Affinity electrophoresis for the identification and characterization of soluble sugar binding by carbohydrate-binding modules (original) (raw)
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Carbohydrate affinity PAGE for the study of carbohydrate-binding proteins
BioTechniques, 1998
Immobilized neoglycoconjugates covalently cross-linked into a polyacrylamide gel can be used to detect and characterize carbohydrate-binding proteins. The neoglycoconjugates comprise two active groups, saccharide and allyl, located on a poly(2-hydroxyethylacrylamide) backbone. The allyl group cross-links with the polyacrylamide gel matrix, while the saccharide groups are available for specific protein interactions. This neoglycoconjugate gel is prepared as a thin layer within the stacking region of a polyacrylamide gel, and electrophoresis is performed according to native, non-denaturing conditions. Carbohydrate-binding proteins, specific for the immobilized neoglycoconjugates, are thus retarded during electrophoresis, while simultaneously permitting the separation of nonbinding proteins according to size and charge. This new approach can be used to study carbohydrate-binding proteins in the pathology of disease or infection.
Carbohydrate-binding domains: multiplicity of biological roles
Applied Microbiology and Biotechnology, 2010
Insoluble polysaccharides can be degraded by a set of hydrolytic enzymes formed by catalytic modules appended to one or more non-catalytic carbohydrate-binding modules (CBM). The most recognized function of these auxiliary domains is to bind polysaccharides, bringing the biocatalyst into close and prolonged vicinity with its substrate, allowing carbohydrate hydrolysis. Examples of insoluble polysaccharides recognized by these enzymes include cellulose, chitin, β-glucans, starch, glycogen, inulin, pullulan, and xylan. Based on their amino acid similarity, CBMs are grouped into 55 families that show notable variation in substrate specificity; as a result, their biological functions are miscellaneous. Carbohydrate or polysaccharide recognition by CBMs is an important event for processes related to metabolism, pathogen defense, polysaccharide biosynthesis, virulence, plant development, etc. Understanding of the CBMs properties and mechanisms in ligand binding is of vital significance for the development of new carbohydrate-recognition technologies and provide the basis for fine manipulation of the carbohydrate–CBM interactions.
Carbohydrate Binding Modules: Biochemical Properties and Novel Applications
2006
SUMMARY Polysaccharide-degrading microorganisms express a repertoire of hydrolytic enzymes that act in synergy on plant cell wall and other natural polysaccharides to elicit the degradation of often-recalcitrant substrates. These enzymes, particularly those that hydrolyze cellulose and hemicellulose, have a complex molecular architecture comprising discrete modules which are normally joined by relatively unstructured linker sequences. This structure is typically comprised of a catalytic module and one or more carbohydrate binding modules (CBMs) that bind to the polysaccharide. CBMs, by bringing the biocatalyst into intimate and prolonged association with its substrate, allow and promote catalysis. Based on their properties, CBMs are grouped into 43 families that display substantial variation in substrate specificity, along with other properties that make them a gold mine for biotechnologists who seek natural molecular “Velcro” for diverse and unusual applications. In this article, w...
Affinity maturation generates greatly improved xyloglucan-specific carbohydrate binding modules
Molecular evolution of carbohydrate binding modules (CBM) is a new approach for the generation of glycan-specific molecular probes. To date, the possibility of performing affinity maturation on CBM has not been investigated. In this study we show that binding characteristics such as affinity can be improved for CBM generated from the CBM4-2 scaffold by using random mutagenesis in combination with phage display technology. Two modified proteins with greatly improved affinity for xyloglucan, a key polysaccharide abundant in the plant kingdom crucial for providing plant support, were generated. Both improved modules differ from other existing xyloglucan probes by binding to galactose-decorated subunits of xyloglucan. The usefulness of the evolved binders was verified by staining of plant sections, where they performed better than the xyloglucan-binding module from which they had been derived. They discriminated non-fucosylated from fucosylated xyloglucan as shown by their ability to stain only the endosperm, rich in non-fucosylated xyloglucan, but not the integument rich in fucosylated xyloglucan, on tamarind seed sections. We conclude that affinity maturation of CBM selected from molecular libraries based on the CBM4-2 scaffold is possible and has the potential to generate new analytical tools for detection of plant carbohydrates.
Affinity purification of glucose-containing oligosaccharide using a monoclonal antibody
Journal of Immunological Methods, 1984
Binding of a human urinary tetrasaccharide by a mouse monoclonal antibody, 61.1, shows an unusually large dependence upon temperature. Association constants determined by equilibrium dialysis double for each 8°C downward shift in temperature from 37°C (8 x 103 M-1) to 4°C (1.7 x 105 M-i ). Purified 61.1 antibody behaves as a specific temperature-sensitive affinity adsorbent when covalently bound to cyanogen bromide-activated Sepharose or non-covalenfly bound via its Fc portion to staphylococcal protein A-Sepharose. A column containing 72 mg of antibody 61.1 bound to 5 ml of staphylococcal protein A-Sepharose can bind up to 0.52 pmol of reduced tetrasaccharide. The relatively large combining sites of most antibodies may permit chromatographic selection based upon structural features more complex than those recognized by most plant lectins.
Analytical Biochemistry, 2010
Characterization of protein-carbohydrate interactions at the molecular level is important for understanding many glycan-mediated processes. Here we present a method for the identification of glycan ligands of carbohydrate-binding proteins. The glycans released from natural sources are labeled with biotinamidocaproyl hydrazide (BACH) and subsequently fractionated by high-performance liquid chromatography. Glycan fractions are screened for binding to carbohydrate-binding proteins (CBPs) using a microtitration plate binding assay; CBPs are immobilized, BACH-glycan fractions are added, and bound BACH-glycans are detected using alkaline phosphatase-conjugated streptavidin. The glycan structures in binding fractions are studied by (tandem) mass spectrometry, exoglycosidase treatment, and rechromatography, thereby revealing the glycan motifs recognized by the CBPs. Subsequent surface plasmon resonance experiments using a reverse setup with immobilization of the BACH-glycan ligands on streptavidincoated surfaces provide more information on glycan-CBP interactions via association and dissociation curves. The presented method is easy and fast, and the required instrumentation is available in many laboratories. The assay is very sensitive given that both the mass spectrometric analysis and the microtitration plate binding assay can be performed on femtomole amounts of BACH-glycans. This approach should be generally applicable to study and structurally identify carbohydrate ligands of anti-glycan antibodies and lectins.
Nature Biotechnology, 2002
We describe microarrays of oligosaccharides as neoglycolipids and their robust display on nitrocellulose. The arrays are sourced from glycoproteins, glycolipids, proteoglycans, polysaccharides, whole organs, or from chemically synthesized oligosaccharides. We show that carbohydrate-recognizing proteins single out their ligands not only in arrays of homogeneous oligosaccharides but also in arrays of heterogeneous oligosaccharides. Initial applications have revealed new findings, including: (i) among O-glycans in brain, a relative abundance of the Lewis x sequence based on N-acetyllactosamine recognized by anti-L5, and a paucity of the Lewis x sequence based on poly-N-acetyllactosamine recognized by anti-SSEA-1; (ii) insights into chondroitin sulfate oligosaccharides recognized by an antiserum and an antibody (CS-56) to chondroitin sulfates; and (iii) binding of the cytokine interferon-γ (IFN-γ) and the chemokine RANTES to sulfated sequences such as HNK-1, sulfo-Lewis x , and sulfo-Lewis a , in addition to glycosaminoglycans. The approach opens the way for discovering new carbohydrate-recognizing proteins in the proteome and for mapping the repertoire of carbohydrate recognition structures in the glycome.
The carbohydrate-binding module family 20 - Diversity, structure, and function
2009
Starch-active enzymes often possess starch-binding domains (SBDs) mediating attachment to starch granules and other high molecular weight substrates. SBDs are divided into nine carbohydrate-binding module (CBM) families, and CBM20 is the earliest-assigned and best characterized family. High diversity characterizes CBM20s, which occur in starch-active glycoside hydrolase families 13, 14, 15, and 77, and enzymes involved in starch or glycogen metabolism, exemplified by the starch-phosphorylating enzyme glucan, water dikinase 3 from Arabidopsis thaliana and the mammalian glycogen phosphatases, laforins. The clear evolutionary relatedness of CBM20s to CBM21s, CBM48s and CBM53s suggests a common clan hosting most of the known SBDs. This review surveys the diversity within the CBM20 family, and makes an evolutionary comparison with CBM21s, CBM48s and CBM53s, discussing intrafamily and interfamily relationships. Data on binding to and enzymatic activity towards soluble ligands and starch granules are summarized for wild-type, mutant and chimeric fusion proteins involving CBM20s. Noticeably, whereas CBM20s in amylolytic enzymes confer moderate binding affinities, with dissociation constants in the low micromolar range for the starch mimic b-cyclodextrin, recent findings indicate that CBM20s in regulatory enzymes have weaker, low millimolar affinities, presumably facilitating dynamic regulation. Structures of CBM20s, including the first example of a full-length glucoamylase featuring both the catalytic domain and the SBD, are summarized, and distinct architectural and functional features of the two SBDs and roles of pivotal amino acids in binding are described. Finally, some applications of SBDs as affinity or immobilization tags and, recently, in biofuel and in planta bioengineering are presented.
GlycoChip: multiarray for the study of carbohydrate-binding proteins
Lab on a Chip, 2003
Biotinylated glycoconjugates which were designed as oligosaccharides attached to 30 kDa polyacrylamide were coated on a microarray platform XNAonGOLD™, which was developed earlier for an oligonucleotide assay. The specificity of antibodies to carbohydrate antigens was analyzed using the glyco-microarray. Comparison of the obtained results with those of common 96-well plate ELISA completely coincided with the found antibody specificities. However, parameters such as the analytical sensitivity of the method and the amount of biotinylated material coated on the microarray platform proved to be worse than expected.