Thermodynamic binding studies of lectins from the diocleinae subtribe to deoxy analogs of the core trimannoside of asparagine-linked oligosaccharides

Applying Pose Clustering and MD Simulations To Eliminate False Positives in Molecular Docking

In this work, we developed a computational protocol that employs multiple molecular docking experiments, followed by pose clustering, molecular dynamic simulations (10 ns), and energy rescoring to produce reliable 3D models of antibody-carbohydrate complexes. The protocol was applied to 10 antibody-carbohydrate co-complexes and three unliganded (apo) antibodies. Pose clustering significantly reduced the number of potential poses. For each system, 15 or fewer clusters out of 100 initial poses were generated and chosen for further analysis. Molecular dynamics (MD) simulations allowed the docked poses to either converge or disperse, and rescoring increased the likelihood that the best-ranked pose was an acceptable pose. This approach is amenable to automation and can be a valuable aid in determining the structure of antibody-carbohydrate complexes provided there is no major side chain rearrangement or backbone conformational change in the H3 loop of the CDR regions. Further, the basic protocol of docking a small ligand to a known binding site, clustering the results, and performing MD with a suitable force field is applicable to any protein ligand system.

Sialyl Lewis(x): a "pre-organized water oligomer"?

Organized and released: Sialyl Lewis(x) (sLe(x)) represents a "pre-organized water oligomer", that is, a surrogate for clustered water molecules attached to a scaffold. The impetus for sLe(x) binding to E-selectin is shown to be the high degree of pre-organization allowing an array of directed hydrogen bonds, and the entropic benefit of the release of water molecules from the large binding interface to bulk water (see picture).

The D-galactose specific lectin of field bean (Dolichos lablab) seed binds sugars with extreme negative cooperativity and half-of-the-sites binding

The field bean (Dolichos lablab) lectin designated as PPO-haemagglutinin (DLL-II) is bifunctional, exhibiting both polyphenol oxidase and haemagglutinating activity. The lectin is unusual in that it binds galactose (Gal), lactose (Lac) and N-acetylgalactosamine (GalNAc) only in the presence of (NH₄)₂SO₄ and exhibits negative cooperativity and half-of-the-sites binding. Circular dichroism, isothermal titration calorimetry and fluorescence quenching were used to assess the sugar binding in the presence of (NH₄)₂O₄. Comparison of the near-UV CD spectra with and without bound sugar revealed ligand induced conformational changes. The intrinsic fluorescence quenching data indicate that DLL-II exhibits weak binding to Gal in the presence of (NH₄)₂SO₄ with a stoichiometry of one bound ligand per dimer. ITC data fitted using a two sets of sites binding model presented a similar picture. The K(a)'s for Gal, Lac and GalNAc in the presence of (NH₄)₂SO₄ were 0.16±0.002, 0.21±0.004 and 8.45±0.78 (×10⁻³) M⁻¹ respectively. The Hill plot for the binding of these sugars to DLL-II was curvilinear with a tangent slope <1.0 indicating negative cooperativity. DLL-II thus exhibits half-of-the-site binding, an extreme form of negative cooperativity in which the second ligand does not bind at all. This is the first report of a legume lectin, exhibiting half-of-the-sites binding.

Protein crystal content analysis by mass spectrometry and preliminary X-ray diffraction of a lectin from Canavalia grandiflora seeds with modulatory role in inflammation

RATIONALE

Lectins are a family of proteins capable of deciphering the glycan code. Several authors have published works about crystallization and mass spectrometry analyses of ConA-like lectins. However, mass spectrometry has never been used to characterize lectin crystal content. In this study, Canavalia grandiflora lectin (ConGF), a ConA-like lectin, was crystallized, part of its primary structure sequenced and the pro-inflammatory activity evaluated. In addition, the crystal content was analyzed by mass spectrometry.

METHODS

ConGF was crystallized in the presence of X-Man by hanging-drop vapor diffusion at 293 K and the protein crystal content was analyzed by electrospray ionization in a SYNAPT HDMS mass spectrometer. Partial sequence was obtained by protein digestion with several proteolytic enzymes and the peptides sequenced by liquid chromatography/tandem mass spectrometry (LC/MS/MS). The pro-inflammatory potential of ConGF was also evaluated in the model of rat paw edema.

RESULTS

The protein crystals consist of mature α chain and β and γ fragments measuring 25 612 ± 2 Da, 12 962 ± 2 Da and 12 667 ± 2 Da, respectively. The crystal belongs to the orthorhombic space group I222 (unit cell parameters: a = 67.70, b = 55.90, c = 107.46 Å), assuming a monomer in the asymmetric unit. The solvent content was calculated as 43.50% and the protein content as 2.5 µg. Furthermore, a significant part of the primary structure (65.8%) was determined by mass spectrometry.

CONCLUSIONS

As far as we know this is the first report of lectin crystal content characterized by mass spectrometry. Like other ConA-like lectins, GonGF induced paw edema however differing in potency and duration. The observed pro-inflammatory activity suggests that ConGF might be a useful tool in the study of inflammation processes and structure/function relationships.

cDNA cloning and 1.75 A crystal structure determination of PPL2, an endochitinase and N-acetylglucosamine-binding hemagglutinin from Parkia platycephala seeds

Parkia platycephala lectin 2 was purified from Parkia platycephala (Leguminosae, Mimosoideae) seeds by affinity chromatography and RP-HPLC. Equilibrium sedimentation and MS showed that Parkia platycephala lectin 2 is a nonglycosylated monomeric protein of molecular mass 29 407+/-15 Da, which contains six cysteine residues engaged in the formation of three intramolecular disulfide bonds. Parkia platycephala lectin 2 agglutinated rabbit erythrocytes, and this activity was specifically inhibited by N-acetylglucosamine. In addition, Parkia platycephala lectin 2 hydrolyzed beta(1-4) glycosidic bonds linking 2-acetoamido-2-deoxy-beta-D-glucopyranose units in chitin. The full-length amino acid sequence of Parkia platycephala lectin 2, determined by N-terminal sequencing and cDNA cloning, and its three-dimensional structure, established by X-ray crystallography at 1.75 A resolution, showed that Parkia platycephala lectin 2 is homologous to endochitinases of the glycosyl hydrolase family 18, which share the (betaalpha)8 barrel topology harboring the catalytic residues Asp125, Glu127, and Tyr182.

Synthesis of monodeoxy analogues of the trisaccharide α-d-Glcp-(1→3)-α-d-Manp-(1→2)-α-d-ManpOMe recognised by Calreticulin/Calnexin

Six (3,4,4',6',3'' or 6'')-monodeoxy analogues of the title trisaccharide (1-6) have been prepared utilising monodeoxy monosaccharide precursors. The reducing end deoxy derivatives were synthesised by N-iodosuccinimide/silver trifluoromethanesulfonate (NIS/AgOTf)-promoted couplings of a common disaccharide thioglycoside donor 10 to suitably protected monodeoxy acceptors 9 and 12, affording trisaccharides, which after deprotection yielded target structures 1 and 2. The non-reducing end deoxy derivatives could similarly be produced by halide-assisted glycosylations of a common disaccharide acceptor 17 with monodeoxy glycosyl bromide donors (obtained from thioglycosides 18 and 20) to yield, after removal of protecting groups, target trisaccharides 3 and 4. The analogues with the deoxy function in the middle mannose residue, were obtained through orthogonal halide-assisted coupling of tetrabenzyl-glucopyranosyl bromide to monodeoxy thioglycoside acceptors to give thioglycoside disaccharides, which subsequently were used as donors in NIS/AgOTf-promoted couplings to a common 2-hydroxy-mannose acceptor 15 to afford trisaccharides; deprotection yielded the final target compounds 5 and 6.

Crystal structure of a lectin from Canavalia maritima (ConM) in complex with trehalose and maltose reveals relevant mutation in ConA-like lectins

The crystal structure of Canavalia maritima lectin (ConM) complexed with trehalose and maltose revealed relevant point mutations in ConA-like lectins. ConM with the disaccharides and other ConA-like lectins complexed with carbohydrates demonstrated significant differences in the position of H-bonds. The main difference in the ConM structure is the replacement of Pro202 by Ser202, a residue that promotes the approximation of Tyr12 to the carbohydrate-binding site. The O-6' of the second glucose ring in maltose interacts with Tyr12, while in trehalose the interaction is established by the O-2' and Tyr12, explaining the higher affinity of ConM for disaccharides compared to monosaccharides.

Embryotoxic activity and differential binding of plant-derived carbohydrate-recognizing proteins towards the sea urchin embryo cells

The embryotoxic activity and differential binding of plant-derived carbohydrate-recognizing proteins on sea urchin (Lytechinus variegatus) embryo cells was investigated. IC50 doses for toxicity on larvae development varied from 0.6 up to 96.3 microg ml(-1) and these effects were largely reversed by previously heating the proteins. Changes in the glycoconjungate status of the cell surface were assessed by time-course binding of the proteins during embryogenesis according to their carbohydrate-binding specificity. Glucose/mannose binding-proteins bound embryo cells at the same stage of development, at a similar stage to the N-acetylglucosamine/N-acetylneuraminic acid binding-protein (WGA) and earlier than galactose specific ones. FITC-conjugates of these proteins confirmed the above results and revealed the presence of specific and differential receptors for them. Inhibition assays using inhibitory glycoproteins significantly diminished the labelled patterns of FITC-conjugates. In conclusion, the assayed proteins exhibited embryotoxicity and their binding requirements were useful for following changes in the pattern of cell surface glycoconjugates on embryo cells of sea urchin. This property could be useful in analyzing other cell types.

Lectins: tools for the molecular understanding of the glycocode

Recent progress in glycobiology has revealed that cell surface oligosaccharides play an essential role in recognition events. More precisely, these saccharides may be complexed by lectins, carbohydrate-binding proteins other than enzymes and antibodies, able to recognise sugars in a highly specific manner. The ubiquity of lectin-carbohydrate interactions opens enormous potential for their exploitation in medicine. Therefore, extraordinary effort is made into the identification of new lectins as well as into the achievement of a deep understanding of their functions and of the precise mechanism of their association with specific ligands. In this review, a summary of the main features of lectins, particularly those found in legumes, will be presented with a focus on the mechanism of carbohydrate-binding. An overview of lectin-carbohydrate interactions will also be given, together with an insight into their energetics. In addition, therapeutic applications of lectins will be discussed.

Energetics of 5-bromo-4-chloro-3-indolyl-alpha-D-mannose binding to the Parkia platycephala seed lectin and its use for MAD phasing

Parkia platycephala belongs to the most primitive group of Leguminosae plants. Its seed lectin is made up of three homologous beta-prism repeats and exhibits binding specificity for mannose/glucose. The properties of the association between the lectin from P. platycephala seeds and monosaccharide ligands were analysed by isothermal titration calorimetry and surface plasmon resonance. The results are consistent with the lectin bearing three thermodynamically identical binding sites for mannose/glucose per monomer with dissociation constants in the millimolar range. Binding of each ligand by the lectin is enthalpically driven. Crystals have been obtained of the lectin in complex with a brominated derivative of mannose (5-bromo-4-chloro-3-indolyl-alpha-D-mannose), which were suitable for deriving an electron-density map by MAD phasing. In agreement with the thermodynamic data, six Br atoms were found in the asymmetric unit of the monoclinic P2(1) crystals, which contained two P. platycephala lectin molecules. The availability of other Br derivatives of monosaccharides (glucose, galactose, fucose) may make this strategy widely useful for structure elucidation of novel lectins or when (as in the case of the P. platycephala lectin) molecular-replacement methods fail.

Thermodynamic, kinetic, and electron microscopy studies of concanavalin A and Dioclea grandiflora lectin cross-linked with synthetic divalent carbohydrates

The jack bean lectin concanavalin A (ConA) and the Dioclea grandiflora lectin (DGL) are highly homologous Man/Glc-specific members of the Diocleinae subtribe. Both lectins bind, cross-link, and precipitate with carbohydrates possessing multiple terminal nonreducing Man residues. The present study investigates the binding and cross-linking interactions of ConA and DGL with a series of synthetic divalent carbohydrates that possess spacer groups with increasing flexibility and length between terminal alpha-mannopyranoside residues. Isothermal titration microcalorimetry was used to determine the thermodynamics of binding of the two lectins to the divalent analogs, and kinetic light scattering and electron microscopy studies were used to characterize the cross-linking interactions of the lectins with the carbohydrates. The results demonstrated that divalent analogs with flexible spacer groups between the two terminal Man residues possess higher affinities for the two lectins as compared with those with inflexible spacer groups. Furthermore, despite their high degree of homology, ConA and DGL exhibit differences in their kinetics of cross-linking and precipitation with the divalent analogs. Electron microscopy shows the loss of organized cross-linked lattices of the two lectins with analogs possessing increased distance between the terminal Man residues. The loss of lattice patterns with the analogs is distinct for each lectin. These results have important implications for the interactions of lectins with multivalent carbohydrate receptors in biological systems.

Isolation of two novel mannan- and L-fucose-binding lectins from the green alga Enteromorpha prolifera: biochemical characterization of EPL-2

EPL-1 and EPL-2 represent lectins isolated from the green alga Enteromorpha prolifera. Both lectins are 20- to 22-kDa single-chain, nonglycosylated proteins. N-terminal sequence analysis of peptides representing over 70% of their primary structures shows that EPL-1 and EPL-2 represent novel proteins. Sedimentation-diffusion equilibrium experiments showed that EPL-1 and EPL-2 had average apparent molecular masses of 60000+/-6000 Da (EPL-1) and 59500+/-3000 Da (EPL-2), indicating that EPL-1 and EPL-2 have a tendency to self-associate into higher order aggregates, possibly homodimers and homotetramers, in equilibrium. The carbohydrate-binding specificity of EPL-2 was studied by enzyme-linked lectin assay and intrinsic fluorescence measurements. The results show that the combining site of EPL-2 is capable of accommodating both D-mannose and L-fucose, which share the conformation of the hydroxyl groups at positions 2 (axial) and 4 (equatorial), and includes subsites for the substituents at O1 and for branched mannose residues.

Evidence of an endogenous lectin receptor in seeds of the legume Cratylia floribunda

Cratylia floribunda seeds were ground and the clean crude saline extract was fractionated into albumin, globulin, prolamin, acidic and basic glutelin protein fractions. These protein fractions were examined for the presence of an endogenous lectin receptor by SDS-polyacrylamide gel electrophoresis, western blot, affinity chromatography on a Sepharose 4B-Cratylia floribunda (CFL) lectin column and kinetic analysis in real time by surface plasmon resonance (SPR). Prolamin was the richest protein fraction although very poor in haemagglutinating activity. Basic glutelin was far the less interesting fraction for lectin activity and protein content, even though this fraction contains considerable amounts of carbohydrates. Lectin was present in all protein fractions as estimated by haemagglutinating assays but basic glutelins were almost devoid of lectin activity. Except for prolamins, protein bands were detected by SDS-PAGE in all other fractions. Western blot using digoxigenin labelled Con A revealed a single band in the albumin, globulin, acidic and basic glutelin fractions, which specifically interacted with ConA. This band migrated exactly at the same position in such fractions and seemed to be more important in the globulins. Affinity chromatography of the protein fractions on a Sepharose-CFL column yielded a peak, which was only recovered after elution with acidic buffered solution or with an alpha-D-mannose solution and the monosaccharide was recognized by the lectin. These results were fully corroborated by real time interaction of immobilized CFL with the different soluble protein fractions suggesting the presence of a lectin receptor within albumins, globulins and basic glutelins. As a whole, the results suggest that the lectin from Cratylia floribunda recognizes a soluble endogenous glycosylated receptor through an interaction mediated by its carbohydrate-binding site.

The amino-acid sequence of the glucose/mannose-specific lectin isolated from Parkia platycephala seeds reveals three tandemly arranged jacalin-related domains

A mannose/glucose-specific lectin was isolated from seeds of Parkia platycephala, the most primitive subfamily of Leguminosae plants. The molecular mass of the purified lectin determined by mass spectrometry was 47 946 +/- 6 Da (by electrospray ionization) and 47 951 +/- 9 Da (by matrix-assisted laser-desoption ionization). The apparent molecular mass of the lectin in solutions of pH in the range 4.5-8.5 determined by analytical ultracentrifugation equilibrium sedimentation was 94 +/- 3 kDa, showing that the protein behaved as a non-pH-dependent dimer. The amino-acid sequence of the Parkia lectin was determined by Edman degradation of overlapping peptides. This is the first report of the primary structure of a Mimosoideae lectin. The protein contained a blocked N-terminus and a single, nonglycosylated polypeptide chain composed of three tandemly arranged homologous domains. Each of these domains shares sequence similarity with jacalin-related lectin monomers from Asteraceae, Convolvulaceae, Moraceae, Musaceae, Gramineae, and Fagaceae plant families. Based on this homology, we predict that each Parkia lectin repeat may display a beta prism fold similar to that observed in the crystal structure of the lectin from Helianthus tuberosus. The P. platycephala lectin also shows sequence similarity with stress- and pathogen-upregulated defence genes of a number of different plants, suggesting a common ancestry for jacalin-related lectins and inducible defence proteins.

Crystal structure of native and Cd/Cd-substituted Dioclea guianensis seed lectin. A novel manganese-binding site and structural basis of dimer-tetramer association

Diocleinae legume lectins are a group of oligomeric proteins whose subunits display a high degree of primary structure and tertiary fold conservation but exhibit considerable diversity in their oligomerisation modes. To elucidate the structural determinants underlaying Diocleinae lectin oligomerisation, we have determined the crystal structures of native and cadmium-substituted Dioclea guianensis (Dguia) seed lectin. These structures have been solved by molecular replacement using concanavalin (ConA) coordinates as the starting model, and refined against data to 2.0 A resolution. In the native (Mn/Ca-Dguia) crystal form (P4(3)2(1)2), the asymmetric unit contains two monomers arranged into a canonical legume lectin dimer, and the tetramer is formed with a symmetry-related dimer. In the Cd/Cd-substituted form (I4(1)22), the asymmetric unit is occupied by a monomer. In both crystal forms, the tetrameric association is achieved by the corresponding symmetry operators. Like other legume lectins, native D. guianensis lectin contains manganese and calcium ions bound in the vicinity of the saccharide-combining site. The architecture of these metal-binding sites (S1 and S2) changed only slightly in the cadmium/cadmium-substituted form. A highly ordered calcium (native lectin) or cadmium (Cd/Cd-substituted lectin) ion is coordinated at the interface between dimers that are not tetrameric partners in a similar manner as the previously identified Cd(2+) in site S3 of a Cd/Ca-ConA. An additional Mn(2+) coordination site (called S5), whose presence has not been reported in crystal structures of any other homologous lectin, is present in both, the Mn/Ca and the Cd/Cd-substituted D. guianensis lectin forms. On the other hand, comparison of the primary and quaternary crystal structures of seed lectins from D. guianensis and Dioclea grandiflora (1DGL) indicates that the loop comprising residues 117-123 is ordered to make interdimer contacts in the D. grandiflora lectin structure, while this loop is disordered in the D. guianensis lectin structure. A single amino acid difference at position 131 (histidine in D. grandiflora and asparagine in D. guianensis) drastically reduces interdimer contacts, accounting for the disordered loop. Further, this amino acid change yields a conformation that may explain why a pH-dependent dimer-tetramer equilibrium exists for the D. guianensis lectin but not for the D. grandiflora lectin.

Glycohistochemistry: the why and how of detection and localization of endogenous lectins

The central dogma of molecular biology limits the downstream flow of genetic information to proteins. Progress from the last two decades of research on cellular glycoconjugates justifies adding the enzymatic production of glycan antennae with information-bearing determinants to this famous and basic pathway. An impressive variety of regulatory processes including cell growth and apoptosis, folding and routing of glycoproteins and cell adhesion/migration have been unravelled and found to be mediated or modulated by specific protein (lectin)-carbohydrate interactions. The conclusion has emerged that it would have meant missing manifold opportunities not to recruit the sugar code to cellular information transfer. Currently, the potential for medical applications in anti-adhesion therapy or drug targeting is one of the major driving forces fuelling progress in glycosciences. In histochemistry, this concept has prompted the introduction of carrier-immobilized carbohydrate ligands (neoglycoconjugates) to visualize the cells' capacity to be engaged in oligosaccharide recognition. After their isolation these tissue lectins will be tested for ligand analysis. Since fine specificities of different lectins can differ despite identical monosaccharide binding, the tissue lectins will eventually replace plant agglutinins to move from glycan profiling and localization to functional considerations. Namely, these two marker types, i.e. neoglycoconjugates and tissue lectins, track down accessible binding sites with relevance for involvement in interactions in situ. The documented interplay of synthetic organic chemistry and biochemistry with cyto- and histochemistry nourishes the optimism that the application of this set of innovative custom-prepared tools will provide important insights into the ways in which glycans can act as hardware in transmitting information during normal tissue development and pathological situations.