Data bank of three-dimensional structures of disaccharides: Part II,N-acetyllactosaminic type N-glycans. Comparison with the crystal structure of a biantennary octasaccharide

Delage, Marie-Madeleine; Bourne, Yves; Cambillau, Christian; Pérez, Serge

doi:10.1007/bf00769847

Cited by 75 publications

(71 citation statements)

References 37 publications

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“…Although the free ligands, on the whole, exhibit greater flexibility about the glycosidic bonds, the average angles are in good agreement with the lowest energy conformations of disaccharide fragments. 55 This indicates that these ligands are bound in low energy conformations, with the largest effect being a decrease in the deviations from these averages. The normal mode analyses show that each ligand pays an entropic penalty upon binding, which is roughly proportional to the number of atoms in the ligand.…”

Section: Discussionmentioning

confidence: 99%

Molecular dynamics simulations of galectin‐1‐oligosaccharide complexes reveal the molecular basis for ligand diversity

et al. 2003

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Galectin-1 is a member of a protein family historically characterized by its ability to bind carbohydrates containing a terminal galactosyl residue. Galectin-1 is found in a variety of mammalian tissues as a homodimer of 14.5-kDa subunits. A number of developmental and regulatory processes have been attributed to the ability of galectin-1 to bind a variety of oligosaccharides containing the Gal-β-(1,4)-GlcNAc (LacNAc II ) sequence. To probe the origin of this permissive binding, solvated molecular dynamics (MD) simulations of several representative galectin-1-ligand complexes have been performed. Simulations of structurally defined complexes have validated the computational approach and expanded upon data obtained from X-ray crystallography and surface plasmon resonance measurements. The MD results indicate that a set of anchoring interactions between the galectin-1 carbohydrate recognition domain (CRD) and the LacNAc core are maintained for a diverse set of ligands and that substituents at the nonreducing terminus of the oligosaccharide extend into the remainder of a characteristic surface groove. The anionic nature of ligands exhibiting relatively high affinities for galectin-1 implicates electrostatic interactions in ligand selectivity, which is confirmed by a generalized Born analysis of the complexes. The results suggest that the search for a single endogenous ligand or function for this lectin may be inappropriate and instead support a more general role for galectin-1, in which the lectin is able to crosslink heterogeneous oligosaccharides displayed on a variety of cell surfaces. Such binding promiscuity provides an explanation for the variety of adhesion phenomena mediated by galectin-1.

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Section: Discussionmentioning

confidence: 99%

Molecular dynamics simulations of galectin‐1‐oligosaccharide complexes reveal the molecular basis for ligand diversity

et al. 2003

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“…However, van der Waals interactions between some of the methoxyl groups and hydrophobic amino acids may make an important contribution to the binding energy and partially explain why, when the methoxyl group population or DE decreases below 45-55%, the enzymatic activity drops very abruptly. In the case of protein-protein interactions, the stabilization from a hydrophobic contact has been estimated to be about half of that produced by complementary polar groups (27), whereas in the case of protein-carbohydrate interactions (28), the favorable effects of electrostatic and van der Waals contacts have been considered to be similar. From the afore-going discussion, it can be postulated that a combination of polar and nonpolar interactions probably contributes to pectin-PME binding.…”

Section: Discussionmentioning

confidence: 99%

Investigation of the Action Patterns of Pectinmethylesterase Isoforms through Kinetic Analyses and NMR Spectroscopy

Catoire¹,

Pierron²,

Morvan³

et al. 1998

Journal of Biological Chemistry

142

110

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Well characterized pectin samples were incubated with cell wall-bound and -solubilized pure isoforms of pectinmethylesterase from mung bean hypocotyls (Vigna radiata). Both enzyme activity and average product structure were determined at intervals along the deesterification pathway at pH 5.6 and 7.6. The latter analyses were performed by 13 C NMR spectroscopy, and the degree of esterification was probed by both 13 C NMR and potentiometric measurements. A dichotomy was observed in the behavior of the ␣ and ␥ isoforms when compared with that of the ␤ isoenzyme. Ideal blockwise deesterification mechanisms reproduced the experimental average structures (methylester distribution) throughout the course of the reaction. In the case of the ␣ and ␥ isoforms, a single chain mechanism associated with a free carboxyl group at the second nearest neighbor position could be postulated at pH 5.6, whereas some multiple attack character was required to reproduce the data at pH 7.6. Several mechanisms that differed from the preceding ones were compatible with the data for the ␤ isoform at the two pH values. Both the nature of the polysaccharides produced in these reactions and the role of pectinmethylesterase in the cell wall-stiffening process along the growth gradient are discussed.Pectins that represent around 30% of the primary plant cell walls play a key role in plant physiology as well as in plant pathology. The general structure of pectic polymers consists of homogalacturonan linear chains (smooth regions) interspersed with highly branched galacturonic chains (hairy regions). Some of the galacturonic residues linked by ␣-1,4 glycosidic bonds are methyl-esterified at the carboxyl group. The degree of methylesterification (DE) 1 varies greatly depending on the plant organ and the degree of differentiation of the cells. Young, plastic cell walls are generally characterized by a high content of highly methylated pectin that decreases in parallel with the loss of extensibility of the walls, whereas the amount of acidic residues increases (1-3). Moreover, the balance between high and low methylated pectins varies inside the wall of a single cell (4) generating microdomains. Not only the number but also the distribution of free, unesterified galacturonate carboxyl groups within the galacturonan regions will control the gellforming capacity of the pectin and thereby the porosity and the extensibility of the apoplasm (5, 6). It is commonly accepted that the polygalacturonic backbone is polymerized in the cisGolgi cisternae, methylesterified in the medial-Golgi, substituted with side chains in the trans-Golgi, and exported to the cell walls as a highly methylated polygalacturonan (7). At a later stage, it is deesterified in muro by cell wall pectinmethylesterases (PMEs). Many proteins exhibiting PME activity have been purified, and their biochemical features such as molecular weight, optimal pH, pI, and substrate specificity have been established (8). In some cases, the corresponding genes have also been cloned and sequenced (9 -11...

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“…The conformations of all of the glycosidic linkages lie in energy minima that were identified previously in energy maps (44,45). In solution, the most flexible one would be the ␣Man1-6Man linkage that could generate several different overall shapes of the biantennary N-glycan.…”

Section: Crystal Structure Of C Orbicularis Lectinmentioning

confidence: 59%

High Affinity Interaction between a Bivalve C-type Lectin and a Biantennary Complex-type N-Glycan Revealed by Crystallography and Microcalorimetry

Gourdine

Cioci

Miguet

et al. 2008

Journal of Biological Chemistry

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Codakine is an abundant 14-kDa mannose-binding C-type lectin isolated from the gills of the sea bivalve Codakia orbicularis. Binding studies using inhibition of hemagglutination indicated specificity for mannose and fucose monosaccharides. Further experiments using a glycan array demonstrated, however, a very fine specificity for N-linked biantennary complex-type glycans. An unusually high affinity was measured by titration microcalorimetry performed with a biantennary Asn-linked nonasaccharide. The crystal structure of the native lectin at 1.3 Å resolution revealed a new type of disulfide-bridged homodimer. Each monomer displays three intramolecular disulfide bridges and contains only one calcium ion located in the canonical binding site that is occupied by a glycerol molecule. The structure of the complex between Asn-linked nonasaccharide and codakine has been solved at 1.7 Å resolution. All residues could be located in the electron density map, except for the capping ␤1-4-linked galactosides. The ␣1-6-linked mannose binds to calcium by coordinating the O3 and O4 hydroxyl groups. The GlcNAc moiety of the ␣1,6 arm engages in several hydrogen bonds with the protein, whereas the GlcNAc on the other antenna is stacked against Trp 108 , forming an extended binding site. This is the first structural report for a bivalve lectin.Lectins are multivalent carbohydrate-binding proteins that play important roles in the social life of cells. A growing repertoire of lectins has been identified in invertebrates (1), where these molecules are involved in self/nonself recognition (2). For example, lectins play a role in aggregation mechanisms in corals and sponges (3) or in sperm-egg recognition in oysters (4). Lectin mediation of symbiosis with algae or bacteria has been observed in coral (5) and nematodes (6). Nevertheless, the most common function assessed for lectins in marine invertebrates is their role in innate immunity by specific binding of polysaccharide-coated pathogenic bacteria (7,8).Different lectins have been identified in bivalves and they most frequently belong to the C-type lectin family. Proteins from this group of calcium-dependent lectins have been reported in oysters (9, 10), scallops (11), and clams (12, 13). C-type lectins are characterized by a carbohydrate recognition domain (CRD) 3 with a conserved fold and the involvement of a calcium ion in carbohydrate binding (14). The crystal structure of mannose-binding protein was the first one to be described (15). The CRD belongs to a larger family sharing a common fold and is referred to as the C-type lectin-like domain (16).Codakine is a 14-kDa C-type lectin purified from the gill of the tropical clam Codakia orbicularis (Linné 1758) by affinity chromatography on a mannose-agarose column (17). It forms homodimers and heterodimers with isoforms 1 (NCBI accession number AAX19697) and 2 (NCBI accession number ABQ40396) (13). A 19-amino acid peptide signal suggests that the lectin travels through a secretory pathway. The 129-amino acid sequence of the mature ...

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Data bank of three-dimensional structures of disaccharides: Part II,N-acetyllactosaminic type N-glycans. Comparison with the crystal structure of a biantennary octasaccharide

Cited by 75 publications

References 37 publications

Molecular dynamics simulations of galectin‐1‐oligosaccharide complexes reveal the molecular basis for ligand diversity

Molecular dynamics simulations of galectin‐1‐oligosaccharide complexes reveal the molecular basis for ligand diversity

Investigation of the Action Patterns of Pectinmethylesterase Isoforms through Kinetic Analyses and NMR Spectroscopy

High Affinity Interaction between a Bivalve C-type Lectin and a Biantennary Complex-type N-Glycan Revealed by Crystallography and Microcalorimetry

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