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S W Homans

Publications and source records attributed to S W Homans.

At least 19 recordsLinked to original sources
PubMed2001

Residual 2H quadrupolar couplings in weakly aligned carbohydrates.

We report a novel two-dimensional NMR pulse scheme for the 1H-detected observation of 2H in isotopically 13C, 2H-enriched carbohydrates. This scheme is used for the indirect observation of residual quadrupolar couplings in 13C, 2H-enriched methyl-beta-D-glucopyranoside weakly aligned in a dilute lyotropic liquid-crystalline medium comprising 20% (w/v) dihexanoyl-phosphatidylcholine/dimyristoyl-phosphatidylcholine (1:3 mol/mol) in D2O. The observed residual quadrupolar couplings are substantially larger than residual dipolar one-bond 13C-1H couplings under the same experimental conditions. These quadrupolar couplings are thus a useful alternative to dipolar couplings for the structural analysis of small molecules that align very weakly in dilute liquid-crystalline media. Moreover, since the quadrupolar coupling constant is very uniform throughout endocyclic deuterons of the carbohydrate, these data suggest that adoption of a single average value of this parameter in 2H relaxation studies on the glycan moieties of glycoproteins and glycopeptides is a valid assumption.

Algorithms↗
PubMed2001

Measurement of one-bond 1H-13C, couplings in backbone-labelled proteins.

NMR dipole-dipole couplings between protein backbone nuclei (1H(alpha), 13C(alpha), 15N, 1H(N), 13C') offer enormous scope for the rapid determination of protein global folds. Here, we show that measurement of one-bond splittings in the protein backbone is facilitated by use of protein that is selectively isotopically enriched only in the backbone atoms. In particular, 1H(alpha)-13C(alpha) couplings can be measured simply and with high sensitivity by use of conventional heteronuclear single quantum correlation (HSQC) techniques.

Amino Acids↗
PubMed2000

Localization of the binding site for the oligosaccharide moiety of Gb3 on verotoxin 1 using NMR residual dipolar coupling measurements.

By use of NMR residual dipolar coupling measurements in a dilute liquid-crystalline solvent, the solution structure has been determined of the complex between the oligosaccharide moiety of globotriaosylceramide (Gb(3)-OS) and the B-subunit homopentamer of verotoxin 1 (VTB). The dipolar coupling data indicate that Gb(3)-OS binds in a single binding site per monomer, which is identical to one of three sites inferred from the X-ray structure of the same complex. We find no evidence within experimental error for occupancy at either of the two additional binding sites observed per monomer in the crystal structure.

Binding Sites↗
PubMed1998

Residual dipolar couplings as new conformational restraints in isotropically 13C-enriched oligosaccharides.

We report the measurement of residual dipolar couplings for l3C-enriched NeuNAcalpha2-3Galbeta1-4Glc in a dilute liquid-crystalline medium. These couplings provide long-range conformational restraints that hitherto have not been available for oligosaccharides. We utilise these restraints in dynamical simulated annealing calculations, which support current models of the solution behaviour of the trisaccharide.

Carbohydrate Conformation↗
PubMed1998

Solution structure of the complex between the B-subunit homopentamer of verotoxin VT-1 from Escherichia coli and the trisaccharide moiety of globotriaosylceramide.

We report the solution structure of the carbohydrate-binding B subunit of verotoxin VT-1 (VTB) from enterohemorrhagic Escherichia coli in association with the trisaccharide Galalpha1-4Galbeta1-4Glcbeta1-O-trimethylsilylethyl , determined by use of stable isotope-assisted NMR techniques. In contrast to the crystal structure of the complex which predicts three binding sites per monomer, only one of these sites is observed with substantial occupancy by the trisaccharide in solution.

Bacterial Toxins↗
PubMed1998

Weak substrate binding to transport proteins studied by NMR.

The weak binding of sugar substrates fails to induce any quantifiable physical changes in the L-fucose-H+ symport protein, FucP, from Escherichia coli, and this protein lacks any strongly binding ligands for competitive binding assays. Access to substrate binding behavior is however possible using NMR methods which rely on substrate immobiliza-tion for detection. Cross-polarization from proton to carbon spins could detect the portion of 13C-labeled substrate associated with 0.2 micromol of the functional transport system overexpressed in the native membranes. The detected substrate was shown to be in the FucP binding site because its signal was diminished by the unlabeled substrates L-fucose and L-galactose but was unaffected by a three- to fivefold molar excess of the non-transportable stereoisomer D-fucose. FucP appeared to bind both anomers of its substrates equally well. An NMR method, designed to measure the rate of substrate exchange, could show that substrate exchanged slowly with the carrier center (>10(-1) s), although its dynamics are not necessarily coupled strongly to this site within the protein. Relaxation measurements support this view that fluctuations in the interaction with substrate would be confined to the binding site in this transport system.

Bacterial Proteins↗
PubMed1998

New conformational constraints in isotopically (13C) enriched oligosaccharides.

Multidimensional heteronuclear NMR studies have been applied to the resonance assignment and conformational analysis of 13C-enriched Neu5Acalpha2-3Galbeta1-4Glc. It is demonstrated that three-dimensional ROESY-HSQC experiments provide through-space distance restraints which cannot be observed with conventional homonuclear 1H techniques due to resonance overlap. In particular, connectivities demonstrating the existence of the "anti" conformation about the Galbeta1-4Glc glycosidic linkage are unambiguously observed. It is shown that 13C isotopic enrichment of the trisaccharide at a level >95% enables straightforward measurement of trans-glycosidic 1H-13C and 13C-13C coupling constants and a Karplus-type relation is derived for the latter. In total 15 conformational restraints were obtained for the trisaccharide in aqueous solution, all of which were in excellent agreement with theoretical parameters computed from a 5 ns molecular dynamics simulation of the glycan.

CA-19-9 Antigen↗
PubMed1997

Structure of a glycoconjugate in solution and in complex with an antibody Fv fragment.

By use of heteronuclear (13C, 1H) NMR methods, the three-dimensional structure and dynamics of the glycoconjugate estrone-3-glucuronide (E3G) uniformly 13C enriched in the glucuronic acid moiety has been probed both in free solution and in association with an anti-E3G antibody single-chain Fv fragment. The glycan is found to exist in multiple conformations in free solution, with particularly large torsional fluctuations about the glycosidic linkage psi. Resonance assignments and distance restraints for the glycoconjugate in the bound state were obtained from heteronuclear proton-carbon-carbon-proton-COSY and isotope-edited NOESY techniques, respectively. Quantitation of the NOE data with a full-relaxation matrix approach showed that the antibody selects a conformation from the solution repertoire which does not correspond with either of the two lowest energy conformations of the free glycan, and the internal energy of the glycan in the bound state is estimated to be at most approximately 15 kcal/mol higher than the global minimum energy conformation. The glucuronide moiety undergoes a stacking interaction with an aromatic ring in the binding site, and both ring-current shifts and nuclear Overhauser effects computed from the predicted bound-state conformation are in good agreement with experiment. The bound-state conformation is also in good agreement with preliminary x-ray data on a related complex.

Carbohydrate Conformation↗
PubMed1996

Structural and conformational analysis of glycan moieties in situ on isotopically 13C, 15N-enriched recombinant human chorionic gonadotropin.

The conformational properties in solution of the glycans on the alpha subunit of recombinant human chorionic gonadotropin are described, using high-resolution multinuclear NMR studies on uniformly 13C, 15N-enriched recombinant glycoprotein expressed in CHO cells. The glycan important for full biological activity of hCG, namely, that at Asn 52, appears to extend into solution both in the isolated alpha subunit and in complex with the beta subunit. The disposition of this glycan with respect to the protein backbone suggests that glycosylation maintains full biological activity of hCG either by interacting with a lectin-like region of the hCG receptor or by reducing the affinity of the hormone for the hCG receptor and preventing its down-regulation.

Carbohydrate Conformation↗
PubMed1996

Conformational studies on the selectin and natural killer cell receptor ligands sulfo- and sialyl-lacto-N-fucopentaoses (SuLNFPII and SLNFPII) using NMR spectroscopy and molecular dynamics simulations. Comparisons with the nonacidic parent molecule LNFPII.

This investigation is focused on the conformational behavior of the blood group Lewisa (Le(a)-active pentasaccharide lacto-N-fucopentaose II (LNFPII) and its sulfated and sialylated analogs, SuLNFPII and SLNFPII. The latter two are more potent oligosaccharide ligands for the animal lectins, E- and L-selectin, and the natural killer cell receptor, NKR-P1, than are the shorter chain analogs based on the trisaccharide Le(a) domain. We report here that the three oligosaccharides based on the fucopentasaccharide have very similar average solution conformations as determined from NMR spectroscopical parameters, in particular 13C chemical shift differences. From restrained simulated annealing and restrained molecular dynamics (MD) simulations performed in order to determine the most probable conformational distributions around the glycosidic linkages we derive models for these oligosaccharides that are in good agreement with experimental parameters, such as rotating-frame Overhauser effects (ROE's) and long-range 1H,13C coupling constants across the glycosidic linkages. In these model structures the Le(a) domain at the non-reducing end of the longer chain oligosaccharides approximates the same rigid structure as in the shorter analogs. The Gal beta 1-4Glc linkage at the reducing end is also rather rigid, showing only little more flexibility than the Le(a) domain. However, the NeuAc alpha 2-3Gal linkage in SLNFPII, and the GlcNAc beta 1-3Gal linkage in all three oligosaccharides are flexible, in each case fluctuating mainly between two minimum energy structures: (phi = -81 degrees, psi = 8 degrees) and (phi = -160 degrees, psi = -20 degrees) for the NeuAc alpha 2-3Gal linkage, as reported previously for the isomeric sequence 3'-sialyl Le(x), and (phi = -25 degrees, psi = -26 degrees) and (phi = 20 degrees, psi = 24 degrees) for the GlcNAc beta 1-3Gal linkage. The flexibility of the latter linkage may allow the lactosyl domain at the reducing end to fit with little strain into extended carbohydrate binding sites on the recognition proteins, and, for the purposes of drug designs, it will be important to establish which conformational distribution is assumed for the GlcNAc beta 1-3Gal linkage in these longer chain oligosaccharides in the bound state.

Animals↗
PubMed1995

Influence of the extent of branching on solution conformations of complex oligosaccharides: a molecular dynamics and NMR study of a penta-antennary "bisected" N-glycan.

The solution conformation of an agalactosyl penta-antennary "bisected" N-linked glycan from hen ovomucoid has been determined using a combination of 1H-NMR NOE measurements and restrained molecular dynamics (MD) simulations. The majority of glycosidic linkages exhibited restricted torsional fluctuations about the global minimum energy configuration, of an extent which was generally less than that observed in N-linked glycans with a smaller number of antennae. The locations of terminal galactose residues in the native glycan, which exhibit branch specificity, could not readily be rationalized in terms of relative accessibility by the relevant galactosyltransferase of the various nonreducing terminal 2-acetamido-2-deoxy-D-glucopyranose (GlcNAc) residues in the agalactosyl glycan, suggesting either that the parent protein exhibits substantial control over glycosylation or that more than one transferase is responsible for galactosylation.

Carbohydrate Conformation↗
PubMed1995

A unique multifucosylated -3GalNAc beta 1-->4GlcNAc beta 1-->3Gal alpha 1- motif constitutes the repeating unit of the complex O-glycans derived from the cercarial glycocalyx of Schistosoma mansoni.

The entire surface of the cercarial stage of the human blood fluke Schistosoma mansoni is covered by a 1-microns thick, highly immunogenic, fucose-rich glycocalyx (GCX). Using strategies based on enzymatic, chemical, and mass spectrometric analysis, we have defined the structures of the major glycans released by reductive elimination from GCX. They comprise a heterogeneous population of multifocosylated complex oligosaccharides with the following nonreducing terminal sequences: [formula: see text] Our structural data suggest that these tri- to pentafucosylated epitopes are carried on type 1, R-->Gal beta-1-->3GalNAc, and type 2, R-->Gal beta 1-->3(R-->GlcNAc beta-1-->6)GalNAc, core structures via repeat units of (3GalNAc beta 1-->4(Fuc alpha 1-->2Fuc alpha 1-->2Fuc alpha 1-->3)GlcNAc beta-1-->3Gal alpha-->)n, where n is mainly 0 and 1, and all sugars are in the pyranose form. The proposed structure represents the first instance where an alpha-galactosylated beta-GalNAc(1-->4)-beta-GlcNAc sequence occurs as a repeating unit in a glycoprotein. It is also unique in being substituted with oligofucosyl appendages. The unusual oligosaccharide structures described here, particularly the potentially immunodominant oligofucosyl moieties, are most likely responsible for the known potency of GCX in modulating various immune responses including complement activation, B cell mitogenesis, and delayed type hypersensitivity in schistosomiasis.

Animals↗
PubMed1995

Proton resonance assignments in oligosaccharides containing multiple monosaccharide residues of the same type.

A technique is described for assisting the resonance assignment process in oligosaccharide proton NMR spectra, where multiple residues of the same type generate extreme resonance overlap in the spectrum. The approach involves the modification of a conventional HOHAHA experiment with constant-time acquisition in t1, which effectively proton decouples the C-1 protons of residues whose resonances overlap, thus affording a significant increase in effective resolution in that dimension. For a sufficiently long spin-lock time, complete one-dimensional subspectra are obtained essentially free of cross talk from adjacent resonances. Further simplification of the assignment process is illustrated by incorporation of the constant-time modification into a three-dimensional HOHAHA-HOHAHA experiment.

Acetylglucosamine↗
PubMed1994

Restrained vs free dynamics simulations of oligosaccharides: application to solution dynamics of biantennary and bisected biantennary N-linked glycans.

We have examined the dynamic behavior in solution of the biantennary glycan GlcNAc beta 1-2Man alpha 1-6(GlcNAc beta 1-2Man alpha 1-3)Man beta 1- 4GlcNAc beta 1-4GlcNAc, and its "bisected" analogue GlcNAc beta 1-2Man alpha 1-6(GlcNAc beta 1-2Man alpha 1-3)(GlcNAc beta 1- 4)Man beta 1-4GlcNAc beta 1-4GlcNAc, by use of both free dynamics simulations and restrained dynamics simulations using distance restraints derived from 1H NMR rotating frame Overhauser effect measurements. Data resulting from each type of simulation are compared with experimental data and are critically evaluated. Both methods suggest that most glycosidic linkages exhibit significant torsional oscillations in solution, and the dynamic behavior of certain linkages, notably Man alpha 1-6Man and Man alpha 1-3Man, were found to be restricted by the presence of the bisecting GlcNAc residue. The average structures so obtained were found to agree closely with those predicted in previous investigations where torsional oscillations about glycosidic linkages were not considered. In particular, the characteristic chemical shift perturbations induced by the bisecting GlcNAc residue could be explained in terms of the dynamic differences between the two glycans.

Acetylglucosamine↗
PubMed1994

Solution structure and dynamics of a glycoinositol phospholipid (GIPL-6) from Leishmania major.

By use of a combination of 1H nuclear Overhauser effect measurements, restrained molecular dynamics simulations, and 13C spin-lattice relaxation time measurements, the solution behavior of the glycan moiety of a complex glycoinositol phospholipid termed GIPL-6, from the protozoan parasite Leishmania major has been determined. The glycan moiety of GIPL-6 has the following structure, which is characterized by the presence of an internal beta-galactofuranose residue: [formula: see text] The glycan does not adopt a single conformation in solution, due to significant torsional variations about the two phosphodiester linkages and certain glycosidic linkages in the molecule. The presence of the internal galactofuranose residue results in an average solution conformation of the oligosaccharide, which resembles a "hairpin," with the galactofuranose residue at the apex.

Animals↗