Structural basis for carbohydrate-binding specificity--a comparative assessment of two engineered carbohydrate-binding modules

Detection, immobilization and purification of carbohydrates can be done using molecular probes that specifically bind to targeted carbohydrate epitopes. Carbohydrate-binding modules (CBMs) are discrete parts of carbohydrate-hydrolyzing enzymes that can be engineered to bind and detect specifically a number of carbohydrates. Design and engineering of CBMs have benefited greatly from structural studies that have helped us to decipher the basis for specificity in carbohydrate-protein interactions. However, more studies are needed to predict which modifications in a CBM would generate probes with predetermined binding properties. In this report, we present the crystal structures of two highly related engineered CBMs with different binding specificity profiles: X-2, which is specific for xylans and the L110F mutant of X-2, which binds xyloglucans and β-glucans in addition to xylans. The structures of the modules were solved both in the apo form and complexed with oligomers of xylose, as well as with an oligomer of glucose in the case of X-2 L110F. The mutation, leucine to phenylalanine, converting the specific module into a cross-reactive one, introduces a crucial hydrogen-π interaction that allows the mutant to retain glucan-based ligands. The cross-reactivity of X-2 L110F is furthermore made possible by the plasticity of the protein, in particular, of residue R142, which permits accommodation of an extra hydroxymethyl group present in cellopentaose and not xylopentaose. Altogether, this study shows, in structural detail, altered protein-carbohydrate interactions that have high impact on the binding properties of a carbohydrate probe but are introduced through simple mutagenesis.     

Aprotinin,a carbohydrate-binding protein

Summary Evidence is presented for a carbohydrate-binding property of aprotinin, which is preserved both in a fluorescein isothiocyanate (FITC) conjugate and a cyanogen bromidelinked Sepharose conjugate of the protein. Both conjugates similarly retain their tryptic and chymotryptic inhibitory properties. The FITC conjugate is shown to be a single species with respect to charge and to molecular weight and shows a specific binding of normal materials containing sialosyl or uronosyl groups, which accords with its histochemical behaviour. The Sepharose-conjugate showed a similar specificity.R.W.S. holds a grant from the Cancer Research Campaign. We thank Dr. G. M. W. Cook for discussion and advice.     

Thermostable carbohydrate-binding modules in affinity chromatography

Affinity chromatography is routinely used mostly on a preparative scale to isolate different biomolecules such as proteins and carbohydrates. To this end a variety of proteins is in common use as ligands. To extend the arsenal of binders intended for separation of carbohydrates, we have explored the use of carbohydrate-binding modules (CBM) in affinity chromatography. The thermostable protein CBM4-2 and two variants (X-6 and A-6) thereof, selected from a newly constructed combinatorial library, were chosen for this study. The CBM4-2 predominantly binds to xylans but also crossreacts with glucose-based oligomers. The two CBM-variants X-6 and A-6 had been selected for binding to xylan and Avicel (a mixture of amorphous and microcrystalline cellulose), respectively. To assess the ability of these proteins to separate carbohydrates, they were immobilized to macroporous microparticulate silica and analyses were conducted at temperatures ranging from 25 to 65 degrees C. With the given set of CBM-variants, we were able to separate cello- and xylo-oligomers under isocratic conditions. The affinities of the CBMs for their targets were weak (in the mM-microM range) and by adjusting the column temperature we could optimize peak resolution and chromatographic retention times. The access to thermostable CBM-variants with diverse affinities and selectivities holds promise to be an efficient tool in the field of affinity chromatography for the separation of carbohydrates.     

Molecular engineering of a thermostable carbohydrate-binding module

Structure–function studies are frequently practiced on the very diverse group of natural carbohydrate-binding modules in order to understand the target recognition of these proteins. We have taken a step further in the study of carbohydrate-binding modules and created variants with novel binding properties by molecular engineering of one such molecule of known 3D-structure. A combinatorial library was created from the sequence encoding a thermostable carbohydrate-binding module, CBM4-2 from a Rhodothermus marinus xylanase, and the phage-display technology was successfully used for selection of variants with specificity towards different carbohydrate polymers (birchwood xylan, Avicel?, ivory nut mannan and recently also xyloglucan), as well as towards a glycoprotein (human IgG4). Our work not only generated a number of binders with properties that would suite a range of biotechnological applications, but analysis the selected binders also helped us to identify residues important for their specificities.     

Molecular engineering of a thermostable carbohydrate-binding module

Structure-function studies are frequently practiced on the very diverse group of natural carbohydrate-binding modules in order to understand the target recognition of these proteins. We have taken a step further in the study of carbohydrate-binding modules and created variants with novel binding properties by molecular engineering of one such molecule of known 3D-structure. A combinatorial library was created from the sequence encoding a thermostable carbohydrate-binding module, CBM4-2 from a Rhodothermus marinus xylanase, and the phage-display technology was successfully used for selection of variants with specificity towards different carbohydrate polymers (birchwood xylan, Avicel™, ivory nut mannan and recently also xyloglucan), as well as towards a glycoprotein (human IgG4). Our work not only generated a number of binders with properties that would suite a range of biotechnological applications, but analysis the selected binders also helped us to identify residues important for their specificities.     

Microglial carbohydrate-binding receptors for neural repair

Microglia are the resident immune cells of the central nervous system (CNS) and perform typical scavenging and innate immune functions. Their capacity to eliminate extracellular aggregates and apoptotic neural material without inflammation is crucial for brain tissue homeostasis and repair. To fulfill these tasks, microglia express a whole set of recognition receptors including toll-like (TLRs), carbohydrate-binding, Fc, complement and cytokine receptors. Receptors recognizing carbohydrate structures are strongly involved in microglial repair function. Carbohydrate-binding receptors can be divided into two major subgroups: the sulfated glycosaminoglycan (SGAG)-binding receptors and the lectins (Siglecs, galectins, selectins). SGAG-binding receptors recognize anionic structural motifs within extended SGAG chains. Siglecs bind to the sialic acid cap of the intact glycocalyx. Other lectin family members such as galectins recognize lactosamine units typically exposed after alteration of the glycocalyx. Dependent on the type of microglial carbohydrate-binding receptors that are stimulated, either a pro-inflammatory cytotoxic or an anti-inflammatory repair-promoting response is evoked. The carbohydrate-binding receptors are also crucial in regulating microglial function such as phagocytosis during neurodegenerative or neuroinflammatory processes. A balance between microglial carbohydrate-binding receptor signaling via an immunoreceptor tyrosine-based activation motif or an immunoreceptor tyrosine-based inhibitory motif is required to polarize microglial cells appropriately so that they create a microenvironment permissive for neural regenerative events.     

Rice lectin: Physico-chemical and carbohydrate-binding properties

Rice seeds contain a 2-acetamido-2-deoxy- -glucose-specific lectin. It has an M_r of 36 000 and is composed of two identical, non-covalently bound subunits of M_r 18 000. Each subunit consists of two disulfide-linked polypeptide chains of M_rs 10 000 and 8000. The lectin activity is highly stable to several chemical denaturants and heat treatment. The lectin interacts with glycoproteins, which have either clustered O-linked oligosaccharides or N-linked oligosaccharides. The N-linked glycoproteins include high -mannose, hybrid and complex biantennary structures.     

CASH--a beta-helix domain widespread among carbohydrate-binding proteins

In this article, we describe a novel, widespread domain (CASH) that is shared by many carbohydrate-binding proteins and sugar hydrolases. This domain occurs in more than 1000 proteins distributed among all three kingdoms of life. The CASH domain is characterized by internal repetitions of glycines and hydrophobic residues that correspond to the repetitive units of a predicted or observed right-handed beta-helix structure of the pectate lyase superfamily.     

Engineered xyloglucan specificity in a carbohydrate-binding module

The field of plant cell wall biology is constantly growing and consequently so is the need for more sensitive and specific probes for individual wall components. Xyloglucan is a key polysaccharide widely distributed in the plant kingdom in both structural and storage tissues that exist in both fucosylated and non-fucosylated variants. Presently, the only xyloglucan marker available is the monoclonal antibody CCRC-M1 that is specific to terminal alpha-1,2-linked fucosyl residues on xyloglucan oligo- and polysaccharides. As a viable alternative to searches for natural binding proteins or creation of new monoclonal antibodies, an approach to select xyloglucan-specific binding proteins from a combinatorial library of the carbohydrate-binding module, CBM4-2, from xylanase Xyn10A of Rhodothermus marinus is described. Using phage display technology in combination with a chemoenzymatic method to anchor xyloglucan to solid supports, the selection of xyloglucan-binding modules with no detectable residual wild-type xylan and beta-glucan-binding ability was achieved.     

Purification and carbohydrate-binding specificity of Agrocybe cylindracea lectin

A lectin was isolated from fruiting bodies of Agrocybe cylindracea by two ion-exchange chromatographies and gel filtration on Toyopearl HW55F. The lectin was homogeneous on polyacrylamide gel electrophoresis and its molecular mass was determined to be 30 000 by gel filtration, and 15 000 by sodium dodecylsulfate polyacrylamide gel electrophoresis, signifying a dimeric protein. Its carbohydrate-binding specificity was investigated both by sugar-hapten inhibition of hemagglutination and by enzyme-linked immunosorbent assay. The inhibition tests showed the affinity of the lectin to be weakly directed toward sialic acid and lactose, and the enhanced affinity toward trisaccharides containing the NeuAcα2,3Galβ-structure. Importantly, the lectin strongly interacted with glycoconjugates containing NeuAcα2,3Galβ1,3GlcNAc-/GalNAc sequences. This revised version was published online in November 2006 with corrections to the Cover Date.     

CBM在多糖底物降解中的应用进展

碳水化合物结合模块(carbohydrate-binding module, CBM)是碳水化合物活性酶的重要组成部分，其功能是识别并结合到特定的多糖底物上以提高催化结构域在底物附近的浓度及催化效率，帮助其更好地降解如纤维素、木聚糖、几丁质和黄原胶等大分子化合物。不同家族的CBM因其来源或结构不同往往会具有不同的底物结合特性。本文从CBM的家族、结构和功能等方面对CBM近年来的研究进行了综述，特别是对其作为融合单元运用到多糖底物的降解和糖苷水解酶改造方面的应用进行了总结。     

Versatile protein microarray based on carbohydrate-binding modules

Non-DNA microarrays, such as protein, peptide and small molecule microarrays, can potentially revolutionize the high-throughput screening tools currently used in basic and pharmaceutical research. However, fundamental obstacles remain that limit their rapid and widespread implementation as an alternative bioanalytical approach. These include the prerequisite for numerous proteins in active and purified form, ineffectual immobilization strategies and inadequate means for quality control of the considerable numbers of multiple reagents. This study describes a simple yet efficient strategy for the production of non-DNA microarrays, based on the tenacious affinity of a carbohydrate-binding module (CBM) for its three-dimensional substrate, i.e., cellulose. Various microarray formats are described, e.g., conventional and single-chain antibody microarrays and peptide microarrays for serodiagnosis of human immunodeficiency virus patients. CBM-based microarray technology overcomes many of the previous obstacles that have hindered fabrication of non-DNA microarrays and provides a technically simple but effective alternative to conventional microarray technology.     

Comparison of the carbohydrate-binding specificities of seven N-acetyl-D-galactosamine-recognizing lectins

Seven plant lectins, Dolichos biflorus agglutinin (DBA), Griffonia simplicifolia agglutinin (GSA, isolectin A4), Helix pomatia agglutinin (HPA), soybean (Glycine max) agglutinin (SBA), Salvia sclarea agglutinin (SSA), Vicia villosa agglutinin (VVA, isolectin B4) and Wistaria floribunda agglutinin (WFA), known to be specific for N-acetyl-D-galactosamine-(GalNAc) bearing glycoconjugates, have been compared by the binding of their radiolabelled derivatives, to eight well-characterized synthetic oligosaccharides immobilized via a spacer on an inert silica matrix (Synsorb). The eight oligosaccharides included the Forssman, the blood group A and the T antigens, as well as alpha GalNAc coupled directly to the support (Tn antigen) and also structures with GalNAc linked alpha or beta to positions 3 or 4 of an unsubstituted Gal. The binding studies clearly distinguished the lectins into alpha GalNAc-specific agglutinins like DBA, GSA and SSA, and lectins which recognize alpha- as well as beta-linked GalNAc residues like HPA, VVA, WFA and SBA. HPA was the only lectin which bound to the beta Gal1----3 alpha GalNAc-Synsorb adsorbent (T antigen) indicating that it also recognizes internal GalNAc residues. Among the alpha GalNAc-specific lectins, DBA strongly recognized blood group A structures while GSA displayed weaker recognition, and SSA bound only slightly to this affinity matrix. In addition, DBA and SSA were able to distinguish between GalNAc linked alpha 1----3 and GalNAc linked alpha 1----4, to the support, the latter being a much weaker ligand. These results were corroborated by the binding of the lectins to biological substrates as determined by their hemagglutination titers with native and enzyme-treated red blood cells carrying known GalNAc determinants, e.g. blood group A, and the Cad and Tn antigens. For SSA, the binding to the alpha GalNAc matrix was inhibited by a number of glycopeptides and glycoproteins confirming the strong preference of this lectin for alpha GalNAc-Ser/Thr-bearing glycoproteins.     

Secretion of the galectin family of mammalian carbohydrate-binding proteins

Galectins are cytosolic proteins that lack any signal sequence for transport into the endoplasmic reticulum and are not glycosylated, although several galectins contain consensus sites for N-glycosylation, indicating that these proteins do not traverse the ER-Golgi network. However, there is abundant evidence for the extracellular localisation of some galectins at cell surfaces, in the extracellular matrix and in cell secretions consistent with other evidence for extracellular roles of galectins as modulators of cell adhesion and signalling. How then are galectins secreted if not through the classical secretory pathway? Do all galectins share the same secretory pathway? Can a particular galectin utilise more than one secretory pathway? If galectins play important extracellular roles how is their secretion regulated in relation to function? These are still largely unanswered questions but recent studies are beginning to give glimpses into some novel aspects of the secretion of these intriguing proteins.     

Selection of a carbohydrate-binding domain with a helix-loop-helix structure

We obtained a novel carbohydrate-binding peptide having a helix-loop-helix scaffold from a random peptide library. The helix-loop-helix peptide library randomized at five amino acid residues was displayed on the major coat protein of a filamentous phage. Affinity selection with a ganglioside, Galbeta1-3GalNAcbeta1-4(Neu5Acalpha2-3)Galbeta1-4Glcbeta1-1'Cer (GM1), gave positive phage clones. Surface plasmon resonance spectroscopy showed that a corresponding 35-mer synthetic peptide had high affinity for GM1 with a dissociation constant of 0.24 microM. This peptide preferentially binds to GM1 rather than asialo GM1 and GM2, suggesting that a terminal galactose and sialic acid are required for the binding as for cholera toxin. Circular dichroism spectroscopic studies indicated that a helical structure is important for the affinity and specificity. Furthermore, alanine scanning at randomized positions showed that arginine and phenylalanine play an especially important role in the recognition of carbohydrates. Such a de novo helix-loop-helix peptide would be available for the design of carbohydrate-binding proteins.     

Identification of a new carbohydrate-binding site of influenza virus

It has recently been shown that the influenza virus can specifically bind the residue of a nonsialylated sulfated oligosaccharide Gal(6SO₃H)β1-4GlcNAcβ (6’SLacNAc). To identify by photoaffinity labeling the virion component that binds 6’SLacNAc, we synthesized a carbohydrate probe containing a ¹²⁵I labeled diazocyclopentadien-2-yl carbonyl group as an aglycone. According to the electrophoretic data, the labeled areas corresponded to a large hemagglutinin subunit, a nucleocapsid protein, and neuraminidase (NA). Probing in the presence of an excess of 6’SLacNAcβ-OCH₂CH₂NHAc glycoside resulted in redistribution of the labeling intensity, with the maximum inhibition being observed for NA. The data obtained indicate that NA is a viral 6’SLacNAc-binding protein.     

Selection of carbohydrate-binding cell phenotypes using oligosaccharide-coated magnetic particles

Neoglycoconjugate coated magnetic beads were assessed for theirability to selectively isolate human cells with known anti-carbohydratereactivity. Four lung cancer cell lines, NCI-H146, NCI-N417D,SKMES-1, EKVX; two acute lymphoblastic leukemia lines, MOLT-4and CCRF-CEM; and the anti- Le^c (isolactosamine) hybridoma,LU-BCRU-G7, were tested. The neoglycoconjugates (biotinylatedpseudopolysaccharides) bound uniformly to streptavidin coatedmagnetic beads as demonstrated by FTTC labeled lectin. Streptavidinbeads alone did not bind to any of the cell types. The anti-Le^c hybridoma cell line, LU BCRU-G7, demonstrated binding onlyto Le^c pseudopolysaccharide coated magnetic beads. Subsequentincubation in the presence of unlabeled pseudopolysaccharideresulted in the release of the beads from the cell surface.Although there was some heterogeneity within the individuallung and leukemic cell lines, positive cells showed strong rosetteformation with the coated beads. The A_dl disaccharide coatedbeads showed binding in all four lung cancer cell lines, withthe Le^c and the H (type1) pseudopolysaccharide-bead conjugatesonly reactive in the N417 and H146 SCLC lines. The range ofL-selectin ligand-coated beads were all successful in bindingto the acute lymphoblastic leukemia cell lines MOLT4 and CCRF-CEM.This approach provides a versatile model for the study of cell-surfacecarbohydrate interactions that should find application in manyareas of cell biology. carbohydrate-coated magnetic beads cell selec-tion lectins neoglycoconjugates pseudopolysaccharides     

Recognition of cellooligosaccharides by a family 28 carbohydrate-binding module

The crystal structures of a carbohydrate-binding module (CBM) family 28 domain of endoglucanase Cel5A from Clostridium josui have been determined in ligand-free and complex forms with cellobiose, cellotetraose, and cellopentaose as the first complex structures of this family. In the cleft of a β-sandwich fold, the ligands are recognized by stacking interactions and hydrogen bonds. Conformations of the bound cellooligosaccharides are similar to those in crystals and solution but clearly different from the cellulose structure. Interestingly, the glucan chain bound on CBM28 is in the opposite direction of that bound to CBM17, although these families share significant structural similarity.