Conformation of the pentasaccharide corresponding to the binding site of heparin for antithrombin III

Ragazzi, Massimo; Ferro, Dino R.; Perly, Bruno; Sînaÿ, Pierre; Petitou, Maurice; Choay, J

doi:10.1016/0008-6215(90)84165-q

Cited by 77 publications

(78 citation statements)

References 33 publications

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“…This observation is consistent with data from circular dichroism studies [Mulloy et al, 1994], which indicated that the overall helical conformations of K5 and several heparin derivatives are very similar to each other, irrespective of sulphation or epimerisation patterns present. Corroborating this observation, several 3D structures of heparin-like molecules have been determined and indeed found to adopt similar solution conformations [Mikhailov et al, 1996[Mikhailov et al, , 1997Mulloy et al, 1993;Ragazzi et al, 1990]. Indeed, it appears that the presence of IdoA does not appreciably affect the local glycosidic linkage conformations or dynamics, while sulphation also leaves the dynamic motions broadly the same [Mulloy et al, 1994;Mulloy and Forster, 2000].…”

Section: Discussionmentioning

confidence: 95%

Investigating the Molecular Basis for the Virulence of <i>Escherichia coli</i> K5 by Nuclear Magnetic Resonance Analysis of the Capsule Polysaccharide

Blundell

Roberts²,

Sheehan³

et al. 2009

Microb Physiol

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The capsular polysaccharide of Escherichia coli K5 has been hypothesised to promote virulence through its molecular mimicry of host heparan sulphate. To test this hypothesis, we have produced pure oligosaccharides from K5 capsular polysaccharide and investigated their conformational properties with ultra-high-field nuclear magnetic resonance (NMR) (900 MHz). Ultra-high-field affords a significant resolution enhancement over previous studies and allowed a full-atomic assignment of the K5 hexasaccharide for the first time. All carbohydrate rings adopt a ⁴C₁ conformation, the amide sidechains have a trans orientation and the hydroxymethyl group is freely exposed to bulk solvent. Initial models of the glycosidic linkage conformation based upon simple interpretation of NOE cross-peaks suggests that the β1→4 linkage adopts a 3D geometry of φ ≈ 60°, ψ ≈ 0° and the α1→4 linkage prefers φ ≈ –30°, ψ ≈ –30° (φ and ψ being defined by dihedral angles involving linkage protons). In this conformation the overall molecular geometries of K5 polysaccharide, heparan sulphate and even fully-sulphated heparin are remarkably similar. These results substantiate the hypothesis that the K5 capsular polysaccharide confers virulence to E. coli K5 by being a 3D molecular mimetic of host heparan sulphate, helping it to evade detection by the mammalian immune system.

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Section: Discussionmentioning

confidence: 95%

Investigating the Molecular Basis for the Virulence of <i>Escherichia coli</i> K5 by Nuclear Magnetic Resonance Analysis of the Capsule Polysaccharide

Blundell

Roberts²,

Sheehan³

et al. 2009

Microb Physiol

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“…However, increased interactions of residues D and E with the activated antithrombin conformation are also likely, given the substantial binding energy resulting from the interaction of residue D and the decreased activation resulting from nonproductive binding of oligosaccharide FGHٞ in the DEF interaction sites. Further stabilization of the activated conformation results from the generation of additional complementary sites of interaction for the more flexible reducing-end residues G and H in this conformation (40). Conformational changes in the reducing-end saccharides, in particular the conformationally flexible iduronate residue G, may be required to align the charges in these residues for an optimal fit with the activated conformation (40).…”

Section: Discussionmentioning

confidence: 99%

“…Further stabilization of the activated conformation results from the generation of additional complementary sites of interaction for the more flexible reducing-end residues G and H in this conformation (40). Conformational changes in the reducing-end saccharides, in particular the conformationally flexible iduronate residue G, may be required to align the charges in these residues for an optimal fit with the activated conformation (40). According to our model, the pentasaccharide functions as a classical allosteric modifier by preferentially binding and stabilizing the activated antithrombin conformation.…”

Section: Discussionmentioning

confidence: 99%

Mechanism of Heparin Activation of Antithrombin

Desai

Petitou

Björk

et al. 1998

Journal of Biological Chemistry

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174

175

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To determine the role of individual saccharide residues of a specific heparin pentasaccharide, denoted DEFGH, in the allosteric activation of the serpin, antithrombin, we studied the effect of deleting pentasaccharide residues on this activation. Binding, spectroscopic, and kinetic analyses demonstrated that deletion of reducing-end residues G and H or nonreducing-end residue D produced variable losses in pentasaccharide binding energy of ϳ15-75% but did not affect the oligosaccharide's ability to conformationally activate the serpin or to enhance the rate at which the serpin inhibited factor Xa. Rapid kinetic studies revealed that elimination of the reducing-end disaccharide marginally affected binding to the native low-heparin-affinity conformational state of antithrombin but greatly affected the conversion of the serpin to the activated high-heparinaffinity state, although the activated conformation was still favored. In contrast, removal of the nonreducingend residue D drastically affected the initial low-heparin-affinity interaction so as to favor an alternative activation pathway wherein the oligosaccharide shifted a preexisiting equilibrium between native and activated serpin conformations in favor of the activated state. These results demonstrate that the nonreducing-end residues of the pentasaccharide function both to recognize the native low-heparin-affinity conformation of antithrombin and to induce and stabilize the activated high-heparin-affinity conformation. Residues at the reducing-end, however, poorly recognize the native conformation and instead function primarily to bind and stabilize the activated antithrombin conformation. Together, these findings establish an important role of the heparin pentasaccharide sequence in preferential binding and stabilization of the activated conformational state of the serpin.

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“…The relative orientation of pyranose rings defined by two torsion angles (U, W) at the (1 ? 4) glycosidic linkage was adjusted according to the experimental data for structurally related heparin-derived oligosaccharides [39,40].…”

Section: Computational Detailsmentioning

confidence: 99%

Molecular structure of basic oligomeric building units of heparan-sulfate glycosaminoglycans

2010

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This study reports in detail the results of systematic large-scale theoretical investigations of the acidic dimeric structural units (D-E, E-F, F-G, and G-H) and pentamer D-E-F-G-H (fondaparinux) of the glycosaminoglycan heparin, and their anionic forms. The geometries and energies of these oligomers have been computed using HF/6-31G(d), Becke3LYP/6-31G(d), and Becke3LYP/ 6-311?G(d,p) methods. The optimized geometries indicate that the most stable structure of these units in the neutral state is stabilized via a system of intramolecular hydrogen bonds. The equilibrium structure of these species changed appreciably upon dissociation. Water has a remarkable effect on the geometry of the anions studied. Because of high negative charge, the solvent effect also resulted in an appreciable energetic stabilization of biologically active anionic forms of these glycosaminoglycans. The stable energy conformations around glycosidic bonds found for dimers and pentamer investigated are compared and discussed with the available experimental X-ray structural data for the structurally related heparinderived pentasaccharides in cocrystals with proteins.

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Conformation of the pentasaccharide corresponding to the binding site of heparin for antithrombin III

Cited by 77 publications

References 33 publications

Investigating the Molecular Basis for the Virulence of <i>Escherichia coli</i> K5 by Nuclear Magnetic Resonance Analysis of the Capsule Polysaccharide

Investigating the Molecular Basis for the Virulence of <i>Escherichia coli</i> K5 by Nuclear Magnetic Resonance Analysis of the Capsule Polysaccharide

Mechanism of Heparin Activation of Antithrombin

Molecular structure of basic oligomeric building units of heparan-sulfate glycosaminoglycans

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