pharma Inc., Park Street, Nangang District, Taipei 11503, Taiwan
| | - Chi-Hui Liang
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan.,The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Dennis R Burton
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Chung-Yi Wu
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan
| | - Chi-Huey Wong
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan.,The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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206
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Gerlach JQ, Griffin MD. Getting to know the extracellular vesicle glycome. MOLECULAR BIOSYSTEMS 2016; 12:1071-81. [PMID: 26888195 DOI: 10.1039/c5mb00835b] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Extracellular vesicles (EVs) are a diverse population of complex biological particles with diameters ranging from approximately 20 to 1000 nm. Tremendous interest in EVs has been generated following a number of recent, high-profile reports describing their potential utility in diagnostic, prognostic, drug delivery, and therapeutic roles. Subpopulations, such as exosomes, are now known to directly participate in cell-cell communication and direct material transfer. Glycomics, the 'omic' portion of the glycobiology field, has only begun to catalog the surface oligosaccharide and polysaccharide structures and also the carbohydrate-binding proteins found on and inside EVs. The EV glycome undoubtedly contains vital clues essential to better understanding the function, biogenesis, release and transfer of vesicles, however getting at this information is technically challenging and made even more so because of the small physical size of the vesicles and the typically minute yield from physiological-scale biological samples. Vesicle micro-heterogeneity which may be related to specific vesicle origins and functions presents a further challenge. A number of primary studies carried out over the past decade have turned up specific and valuable clues regarding the composition and roles of glycan structures and also glycan binding proteins involved EV biogenesis and transfer. This review explores some of the major EV glycobiological research carried out to date and discusses the potential implications of these findings across the life sciences.
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Affiliation(s)
- Jared Q Gerlach
- Regenerative Medicine Institute (REMEDI) at CÚRAM Centre for Research in Medical Devices, School of Medicine, College of Medicine, Nursing and Health Sciences, National University of Ireland, Galway, Ireland.
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207
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Factors Affecting Anti-Glycan IgG and IgM Repertoires in Human Serum. Sci Rep 2016; 6:19509. [PMID: 26781493 PMCID: PMC4726023 DOI: 10.1038/srep19509] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 12/09/2015] [Indexed: 02/06/2023] Open
Abstract
Serum anti-glycan antibodies play important roles in many immune processes and are of particular interest as biomarkers for many diseases. Changes in anti-glycan antibodies can occur with the onset of disease or in response to stimuli such as pathogens and vaccination. Understanding relationships between anti-glycan antibody repertoires and genetic and environment factors is critical for basic research and clinical applications, but little information is available. In this study we evaluated the effects of age, race, gender, and blood type on anti-glycan antibody profiles in the serum of 135 healthy subjects. As expected, IgG and IgM antibody signals to blood group antigens correlated strongly with blood type. Interestingly, antibodies to other non-ABH glycans, such as the alpha-Gal antigen, also correlated with blood type. A statistically significant decline in IgM signals with age was observed for many antibody subpopulations, but not for IgG. Moreover, statistically significant correlations between race and IgG levels to certain LacNAc-containing glycans were observed. The results have important implications for designing studies and interpreting results in the area of biomarker discovery and for the development of vaccines. The study also highlights the importance of collecting and reporting patient information that could affect serum anti-glycan antibody levels.
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208
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Pai J, Hyun JY, Jeong J, Loh S, Cho EH, Kang YS, Shin I. Carbohydrate microarrays for screening functional glycans. Chem Sci 2016; 7:2084-2093. [PMID: 29899934 PMCID: PMC5968531 DOI: 10.1039/c5sc03789a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 12/10/2015] [Indexed: 12/27/2022] Open
Abstract
Carbohydrate microarrays were used for the simultaneous screening of various glycans whose binding to the cell-surface lectin elicits cellular response.
Carbohydrate microarrays have become robust and powerful tools for the rapid analysis of glycan-associated binding events. However, this microarray technology has rarely been applied in studies of glycan-mediated cellular responses. Herein we describe a carbohydrate microarray-based approach for the rapid screening of biologically active glycans that stimulate the production of reactive oxygen species (ROS) through binding to the cell-surface lectin. We employed a microarray assay and a fluorescent ROS probe to identify the functional glycans which enhance ROS production. Cells binding to glycans on the microarrays produced ROS, whose levels were decreased in the presence of a ROS scavenger or a NADPH oxidase inhibitor. The present study leads us to suggest that glycan microarrays are applicable to the simultaneous screening of various glycans whose binding to the cell-surface lectin elicits cellular response.
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Affiliation(s)
- Jaeyoung Pai
- Center for Biofunctional Molecules , Department of Chemistry , Yonsei University , Seoul 03722 , Korea .
| | - Ji Young Hyun
- Center for Biofunctional Molecules , Department of Chemistry , Yonsei University , Seoul 03722 , Korea .
| | - Jieun Jeong
- Center for Biofunctional Molecules , Department of Chemistry , Yonsei University , Seoul 03722 , Korea .
| | - Sohee Loh
- Department of Biomedical Science and Technology , Department of Veterinary Pharmacology and Toxicology , College of Veterinary Medicine , Konkuk University , Seoul 05029 , Korea
| | - Eun-Hee Cho
- Department of Biomedical Science and Technology , Department of Veterinary Pharmacology and Toxicology , College of Veterinary Medicine , Konkuk University , Seoul 05029 , Korea
| | - Young-Sun Kang
- Department of Biomedical Science and Technology , Department of Veterinary Pharmacology and Toxicology , College of Veterinary Medicine , Konkuk University , Seoul 05029 , Korea
| | - Injae Shin
- Center for Biofunctional Molecules , Department of Chemistry , Yonsei University , Seoul 03722 , Korea .
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209
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Abstract
We describe the method to prepare neoglycoproteins from the conjugation of bovine serum albumin and pyridylaminated glycans. Large quantities of glycans (>1 mg) can be pyridylaminated and then converted to their 1-amino-1-deoxy derivatives by reaction with hydrogen followed by hydrazine. These pyridylaminated glycans can then be conjugated to bovine serum albumin via esterification with N-( m-maleimidobenzoyloxy)succinimide to form a neoglycoprotein, e.g., glycosylated bovine serum albumin. As a demonstration, we prepared High-mannose bovine serum albumin, which was immobilized on an activated glass slide. Then, we showed that the neoglycoprotein bind to Cy3-labeled Lens culinaris agglutinin, a mannose-specific plant lectin, as detected using an evanescent-field-activated fluorescence scanner system.
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Affiliation(s)
- Shin-Ichi Nakakita
- Department of Functional Glycomics, Life Science Research Center, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan.
| | - Jun Hirabayashi
- Department of Functional Glycomics, Life Science Research Center, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan
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210
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Sankaran S, van Weerd J, Voskuhl J, Karperien M, Jonkheijm P. Photoresponsive Cucurbit[8]uril-Mediated Adhesion of Bacteria on Supported Lipid Bilayers. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:6187-96. [PMID: 26469773 DOI: 10.1002/smll.201502471] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Indexed: 05/16/2023]
Abstract
In this work, the development of a photoresponsive platform for the presentation of bioactive ligands to study receptor-ligand interactions has been described. For this purpose, supramolecular host-guest chemistry and supported lipid bilayers (SLBs) have been combined in a microfluidic device. Quartz crystal microbalance with dissipation monitoring (QCM-D) studies on methyl viologen (MV)-functionalized oligo ethylene glycol-based self-assembled monolayers, gel and liquid-state SLBs have been compared for their nonfouling properties in the case of ConA and bacteria. In combination with bacterial adhesion test, negligible nonspecific bacterial adhesion is observed only in the case of methyl-viologen-modified liquid-state SLBs. Therefore, liquid-state SLBs have been identified as most suitable for studying specific cell interactions when MV is incorporated as a guest on the surface. The photoswitchable supramolecular ternary complex is formed by assembling cucurbit[8]uril (CB[8]) and an azobenzene-mannose conjugate (Azo-Man) onto MV-functionalized liquid-state SLBs and the assembly process has been characterized using QCM-D and fluorescence techniques. Mannose has been found to enable binding of E. coli via cell-surface receptors on the nonfouling supramolecular SLBs. Optical switching of the azobenzene moiety allows us to "erase" the bioactive surface after bacterial binding, providing the potential to develop reusable sensors. Localized photorelease of bacterial cells has also been shown indicating the possibility of optically guiding cellular growth, migration, and intercellular interactions.
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Affiliation(s)
- Shrikrishnan Sankaran
- Molecular Nanofabrication Group of the MESA+ Institute for Nanotechnology, Bioinspired Molecular Engineering Laboratory of the MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, P.O. Box 217, 7500, AE Enschede, The Netherlands
| | - Jasper van Weerd
- Molecular Nanofabrication Group of the MESA+ Institute for Nanotechnology, Bioinspired Molecular Engineering Laboratory of the MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, P.O. Box 217, 7500, AE Enschede, The Netherlands
- Department of Developmental Bioengineering of the MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, P.O. Box 217, 7500, AE Enschede, The Netherlands
| | - Jens Voskuhl
- Molecular Nanofabrication Group of the MESA+ Institute for Nanotechnology, Bioinspired Molecular Engineering Laboratory of the MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, P.O. Box 217, 7500, AE Enschede, The Netherlands
| | - Marcel Karperien
- Department of Developmental Bioengineering of the MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, P.O. Box 217, 7500, AE Enschede, The Netherlands
| | - Pascal Jonkheijm
- Molecular Nanofabrication Group of the MESA+ Institute for Nanotechnology, Bioinspired Molecular Engineering Laboratory of the MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, P.O. Box 217, 7500, AE Enschede, The Netherlands
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211
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Macauley MS, Kawasaki N, Peng W, Wang SH, He Y, Arlian BM, McBride R, Kannagi R, Khoo KH, Paulson JC. Unmasking of CD22 Co-receptor on Germinal Center B-cells Occurs by Alternative Mechanisms in Mouse and Man. J Biol Chem 2015; 290:30066-77. [PMID: 26507663 DOI: 10.1074/jbc.m115.691337] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Indexed: 11/06/2022] Open
Abstract
CD22 is an inhibitory B-cell co-receptor whose function is modulated by sialic acid (Sia)-bearing glycan ligands. Glycan remodeling in the germinal center (GC) alters CD22 ligands, with as yet no ascribed biological consequence. Here, we show in both mice and humans that loss of high affinity ligands on GC B-cells unmasks the binding site of CD22 relative to naive and memory B-cells, promoting recognition of trans ligands. The conserved modulation of CD22 ligands on GC B-cells is striking because high affinity glycan ligands of CD22 are species-specific. In both species, the high affinity ligand is based on the sequence Siaα2-6Galβ1-4GlcNAc, which terminates N-glycans. The human ligand has N-acetylneuraminic acid (Neu5Ac) as the sialic acid, and the high affinity ligand on naive B-cells contains 6-O-sulfate on the GlcNAc. On human GC B-cells, this sulfate modification is lost, giving rise to lower affinity CD22 ligands. Ligands of CD22 on naive murine B-cells do not contain the 6-O-sulfate modification. Instead, the high affinity ligand for mouse CD22 has N-glycolylneuraminic acid (Neu5Gc) as the sialic acid, which is replaced on GC B-cells with Neu5Ac. Human naive and memory B-cells express sulfated glycans as high affinity CD22 ligands, which are lost on GC B-cells. In mice, Neu5Gc-containing glycans serve as high affinity CD22 ligands that are replaced by Neu5Ac-containing glycans on GC B-cells. Our results demonstrate that loss of high affinity CD22 ligands on GC B-cells occurs in both mice and humans through alternative mechanisms, unmasking CD22 relative to naive and memory B-cells.
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Affiliation(s)
| | | | | | | | - Yuan He
- Cell and Molecular Biology, and
| | | | | | - Reiji Kannagi
- Biomedical Science, Academia Sinica, Taipei 115, Taiwan
| | | | - James C Paulson
- From the Departments of Chemical Physiology, Cell and Molecular Biology, and Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037 and
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212
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Dupin L, Zuttion F, Géhin T, Meyer A, Phaner-Goutorbe M, Vasseur JJ, Souteyrand E, Morvan F, Chevolot Y. Effects of the Surface Densities of Glycoclusters on the Determination of Their IC50andKdValue Determination by Using a Microarray. Chembiochem 2015; 16:2329-36. [DOI: 10.1002/cbic.201500371] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Indexed: 01/21/2023]
Affiliation(s)
- Lucie Dupin
- Institut des Nanotechnologies de Lyon (INL); UMR 5270 CNRS; Ecole Centrale de Lyon; Université de Lyon; 36 Avenue Guy de Collongue 69134 Ecully France
| | - Francesca Zuttion
- Institut des Nanotechnologies de Lyon (INL); UMR 5270 CNRS; Ecole Centrale de Lyon; Université de Lyon; 36 Avenue Guy de Collongue 69134 Ecully France
| | - Thomas Géhin
- Institut des Nanotechnologies de Lyon (INL); UMR 5270 CNRS; Ecole Centrale de Lyon; Université de Lyon; 36 Avenue Guy de Collongue 69134 Ecully France
| | - Albert Meyer
- Institut des Biomolécules Max Mousseron (IBMM); UMR 5247 CNRS; UM; ENSCM; Université de Montpellier; Place E. Bataillon CC1704 34095 Montpellier Cedex 5 France
| | - Magali Phaner-Goutorbe
- Institut des Nanotechnologies de Lyon (INL); UMR 5270 CNRS; Ecole Centrale de Lyon; Université de Lyon; 36 Avenue Guy de Collongue 69134 Ecully France
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron (IBMM); UMR 5247 CNRS; UM; ENSCM; Université de Montpellier; Place E. Bataillon CC1704 34095 Montpellier Cedex 5 France
| | - Eliane Souteyrand
- Institut des Nanotechnologies de Lyon (INL); UMR 5270 CNRS; Ecole Centrale de Lyon; Université de Lyon; 36 Avenue Guy de Collongue 69134 Ecully France
| | - François Morvan
- Institut des Biomolécules Max Mousseron (IBMM); UMR 5247 CNRS; UM; ENSCM; Université de Montpellier; Place E. Bataillon CC1704 34095 Montpellier Cedex 5 France
| | - Yann Chevolot
- Institut des Nanotechnologies de Lyon (INL); UMR 5270 CNRS; Ecole Centrale de Lyon; Université de Lyon; 36 Avenue Guy de Collongue 69134 Ecully France
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213
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Abstract
Chronic liver diseases are a serious health problem worldwide. The biosynthesis of proteins takes place in the liver, and protein glycosylation is the most common form of post-translational modification of proteins, with as many as 70% of all human proteins estimated to contain one or more glycan chains. Protein glycosylation is the enzymatic addition of sugars or oligosaccharides to proteins, which increases the diversity of the proteome to a level unmatched by any other post-translational modifications because of the various aspects of modification, including glycosidic bond, glycan composition, glycan structure, and glycan length. Changes in the glycan structures of proteins are an indication for liver damage, which plays an important role in the pathogenesis and progression of various liver diseases. The aim of this paper is to give an overview of the altered protein glycosylation in different etiologies of hepatitis, liver fibrosis/cirrhosis, hepatocellular carcinoma, alcoholic and fatty liver diseases based on the analysis of serum and saliva using the glycomics technology.
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214
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Belardi B, Bertozzi CR. Chemical Lectinology: Tools for Probing the Ligands and Dynamics of Mammalian Lectins In Vivo. ACTA ACUST UNITED AC 2015; 22:983-93. [PMID: 26256477 DOI: 10.1016/j.chembiol.2015.07.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 06/29/2015] [Accepted: 07/08/2015] [Indexed: 02/06/2023]
Abstract
The importance and complexity associated with the totality of glycan structures, i.e. the glycome, has garnered significant attention from chemists and biologists alike. However, what is lacking from this biochemical picture is how cells, tissues, and organisms interpret glycan patterns and translate this information into appropriate responses. Lectins, glycan-binding proteins, are thought to bridge this gap by decoding the glycome and dictating cell fate based on the underlying chemical identities and properties of the glycome. Yet, our understanding of the in vivo ligands and function for most lectins is still incomplete. This review focuses on recent advances in chemical tools to study the specificity and dynamics of mammalian lectins in live cells. A picture emerges of lectin function that is highly sensitive to its organization, which in turn drastically shapes immunity and cancer progression. We hope this review will inspire biologists to make use of these new techniques and stimulate chemists to continue developing innovative approaches to probe lectin biology in vivo.
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Affiliation(s)
- Brian Belardi
- Departments of Chemistry and Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Carolyn R Bertozzi
- Department of Chemistry and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305-4401, USA.
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215
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Defaus S, Gupta P, Andreu D, Gutiérrez-Gallego R. Mammalian protein glycosylation--structure versus function. Analyst 2015; 139:2944-67. [PMID: 24779027 DOI: 10.1039/c3an02245e] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Carbohydrates fulfil many common as well as extremely important functions in nature. They show a variety of molecular displays--e.g., free mono-, oligo-, and polysaccharides, glycolipids, proteoglycans, glycoproteins, etc.--with particular roles and localizations in living organisms. Structure-specific peculiarities are so many and diverse that it becomes virtually impossible to cover them all from an analytical perspective. Hence this manuscript, focused on mammalian glycosylation, rather than a complete list of analytical descriptors or recognized functions for carbohydrate structures, comprehensively reviews three central issues in current glycoscience, namely (i) structural analysis of glycoprotein glycans, covering both classical and novel approaches for teasing out the structural puzzle as well as potential pitfalls of these processes; (ii) an overview of functions attributed to carbohydrates, covering from monosaccharide to complex, well-defined epitopes and full glycans, including post-glycosylational modifications, and (iii) recent technical advances allowing structural identification of glycoprotein glycans with simultaneous assignation of biological functions.
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Affiliation(s)
- S Defaus
- Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona Biomedical Research Park, 08003 Barcelona, Spain.
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216
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Stowell SR, Ju T, Cummings RD. Protein glycosylation in cancer. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2015; 10:473-510. [PMID: 25621663 DOI: 10.1146/annurev-pathol-012414-040438] [Citation(s) in RCA: 574] [Impact Index Per Article: 63.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Neoplastic transformation results in a wide variety of cellular alterations that impact the growth, survival, and general behavior of affected tissue. Although genetic alterations underpin the development of neoplastic disease, epigenetic changes can exert an equally significant effect on neoplastic transformation. Among neoplasia-associated epigenetic alterations, changes in cellular glycosylation have recently received attention as a key component of neoplastic progression. Alterations in glycosylation appear to not only directly impact cell growth and survival but also facilitate tumor-induced immunomodulation and eventual metastasis. Many of these changes may support neoplastic progression, and unique alterations in tumor-associated glycosylation may also serve as a distinct feature of cancer cells and therefore provide novel diagnostic and even therapeutic targets.
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217
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Wu B, Wei N, Thon V, Wei M, Yu Z, Xu Y, Chen X, Liu J, Wang PG, Li T. Facile chemoenzymatic synthesis of biotinylated heparosan hexasaccharide. Org Biomol Chem 2015; 13:5098-101. [PMID: 25858766 PMCID: PMC4472006 DOI: 10.1039/c5ob00462d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A biotinylated heparosan hexasaccharide was synthesized using a one-pot multi-enzyme strategy, in situ activation and transfer of N-trifluoroacetylglucosamine (GlcNTFA) to a heparin backbone significantly improved the synthetic efficiency. The biotinylated hexasaccharide could serve as a flexible core to diversify its conversion into heparan sulfate isoforms with potential biological applications and therapeutics.
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Affiliation(s)
- Baolin Wu
- Center for Diagnostics and Therapeutics, Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Na Wei
- Center for Diagnostics and Therapeutics, Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Vireak Thon
- Center for Diagnostics and Therapeutics, Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Mohui Wei
- Center for Diagnostics and Therapeutics, Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Zaikuan Yu
- Center for Diagnostics and Therapeutics, Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Yongmei Xu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Xi Chen
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Jian Liu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Peng George Wang
- Center for Diagnostics and Therapeutics, Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Tiehai Li
- Center for Diagnostics and Therapeutics, Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
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218
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Fernández-Tejada A, Cañada FJ, Jiménez-Barbero J. Glycans in Medicinal Chemistry: An Underexploited Resource. ChemMedChem 2015; 10:1291-5. [PMID: 25974358 DOI: 10.1002/cmdc.201500107] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Indexed: 11/05/2022]
Abstract
The biological relevance of glycans as mediators of key physiological processes, including disease-related mechanisms, makes them attractive targets for a wide range of medical applications. Despite their important biological roles, especially as molecular recognition elements, carbohydrates have not been fully exploited as therapeutics mainly due to the scarcity of structure-activity correlations and their non-drug-like properties. A more detailed understanding of the complex carbohydrate structures and their associated functions should contribute to the development of new glycan-based pharmaceuticals. Recent significant progress in oligosaccharide synthesis and chemical glycobiology has renewed the interest of the medicinal chemistry community in carbohydrates. This promises to increase our possibilities to harness them in drug discovery efforts for the development of new and more effective, synthetic glycan-based therapeutics and vaccines.
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Affiliation(s)
- Alberto Fernández-Tejada
- Chemical and Physical Biology, Centro de Investigaciones Biológicas (CIB-CSIC), Ramiro de Maeztu 9, 28040 Madrid (Spain).
| | - F Javier Cañada
- Chemical and Physical Biology, Centro de Investigaciones Biológicas (CIB-CSIC), Ramiro de Maeztu 9, 28040 Madrid (Spain)
| | - Jesús Jiménez-Barbero
- CIC bioGUNE: Center for Cooperative Research in Biosciences, Bizkaia Technology Park, 48160 Derio (Spain). .,Ikerbasque, Basque Foundation for Science, María López de Haro 13, 48009 Bilbao (Spain).
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219
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Prudden AR, Chinoy ZS, Wolfert MA, Boons GJ. A multifunctional anomeric linker for the chemoenzymatic synthesis of complex oligosaccharides. Chem Commun (Camb) 2015; 50:7132-5. [PMID: 24854112 DOI: 10.1039/c4cc02222j] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new anomeric linker has been developed that facilitates the purification of glycans prepared by chemoenzymatic approaches and can readily give compounds that are appropriately modified for microarray development or glycan derivatives with a free reducing end that are needed as standards for the development of analytical protocols.
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Affiliation(s)
- Anthony R Prudden
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, USA.
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220
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Novoa A, Winssinger N. DNA display of glycoconjugates to emulate oligomeric interactions of glycans. Beilstein J Org Chem 2015; 11:707-19. [PMID: 26113879 PMCID: PMC4462854 DOI: 10.3762/bjoc.11.81] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 05/06/2015] [Indexed: 12/21/2022] Open
Abstract
Glycans (carbohydrate portion of glycoproteins and glycolipids) frequently exert their function through oligomeric interactions involving multiple carbohydrate units. In efforts to recapitulate the diverse spatial arrangements of the carbohydrate units, assemblies based on hybridization of nucleic acid conjugates have been used to display simplified ligands with tailored interligand distances and valences. The programmability of the assemblies lends itself to a combinatorial display of multiple ligands. Recent efforts in the synthesis and applications of such conjugates are discussed.
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Affiliation(s)
- Alexandre Novoa
- Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva 30, quai Ernest Ansermet, 1211 Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva 30, quai Ernest Ansermet, 1211 Geneva, Switzerland
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221
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A multivariate approach for high throughput pectin profiling by combining glycan microarrays with monoclonal antibodies. Carbohydr Res 2015; 409:41-7. [DOI: 10.1016/j.carres.2015.03.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Revised: 03/22/2015] [Accepted: 03/27/2015] [Indexed: 11/18/2022]
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222
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Song X, Heimburg-Molinaro J, Smith DF, Cummings RD. Glycan microarrays of fluorescently-tagged natural glycans. Glycoconj J 2015; 32:465-73. [PMID: 25877830 DOI: 10.1007/s10719-015-9584-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 03/02/2015] [Accepted: 03/19/2015] [Indexed: 01/22/2023]
Abstract
This review discusses the challenges facing research in 'functional glycomics' and the novel technologies that are being developed to advance the field. The structural complexity of glycans and glycoconjugates makes studies of both their structures and recognition difficult. However, these intricate structures can be captured from their natural sources, isolated and fluorescently-tagged for detailed structural analysis and for presentation on glycan microarrays for functional recognition by glycan-binding proteins. These advances in glycan preparation and manipulation enable the streamlining of functional glycomics studies and will help to propel the field forward in studying natural, biologically relevant glycans.
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Affiliation(s)
- Xuezheng Song
- Department of Biochemistry, The National Center for Functional Glycomics, Emory University School of Medicine, Atlanta, GA, 30322, USA. .,Department of Biochemistry, O. Wayne Rollins Research Center, Emory University School of Medicine, 1510 Clifton Road, Suite 4025, Atlanta, GA, 30322, USA.
| | - Jamie Heimburg-Molinaro
- Department of Biochemistry, The National Center for Functional Glycomics, Emory University School of Medicine, Atlanta, GA, 30322, USA.,Department of Biochemistry, O. Wayne Rollins Research Center, Emory University School of Medicine, 1510 Clifton Road, Suite 4025, Atlanta, GA, 30322, USA
| | - David F Smith
- Department of Biochemistry, The National Center for Functional Glycomics, Emory University School of Medicine, Atlanta, GA, 30322, USA.,Department of Biochemistry, O. Wayne Rollins Research Center, Emory University School of Medicine, 1510 Clifton Road, Suite 4025, Atlanta, GA, 30322, USA
| | - Richard D Cummings
- Department of Biochemistry, The National Center for Functional Glycomics, Emory University School of Medicine, Atlanta, GA, 30322, USA.,Department of Biochemistry, O. Wayne Rollins Research Center, Emory University School of Medicine, 1510 Clifton Road, Suite 4025, Atlanta, GA, 30322, USA
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223
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Muthana SM, Xia L, Campbell CT, Zhang Y, Gildersleeve JC. Competition between serum IgG, IgM, and IgA anti-glycan antibodies. PLoS One 2015; 10:e0119298. [PMID: 25807519 PMCID: PMC4373866 DOI: 10.1371/journal.pone.0119298] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 01/29/2015] [Indexed: 12/31/2022] Open
Abstract
Anti-glycan antibodies are an abundant subpopulation of serum antibodies with critical functions in many immune processes. Changes in the levels of these antibodies can occur with the onset of disease, exposure to pathogens, or vaccination. As a result, there has been significant interest in exploiting anti-glycan antibodies as biomarkers for many diseases. Serum contains a mixture of anti-glycan antibodies that can recognize the same antigen, and competition for binding can potentially influence the detection of antibody subpopulations that are more relevant to disease processes. The most abundant antibody isotypes in serum are IgG, IgM, and IgA, but little is known regarding how these different isotypes compete for the same glycan antigen. In this study, we developed a multiplexed glycan microarray assay and applied it to evaluate how different isotypes of anti-glycan antibodies (IgA, IgG, and IgM) compete for printed glycan antigens. While IgG and IgA antibodies typically outcompete IgM for peptide or protein antigens, we found that IgM outcompete IgG and IgA for many glycan antigens. To illustrate the importance of this effect, we provide evidence that IgM competition can account for the unexpected observation that IgG of certain antigen specificities appear to be preferentially transported from mothers to fetuses. We demonstrate that IgM in maternal sera compete with IgG resulting in lower than expected IgG signals. Since cord blood contains very low levels of IgM, competition only affects maternal IgG signals, making it appear as though certain IgG antibodies are higher in cord blood than matched maternal blood. Taken together, the results highlight the importance of competition for studies involving anti-glycan antibodies.
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Affiliation(s)
- Saddam M. Muthana
- Chemical Biology Laboratory, National Cancer Institute, NIH, 376 Boyles St., Frederick, MD, 21702, United States of America
| | - Li Xia
- Chemical Biology Laboratory, National Cancer Institute, NIH, 376 Boyles St., Frederick, MD, 21702, United States of America
| | - Christopher T. Campbell
- Chemical Biology Laboratory, National Cancer Institute, NIH, 376 Boyles St., Frederick, MD, 21702, United States of America
| | - Yalong Zhang
- Chemical Biology Laboratory, National Cancer Institute, NIH, 376 Boyles St., Frederick, MD, 21702, United States of America
| | - Jeffrey C. Gildersleeve
- Chemical Biology Laboratory, National Cancer Institute, NIH, 376 Boyles St., Frederick, MD, 21702, United States of America
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224
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Tang H, Singh S, Partyka K, Kletter D, Hsueh P, Yadav J, Ensink E, Bern M, Hostetter G, Hartman D, Huang Y, Brand RE, Haab BB. Glycan motif profiling reveals plasma sialyl-lewis x elevations in pancreatic cancers that are negative for sialyl-lewis A. Mol Cell Proteomics 2015; 14:1323-33. [PMID: 25733690 DOI: 10.1074/mcp.m114.047837] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Indexed: 12/24/2022] Open
Abstract
The sialyl-Lewis A (sLeA) glycan forms the basis of the CA19-9 assay and is the current best biomarker for pancreatic cancer, but because it is not elevated in ∼25% of pancreatic cancers, it is not useful for early diagnosis. We hypothesized that sLeA-low tumors secrete glycans that are related to sLeA but not detectable by CA19-9 antibodies. We used a method called motif profiling to predict that a structural isomer of sLeA called sialyl-Lewis X (sLeX) is elevated in the plasma of some sLeA-low cancers. We corroborated this prediction in a set of 48 plasma samples and in a blinded set of 200 samples. An antibody sandwich assay formed by the capture and detection of sLeX was elevated in 13 of 69 cancers that were not elevated in sLeA, and a novel hybrid assay of sLeA capture and sLeX detected 24 of 69 sLeA-low cancers. A two-marker panel based on combined sLeA and sLeX detection differentiated 109 pancreatic cancers from 91 benign pancreatic diseases with 79% accuracy (74% sensitivity and 78% specificity), significantly better than sLeA alone, which yielded 68% accuracy (65% sensitivity and 71% specificity). Furthermore, sLeX staining was evident in tumors that do not elevate plasma sLeA, including those with poorly differentiated ductal adenocarcinoma. Thus, glycan-based biomarkers could characterize distinct subgroups of patients. In addition, the combined use of sLeA and sLeX, or related glycans, could lead to a biomarker panel that is useful in the clinical diagnosis of pancreatic cancer. Précis: This paper shows that a structural isomer of the current best biomarker for pancreatic cancer, CA19-9, is elevated in the plasma of patients who are low in CA19-9, potentially enabling more comprehensive detection and classification of pancreatic cancers.
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Affiliation(s)
| | | | | | | | - Peter Hsueh
- §Van Andel Research Institute, Grand Rapids, MI
| | | | | | | | | | | | - Ying Huang
- **University of Pittsburgh School of Medicine, Pittsburgh, PA
| | | | - Brian B Haab
- §Van Andel Research Institute, Grand Rapids, MI;
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225
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Ananikov VP, Khokhlova EA, Egorov MP, Sakharov AM, Zlotin SG, Kucherov AV, Kustov LM, Gening ML, Nifantiev NE. Organic and hybrid molecular systems. MENDELEEV COMMUNICATIONS 2015. [DOI: 10.1016/j.mencom.2015.03.001] [Citation(s) in RCA: 164] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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226
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Schmidt D, Schuhmacher F, Geissner A, Seeberger PH, Pfrengle F. Automated Synthesis of Arabinoxylan-Oligosaccharides Enables Characterization of Antibodies that Recognize Plant Cell Wall Glycans. Chemistry 2015; 21:5709-13. [DOI: 10.1002/chem.201500065] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Indexed: 11/06/2022]
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227
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Palma AS, Liu Y, Zhang H, Zhang Y, McCleary BV, Yu G, Huang Q, Guidolin LS, Ciocchini AE, Torosantucci A, Wang D, Carvalho AL, Fontes CMGA, Mulloy B, Childs RA, Feizi T, Chai W. Unravelling glucan recognition systems by glycome microarrays using the designer approach and mass spectrometry. Mol Cell Proteomics 2015; 14:974-88. [PMID: 25670804 PMCID: PMC4390274 DOI: 10.1074/mcp.m115.048272] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Indexed: 11/06/2022] Open
Abstract
Glucans are polymers of d-glucose with differing linkages in linear or branched sequences. They are constituents of microbial and plant cell-walls and involved in important bio-recognition processes, including immunomodulation, anticancer activities, pathogen virulence, and plant cell-wall biodegradation. Translational possibilities for these activities in medicine and biotechnology are considerable. High-throughput micro-methods are needed to screen proteins for recognition of specific glucan sequences as a lead to structure–function studies and their exploitation. We describe construction of a “glucome” microarray, the first sequence-defined glycome-scale microarray, using a “designer” approach from targeted ligand-bearing glucans in conjunction with a novel high-sensitivity mass spectrometric sequencing method, as a screening tool to assign glucan recognition motifs. The glucome microarray comprises 153 oligosaccharide probes with high purity, representing major sequences in glucans. Negative-ion electrospray tandem mass spectrometry with collision-induced dissociation was used for complete linkage analysis of gluco-oligosaccharides in linear “homo” and “hetero” and branched sequences. The system is validated using antibodies and carbohydrate-binding modules known to target α- or β-glucans in different biological contexts, extending knowledge on their specificities, and applied to reveal new information on glucan recognition by two signaling molecules of the immune system against pathogens: Dectin-1 and DC-SIGN. The sequencing of the glucan oligosaccharides by the MS method and their interrogation on the microarrays provides detailed information on linkage, sequence and chain length requirements of glucan-recognizing proteins, and are a sensitive means of revealing unsuspected sequences in the polysaccharides.
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Affiliation(s)
- Angelina S Palma
- From the ‡Glycosciences Laboratory, Department of Medicine, Imperial College London, United Kingdom; §UCIBIO-REQUIMTE, Department of Chemistry, Faculty of Science and Technology, NOVA University of Lisbon;
| | - Yan Liu
- From the ‡Glycosciences Laboratory, Department of Medicine, Imperial College London, United Kingdom
| | - Hongtao Zhang
- From the ‡Glycosciences Laboratory, Department of Medicine, Imperial College London, United Kingdom
| | - Yibing Zhang
- From the ‡Glycosciences Laboratory, Department of Medicine, Imperial College London, United Kingdom
| | | | - Guangli Yu
- ‖Key Laboratory of Marine Drugs, Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China
| | - Qilin Huang
- **Department of Chemistry, Wuhan University, Wuhan, China
| | - Leticia S Guidolin
- ‡‡Instituto de Investigaciones Biotecnológicas "Dr. Rodolfo A. Ugalde", Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Andres E Ciocchini
- ‡‡Instituto de Investigaciones Biotecnológicas "Dr. Rodolfo A. Ugalde", Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Antonella Torosantucci
- §§Department of Infectious, Parasitic and Immune-mediated Diseases, Istituto Superiore di Sanitá, Rome, Italy
| | - Denong Wang
- ¶¶Tumor Glycomics Laboratory, SRI International Biosciences Division, Menlo Park, CA
| | - Ana Luísa Carvalho
- §UCIBIO-REQUIMTE, Department of Chemistry, Faculty of Science and Technology, NOVA University of Lisbon
| | - Carlos M G A Fontes
- ‖‖CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Portugal
| | - Barbara Mulloy
- From the ‡Glycosciences Laboratory, Department of Medicine, Imperial College London, United Kingdom
| | - Robert A Childs
- From the ‡Glycosciences Laboratory, Department of Medicine, Imperial College London, United Kingdom
| | - Ten Feizi
- From the ‡Glycosciences Laboratory, Department of Medicine, Imperial College London, United Kingdom
| | - Wengang Chai
- From the ‡Glycosciences Laboratory, Department of Medicine, Imperial College London, United Kingdom;
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228
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Tang H, Hsueh P, Kletter D, Bern M, Haab B. The detection and discovery of glycan motifs in biological samples using lectins and antibodies: new methods and opportunities. Adv Cancer Res 2015; 126:167-202. [PMID: 25727148 DOI: 10.1016/bs.acr.2014.11.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Recent research has uncovered unexpected ways that glycans contribute to biology, as well as new strategies for combatting disease using approaches involving glycans. To make full use of glycans for clinical applications, we need more detailed information on the location, nature, and dynamics of glycan expression in vivo. Such studies require the use of specimens acquired directly from patients. Effective studies of clinical specimens require low-volume assays, high precision measurements, and the ability to process many samples. Assays using affinity reagents-lectins and glycan-binding antibodies-can meet these requirements, but further developments are needed to make the methods routine and effective. Recent advances in the use of glycan-binding proteins involve improved determination of specificity using glycan arrays; the availability of databases for mining and analyzing glycan array data; lectin engineering methods; and the ability to quantitatively interpret lectin measurements. Here, we describe many of the challenges and opportunities involved in the application of these new approaches to the study of biological samples. The new tools hold promise for developing methods to improve the outcomes of patients afflicted with diseases characterized by aberrant glycan expression.
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Affiliation(s)
- Huiyuan Tang
- Van Andel Research Institute, Grand Rapids, MI, USA
| | - Peter Hsueh
- Van Andel Research Institute, Grand Rapids, MI, USA
| | | | | | - Brian Haab
- Van Andel Research Institute, Grand Rapids, MI, USA.
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229
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Anish C, Schumann B, Pereira CL, Seeberger PH. Chemical biology approaches to designing defined carbohydrate vaccines. ACTA ACUST UNITED AC 2015; 21:38-50. [PMID: 24439205 DOI: 10.1016/j.chembiol.2014.01.002] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 12/27/2013] [Accepted: 01/02/2014] [Indexed: 01/08/2023]
Abstract
Carbohydrate antigens have shown promise as important targets for developing effective vaccines and pathogen detection strategies. Modifying purified microbial glycans through synthetic routes or completely synthesizing antigenic motifs are attractive options to advance carbohydrate vaccine development. However, limited knowledge on structure-property correlates hampers the discovery of immunoprotective carbohydrate epitopes. Recent advancements in tools for glycan modification, high-throughput screening of biological samples, and 3D structural analysis may facilitate antigen discovery process. This review focuses on advances that accelerate carbohydrate-based vaccine development and various technologies that are driving these efforts. Herein we provide a critical overview of approaches and resources available for rational design of better carbohydrate antigens. Structurally defined and fully synthetic oligosaccharides, designed based on molecular understanding of antigen-antibody interactions, offer a promising alternative for developing future carbohydrate vaccines.
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Affiliation(s)
- Chakkumkal Anish
- Department for Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam, Germany.
| | - Benjamin Schumann
- Department for Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Claney Lebev Pereira
- Department for Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam, Germany
| | - Peter H Seeberger
- Department for Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany.
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230
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Hu Y, Tabor RF, Wilkinson BL. Sweetness and light: design and applications of photo-responsive glycoconjugates. Org Biomol Chem 2015; 13:2216-25. [DOI: 10.1039/c4ob02296c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photoswitchable glycoconjugates are promising tools for studying biomolecular interactions and for the development of stimuli-responsive materials.
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Affiliation(s)
- Yingxue Hu
- School of Chemistry
- Monash University
- Australia
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231
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Abstract
Carbohydrate antigens are important targets for the immune system, but identification of key glycan antigens is challenging. Direct analysis of glycomes by mass spectrometry is difficult, and detection reagents, such as monoclonal antibodies and lectins, are only available for a small subset of glycans. An alternative approach involves profiling serum anti-glycan antibody populations to identify unique antibodies or changes in antibody subpopulations. Glycan microarray technology allows rapid evaluation of hundreds to thousands of antigen-antibody interactions in a single experiment. This high-throughput format is particularly useful in profiling complex anti-glycan antibodies in serum. Here we elaborate the use of this technology to explore clinically relevant carbohydrate antigens by profiling serum anti-glycan antibodies. Detailed protocols from glycan microarray fabrication to microarray binding assays and analysis of microarray data are presented.
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232
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Jiang QL, Zhang S, Tian M, Zhang SY, Xie T, Chen DY, Chen YJ, He J, Liu J, Ouyang L, Jiang X. Plant lectins, from ancient sugar-binding proteins to emerging anti-cancer drugs in apoptosis and autophagy. Cell Prolif 2014; 48:17-28. [PMID: 25488051 DOI: 10.1111/cpr.12155] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 08/28/2014] [Indexed: 02/06/2023] Open
Abstract
Ubiquitously distributed in different plant species, plant lectins are highly diverse carbohydrate-binding proteins of non-immune origin. They have interesting pharmacological activities and currently are of great interest to thousands of people working on biomedical research in cancer-related problems. It has been widely accepted that plant lectins affect both apoptosis and autophagy by modulating representative signalling pathways involved in Bcl-2 family, caspase family, p53, PI3K/Akt, ERK, BNIP3, Ras-Raf and ATG families, in cancer. Plant lectins may have a role as potential new anti-tumour agents in cancer drug discovery. Thus, here we summarize these findings on pathway- involved plant lectins, to provide a comprehensive perspective for further elucidating their potential role as novel anti-cancer drugs, with respect to both apoptosis and autophagy in cancer pathogenesis, and future therapy.
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Affiliation(s)
- Q-L Jiang
- State Key Laboratory of Biotherapy & Collaborative Innovation Center of Biotherapy, Department of Dermatology, Department of Emergency Medicine, West China Hospital, Sichuan University, Chengdu, 610041, China; School of Pharmacy and The First Affiliated Hospital of Chengdu Medical College, Chengdu Medical College, Chengdu, Sichuan, 610500, China; Sichuan Province College Key Laboratory of Structure-Specific Small Molecule Drugs, Chengdu Medical College, Chengdu, Sichuan, 610500, China
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233
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Kurochkina NA, Budanova UA, Sebyakin YL. Design and synthesis of cluster neoglycoconjugates based on D-glucose. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2014. [DOI: 10.1134/s1070428014100157] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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234
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Gahoi N, Ray S, Srivastava S. Array-based proteomic approaches to study signal transduction pathways: prospects, merits and challenges. Proteomics 2014; 15:218-31. [PMID: 25266292 DOI: 10.1002/pmic.201400261] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Revised: 09/17/2014] [Accepted: 09/25/2014] [Indexed: 01/17/2023]
Abstract
Very often dysfunctional aspects of various signalling networks are found to be associated with human diseases and disorders. The major characteristics of signal transduction pathways are specificity, amplification of the signal, desensitisation and integration, which is accomplished not solely, but majorly by proteins. Array-based profiling of protein-protein and other biomolecular interactions is a versatile approach, which holds immense potential for multiplex interactome mapping and provides an inclusive representation of the signal transduction pathways and networks. Protein microarrays such as analytical protein microarrays (antigen-antibody interactions, autoantibody screening), RP microarrays (interaction of a particular ligand with all the possible targets in cell), functional protein microarrays (protein-protein or protein-ligand interactions) are implemented for various applications, including analysis of protein interactions and their significance in signalling cascades. Additionally, successful amalgamation of the array-based approaches with different label-free detection techniques allows real-time analysis of interaction kinetics of multiple interaction events simultaneously. This review discusses the prospects, merits and limitations of different variants of array-based techniques and their promising applications for studying the modifications and interactions of biomolecules, and highlights the studies associated with signal transduction pathways and their impact on disease pathobiology.
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Affiliation(s)
- Nikita Gahoi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
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235
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Kitova EN, El-Hawiet A, Klassen JS. Screening carbohydrate libraries for protein interactions using the direct ESI-MS assay. Applications to libraries of unknown concentration. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1908-16. [PMID: 25135608 DOI: 10.1007/s13361-014-0964-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 07/02/2014] [Accepted: 07/04/2014] [Indexed: 05/22/2023]
Abstract
A semiquantitative electrospray ionization mass spectrometry (ESI-MS) binding assay suitable for analyzing mixtures of oligosaccharides, at unknown concentrations, for interactions with target proteins is described. The assay relies on the differences in the ratio of the relative abundances of the ligand-bound and free protein ions measured by ESI-MS at two or more initial protein concentrations to distinguish low affinity (≤10(3) M(-1)) ligands from moderate and high affinity (>10(5) M(-1)) ligands present in the library and to rank their affinities. Control experiments were performed on solutions of a single chain antibody and a mixture of synthetic oligosaccharides, with known affinities, in the absence and presence of a 40-component carbohydrate library to demonstrate the implementation and reliability of the assay. The application of the assay for screening natural libraries of carbohydrates against proteins is also demonstrated using mixtures of human milk oligosaccharides, isolated from breast milk, and fragments of a bacterial toxin and human galectin 3.
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Affiliation(s)
- Elena N Kitova
- Alberta Glycomics Center and Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
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236
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Çelik E, Ollis AA, Lasanajak Y, Fisher AC, Gür G, Smith DF, DeLisa MP. Glycoarrays with engineered phages displaying structurally diverse oligosaccharides enable high-throughput detection of glycan-protein interactions. Biotechnol J 2014; 10:199-209. [PMID: 25263089 DOI: 10.1002/biot.201400354] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 08/21/2014] [Accepted: 09/24/2014] [Indexed: 02/02/2023]
Abstract
Glycan microarrays have become a powerful platform to investigate the interactions of carbohydrates with a variety of biomolecules. However, the number and diversity of glycans available for use in such arrays represent a key bottleneck in glycan array fabrication. To address this challenge, we describe a novel glycan array platform based on surface patterning of engineered glycophages that display unique carbohydrate epitopes. Specifically, we show that glycophages are compatible with surface immobilization procedures and that phage-displayed oligosaccharides retain the ability to be recognized by different glycan-binding proteins (e.g. antibodies and lectins) after immobilization. A key advantage of glycophage arrays is that large quantities of glycophages can be produced biosynthetically from recombinant bacteria and isolated directly from bacterial supernatants without laborious purification steps. Taken together, the glycophage array technology described here should help to expand the diversity of glycan libraries and provide a complement to the existing toolkit for high-throughput analysis of glycan-protein interactions.
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Affiliation(s)
- Eda Çelik
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA; Department of Chemical Engineering, Hacettepe University, Beytepe, Ankara, Turkey; Bioengineering Division, Institute of Science, Hacettepe University, Beytepe, Ankara, Turkey
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237
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Garcia-Martin F, Matsushita T, Hinou H, Nishimura SI. Fast epitope mapping for the anti-MUC1 monoclonal antibody by combining a one-bead-one-glycopeptide library and a microarray platform. Chemistry 2014; 20:15891-902. [PMID: 25303614 DOI: 10.1002/chem.201403239] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 07/13/2014] [Indexed: 12/25/2022]
Abstract
Anti-MUC1 monoclonal antibodies (mAbs) are powerful tools that can be used to recognize cancer-related MUC1 molecules, the O-glycosylation status of which is believed to affect binding affinity. We demonstrate the feasibility of using a rapid screening methodology to elucidate those effects. The approach involves i) "one-bead-one-compound"-based preparation of bilayer resins carrying glycopeptides on the shell and mass-tag tripeptides coding O-glycan patterns in the core, ii) on-resin screening with an anti-MUC1 mAb, iii) separating positive resins by utilizing secondary antibody conjugation with magnetic beads, and (iv) decoding the mass-tag that is detached from the positive resins pool by using mass spectrometric analysis. We tested a small library consisting of 27 MUC1 glycopeptides with different O-glycosylations against anti-MUC1 mAb clone VU-3C6. Qualitative mass-tag analysis showed that increasing the number of glycans leads to an increase in the binding affinity. Six glycopeptides selected from the library were validated by using a microarray-based assay. Our screening provides valuable information on O-glycosylations of epitopes leading to high affinity with mAb.
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Affiliation(s)
- Fayna Garcia-Martin
- Faculty of Advanced Life Science and Graduate School of Life Science, Hokkaido University, N21, W11, Kita-ku, Sapporo 001-0021 (Japan), Fax: (+81) 11-706-9042
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238
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Zhao H, Yang Y, von Itzstein M, Zhou Y. Carbohydrate-binding protein identification by coupling structural similarity searching with binding affinity prediction. J Comput Chem 2014; 35:2177-83. [PMID: 25220682 DOI: 10.1002/jcc.23730] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 05/27/2014] [Accepted: 08/25/2014] [Indexed: 02/03/2023]
Abstract
Carbohydrate-binding proteins (CBPs) are potential biomarkers and drug targets. However, the interactions between carbohydrates and proteins are challenging to study experimentally and computationally because of their low binding affinity, high flexibility, and the lack of a linear sequence in carbohydrates as exists in RNA, DNA, and proteins. Here, we describe a structure-based function-prediction technique called SPOT-Struc that identifies carbohydrate-recognizing proteins and their binding amino acid residues by structural alignment program SPalign and binding affinity scoring according to a knowledge-based statistical potential based on the distance-scaled finite-ideal gas reference state (DFIRE). The leave-one-out cross-validation of the method on 113 carbohydrate-binding domains and 3442 noncarbohydrate binding proteins yields a Matthews correlation coefficient of 0.56 for SPalign alone and 0.63 for SPOT-Struc (SPalign + binding affinity scoring) for CBP prediction. SPOT-Struc is a technique with high positive predictive value (79% correct predictions in all positive CBP predictions) with a reasonable sensitivity (52% positive predictions in all CBPs). The sensitivity of the method was changed slightly when applied to 31 APO (unbound) structures found in the protein databank (14/31 for APO versus 15/31 for HOLO). The result of SPOT-Struc will not change significantly if highly homologous templates were used. SPOT-Struc predicted 19 out of 2076 structural genome targets as CBPs. In particular, one uncharacterized protein in Bacillus subtilis (1oq1A) was matched to galectin-9 from Mus musculus. Thus, SPOT-Struc is useful for uncovering novel carbohydrate-binding proteins. SPOT-Struc is available at http://sparks-lab.org.
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Affiliation(s)
- Huiying Zhao
- Indiana University School of Informatics, Indiana University Purdue University, Indianapolis, 719 Indiana Ave, Suite 319, Indianapolis, Indiana, 46202; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, 46202
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239
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Claes D, Memmel E, Holzapfel M, Seibel J, Maison W. High-Affinity Carbohydrate Binding by Trimeric Benzoboroxoles Measured on Carbohydrate Arrays. Chembiochem 2014; 15:2450-7. [DOI: 10.1002/cbic.201402297] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Indexed: 11/06/2022]
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240
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Hushegyi A, Tkac J. Are glycan biosensors an alternative to glycan microarrays? ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2014; 6:6610-6620. [PMID: 27231487 PMCID: PMC4878710 DOI: 10.1039/c4ay00692e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Complex carbohydrates (glycans) play an important role in nature and study of their interaction with proteins or intact cells can be useful for understanding many physiological and pathological processes. Such interactions have been successfully interrogated in a highly parallel way using glycan microarrays, but this technique has some limitations. Thus, in recent years glycan biosensors in numerous progressive configurations have been developed offering distinct advantages compared to glycan microarrays. Thus, in this review advances achieved in the field of label-free glycan biosensors are discussed.
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Affiliation(s)
- A Hushegyi
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava 845 38, Slovakia
| | - J Tkac
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, Bratislava 845 38, Slovakia
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241
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Novoa A, Machida T, Barluenga S, Imberty A, Winssinger N. PNA-encoded synthesis (PES) of a 10 000-member hetero-glycoconjugate library and microarray analysis of diverse lectins. Chembiochem 2014; 15:2058-65. [PMID: 25158314 DOI: 10.1002/cbic.201402280] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Indexed: 11/07/2022]
Abstract
Identification of selective and synthetically tractable ligands to glycan-binding proteins is important in glycoscience. Carbohydrate arrays have had a tremendous impact on profiling glycan-binding proteins and as analytical tools. We report a highly miniaturized synthetic format to access nucleic-acid-encoded hetero-glycoconjugate libraries with an unprecedented diversity in the combinations of glycans, linkers, and capping groups. Novel information about plant and bacterial lectin specificity was obtained by microarray profiling, and we show that a ligand identified on the array can be converted to a high-affinity soluble ligand by straightforward chemistry.
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Affiliation(s)
- Alexandre Novoa
- Department of Organic Chemistry, University of Geneva, Quai Ernest Ansermet 30, 1211 Geneva 4 (Switzerland)
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242
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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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243
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Venkataram Prasad BV, Shanker S, Hu L, Choi JM, Crawford SE, Ramani S, Czako R, Atmar RL, Estes MK. Structural basis of glycan interaction in gastroenteric viral pathogens. Curr Opin Virol 2014; 7:119-27. [PMID: 25073118 PMCID: PMC4251800 DOI: 10.1016/j.coviro.2014.05.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 05/28/2014] [Indexed: 01/12/2023]
Abstract
A critical event in the life cycle of a virus is its initial attachment to host cells. This involves recognition by the viruses of specific receptors on the cell surface, including glycans. Viruses typically exhibit strain-dependent variations in recognizing specific glycan receptors, a feature that contributes significantly to cell tropism, host specificity, host adaptation and interspecies transmission. Examples include influenza viruses, noroviruses, rotaviruses, and parvoviruses. Both rotaviruses and noroviruses are well known gastroenteric pathogens that are of significant global health concern. While rotaviruses, in the family Reoviridae, are the major causative agents of life-threatening diarrhea in children, noroviruses, which belong to the Caliciviridae family, cause epidemic and sporadic cases of acute gastroenteritis across all age groups. Both exhibit enormous genotypic and serotypic diversity. Consistent with this diversity each exhibits strain-dependent variations in the types of glycans they recognize for cell attachment. This chapter reviews the current status of the structural biology of such strain-dependent glycan specificities in these two families of viruses.
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Affiliation(s)
- B V Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, United States; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, United States.
| | - Sreejesh Shanker
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Jae-Mun Choi
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Sue E Crawford
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Sasirekha Ramani
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Rita Czako
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Robert L Atmar
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, United States
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244
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Yu Y, Lasanajak Y, Song X, Hu L, Ramani S, Mickum ML, Ashline DJ, Prasad BVV, Estes MK, Reinhold VN, Cummings RD, Smith DF. Human milk contains novel glycans that are potential decoy receptors for neonatal rotaviruses. Mol Cell Proteomics 2014; 13:2944-60. [PMID: 25048705 DOI: 10.1074/mcp.m114.039875] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Human milk contains a rich set of soluble, reducing glycans whose functions and bioactivities are not well understood. Because human milk glycans (HMGs) have been implicated as receptors for various pathogens, we explored the functional glycome of human milk using shotgun glycomics. The free glycans from pooled milk samples of donors with mixed Lewis and Secretor phenotypes were labeled with a fluorescent tag and separated via multidimensional HPLC to generate a tagged glycan library containing 247 HMG targets that were printed to generate the HMG shotgun glycan microarray (SGM). To investigate the potential role of HMGs as decoy receptors for rotavirus (RV), a leading cause of severe gastroenteritis in children, we interrogated the HMG SGM with recombinant forms of VP8* domains of the RV outer capsid spike protein VP4 from human neonatal strains N155(G10P[11]) and RV3(G3P[6]) and a bovine strain, B223(G10P[11]). Glycans that were bound by RV attachment proteins were selected for detailed structural analyses using metadata-assisted glycan sequencing, which compiles data on each glycan based on its binding by antibodies and lectins before and after exo- and endo-glycosidase digestion of the SGM, coupled with independent MS(n) analyses. These complementary structural approaches resulted in the identification of 32 glycans based on RV VP8* binding, many of which are novel HMGs, whose detailed structural assignments by MS(n) are described in a companion report. Although sialic acid has been thought to be important as a surface receptor for RVs, our studies indicated that sialic acid is not required for binding of glycans to individual VP8* domains. Remarkably, each VP8* recognized specific glycan determinants within a unique subset of related glycan structures where specificity differences arise from subtle differences in glycan structures.
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Affiliation(s)
- Ying Yu
- From the ‡Department of Biochemistry and the National Center for Functional Glycomics, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Yi Lasanajak
- From the ‡Department of Biochemistry and the National Center for Functional Glycomics, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Xuezheng Song
- From the ‡Department of Biochemistry and the National Center for Functional Glycomics, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Liya Hu
- §Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Sasirekha Ramani
- ¶Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030
| | - Megan L Mickum
- From the ‡Department of Biochemistry and the National Center for Functional Glycomics, Emory University School of Medicine, Atlanta, Georgia 30322
| | - David J Ashline
- ‖Glycomics Center, University of New Hampshire, Durham, New Hampshire 03824
| | - B V Venkataram Prasad
- §Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030; ¶Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030
| | - Mary K Estes
- ¶Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030
| | - Vernon N Reinhold
- ‖Glycomics Center, University of New Hampshire, Durham, New Hampshire 03824
| | - Richard D Cummings
- From the ‡Department of Biochemistry and the National Center for Functional Glycomics, Emory University School of Medicine, Atlanta, Georgia 30322;
| | - David F Smith
- From the ‡Department of Biochemistry and the National Center for Functional Glycomics, Emory University School of Medicine, Atlanta, Georgia 30322;
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245
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Santos F, MartÃnez-GarcÃa M, Parro VÃ, Antón J. Microarray tools to unveil viral-microbe interactions in nature. Front Ecol Evol 2014. [DOI: 10.3389/fevo.2014.00031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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246
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Liu G, Neelamegham S. A computational framework for the automated construction of glycosylation reaction networks. PLoS One 2014; 9:e100939. [PMID: 24978019 PMCID: PMC4076241 DOI: 10.1371/journal.pone.0100939] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 06/02/2014] [Indexed: 11/18/2022] Open
Abstract
Glycosylation is among the most common and complex post-translational modifications identified to date. It proceeds through the catalytic action of multiple enzyme families that include the glycosyltransferases that add monosaccharides to growing glycans, and glycosidases which remove sugar residues to trim glycans. The expression level and specificity of these enzymes, in part, regulate the glycan distribution or glycome of specific cell/tissue systems. Currently, there is no systematic method to describe the enzymes and cellular reaction networks that catalyze glycosylation. To address this limitation, we present a streamlined machine-readable definition for the glycosylating enzymes and additional methodologies to construct and analyze glycosylation reaction networks. In this computational framework, the enzyme class is systematically designed to store detailed specificity data such as enzymatic functional group, linkage and substrate specificity. The new classes and their associated functions enable both single-reaction inference and automated full network reconstruction, when given a list of reactants and/or products along with the enzymes present in the system. In addition, graph theory is used to support functions that map the connectivity between two or more species in a network, and that generate subset models to identify rate-limiting steps regulating glycan biosynthesis. Finally, this framework allows the synthesis of biochemical reaction networks using mass spectrometry (MS) data. The features described above are illustrated using three case studies that examine: i) O-linked glycan biosynthesis during the construction of functional selectin-ligands; ii) automated N-linked glycosylation pathway construction; and iii) the handling and analysis of glycomics based MS data. Overall, the new computational framework enables automated glycosylation network model construction and analysis by integrating knowledge of glycan structure and enzyme biochemistry. All the implemented features are provided as part of the Glycosylation Network Analysis Toolbox (GNAT), an open-source, platform-independent, MATLAB based toolbox for studies of Systems Glycobiology.
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Affiliation(s)
- Gang Liu
- Department of Chemical and Biological Engineering, and The NY State Center for Excellence in Bioinformatics and Life Sciences, State University of New York, Buffalo, New York, United States of America
| | - Sriram Neelamegham
- Department of Chemical and Biological Engineering, and The NY State Center for Excellence in Bioinformatics and Life Sciences, State University of New York, Buffalo, New York, United States of America
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247
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Chandrasekaran V, Jacob H, Petersen F, Kathirvel K, Tuczek F, Lindhorst TK. Synthesis and Surface-Spectroscopic Characterization of Photoisomerizable glyco-SAMs on Au(111). Chemistry 2014; 20:8744-52. [DOI: 10.1002/chem.201402075] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Indexed: 12/31/2022]
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248
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Kaus K, Lary JW, Cole JL, Olson R. Glycan specificity of the Vibrio vulnificus hemolysin lectin outlines evolutionary history of membrane targeting by a toxin family. J Mol Biol 2014; 426:2800-12. [PMID: 24862282 DOI: 10.1016/j.jmb.2014.05.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 05/15/2014] [Accepted: 05/18/2014] [Indexed: 01/22/2023]
Abstract
Pore-forming toxins (PFTs) are a class of pathogen-secreted molecules that oligomerize to form transmembrane channels in cellular membranes. Determining the mechanism for how PFTs bind membranes is important in understanding their role in disease and for developing possible ways to block their action. Vibrio vulnificus, an aquatic pathogen responsible for severe food poisoning and septicemia in humans, secretes a PFT called V. vulnificus hemolysin (VVH), which contains a single C-terminal targeting domain predicted to resemble a β-trefoil lectin fold. In order to understand the selectivity of the lectin for glycan motifs, we expressed the isolated VVH β-trefoil domain and used glycan-chip screening to identify that VVH displays a preference for terminal galactosyl groups including N-acetyl-d-galactosamine and N-acetyl-d-lactosamine. The X-ray crystal structure of the VVH lectin domain solved to 2.0Å resolution reveals a heptameric ring arrangement similar to the oligomeric form of the related, but inactive, lectin from Vibrio cholerae cytolysin. Structures bound to glycerol, N-acetyl-d-galactosamine, and N-acetyl-d-lactosamine outline a common and versatile mode of recognition allowing VVH to target a wide variety of cell-surface ligands. Sequence analysis in light of our structural and functional data suggests that VVH may represent an earlier step in the evolution of Vibrio PFTs.
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Affiliation(s)
- Katherine Kaus
- Department of Molecular Biology and Biochemistry, Wesleyan University, 52 Lawn Avenue, Middletown, CT 06459, USA
| | - Jeffrey W Lary
- Biotechnology-Bioservices Center, University of Connecticut, Storrs, CT 06269, USA
| | - James L Cole
- Biotechnology-Bioservices Center, University of Connecticut, Storrs, CT 06269, USA; Department of Molecular and Cell Biology and Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
| | - Rich Olson
- Department of Molecular Biology and Biochemistry, Wesleyan University, 52 Lawn Avenue, Middletown, CT 06459, USA.
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249
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Kamiya Y, Satoh T, Kato K. Recent advances in glycoprotein production for structural biology: toward tailored design of glycoforms. Curr Opin Struct Biol 2014; 26:44-53. [PMID: 24841384 DOI: 10.1016/j.sbi.2014.03.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Revised: 03/20/2014] [Accepted: 03/25/2014] [Indexed: 01/01/2023]
Abstract
Because of the complexity, heterogeneity, and flexibility of the glycans, the structural analysis of glycoproteins has been eschewed until recently, with a few prominent exceptions. This aversion may have branded structural biologists as glycophobics. However, recent technological advancements in glycoprotein expression systems, employing genetically engineered production vehicles derived from mammalian, insect, yeast, and even bacterial cells, have yielded encouraging breakthroughs. The major advance is the active control of glycoform expression of target glycoproteins based on the genetic manipulation of glycan biogenetic pathways, which was previously overlooked, abolished, or considered unmanageable. Moreover, synthetic and/or chemoenzymatic approaches now enable the preparation of glycoproteins with uniform glycoforms designed in a tailored fashion.
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Affiliation(s)
- Yukiko Kamiya
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan; Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Tadashi Satoh
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan; JST, PRESTO, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Koichi Kato
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan; Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan; The Glycoscience Institute, Ochanomizu University, 2-1-1 Ohtsuka, Bunkyo-ku, Tokyo 112-8610, Japan; GLYENCE Co., Ltd., 2-22-8 Chikusa, Chikusa-ku, Nagoya 464-0858, Japan.
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250
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Leney AC, Fan X, Kitova EN, Klassen JS. Nanodiscs and Electrospray Ionization Mass Spectrometry: A Tool for Screening Glycolipids Against Proteins. Anal Chem 2014; 86:5271-7. [DOI: 10.1021/ac4041179] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Aneika C. Leney
- Alberta Glycomics Centre
and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Xuxin Fan
- Alberta Glycomics Centre
and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Elena N. Kitova
- Alberta Glycomics Centre
and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - John S. Klassen
- Alberta Glycomics Centre
and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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