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1.
A tetrasaccharide related to the blood group oligosaccharides, known as sialyl LewisX, has been proposed as the receptor for the lectin responsible for leukocyte adhesion named alternatively as E-selectin or ELAM-1. The 13C- and 1H-nmr spectra have been completely assigned for a tetrasaccharide model of this receptor, Neu5Ac α-(2 → 3)-Gal β-(1 → 4)-[ Fuc α-(1 → 3)-] GlcNAc β-NHAc. Quantitative nuclear Overhauser data (NOESY) have been recorded and analyzed by a complete spin matrix simulation method. Conformational space was exhaustively searched and all conformational models whose simulated NOESY spectra matched the experiment were found. Molecular mechanics and molecular dynamics calculations were carried out to test whether the experimental conformations are low energy and thus likely to represent true single conformations for the tetrasaccharide. It was concluded that while the LewisX trisaccharide portion of the compound adopts a single conformation, there is likely to be some flexibility about the Neu5Ac α-(2 → 3)-linkage. A model featuring fast exchange between two different conformations of this linkage is found to be consistent with both the nmr experiments and the molecular dynamics simulations. © 1994 John Wiley & Sons, Inc.  相似文献   

2.
M Martin-Pastor  C A Bush 《Biochemistry》1999,38(25):8045-8055
For complex oligosaccharides, which are relatively rigid with modest excursions from a single minimum energy conformation, it is straightforward to build conformational models from NOE data. Other oligosaccharides are more flexible with transitions between distinct minima separated by substantial energy barriers. We show that modeling based on scalar coupling data is superior to NOE-based modeling for the latter case. Long range 13C-13C and 13C-1H coupling constants measured for the heptasaccharide repeating subunit of the cell wall polysaccharide from Streptococcus mitis J22 are correlated with individual glycosidic dihedral angles, effectively uncoupling the degrees of freedom of the oligosaccharide and allowing a search for combinations of dihedral angles which are energetically reasonable, i.e., with no bad van der Waals contacts, and which can be combined to satisfy all the measured J values. Allowed values of the individual angles can then be combined to search for overall oligosaccharide conformations which contribute to the ensemble. We show that while the polysaccharide from S. mitis J22 is flexible, requiring multiple conformations, most of the flexibility is localized to a few bonds and only a rather small number of conformations is required to reproduce the experimental NOE and scalar coupling data.  相似文献   

3.
P Cagas  C A Bush 《Biopolymers》1990,30(11-12):1123-1138
Through control of both the nmr probe temperature and of the solvent viscosity, phase-sensitive two-dimensional 1H nuclear Overhauser data (NOESY) at 300 and 500 MHz are obtained with excellent signal-to-noise ratios for Lewis blood group penta- and hexasaccharides isolated from human milk. Relatively long mixing times are required to produce measurable NOE intensities in these oligosaccharides, which makes a full relaxation matrix analysis necessary. By measurements of selective T1 for a few isolated 1H resonances, it was possible to generate a simulation of the complete NOESY spectrum at arbitrary mixing time for comparison with the experimental data. From an exhaustive search of the conformational space, it was found that only a small range of glycosidic dihedral angles of the nonreducing terminal Lewis blood group determinant fragments of the milk oligosaccharides LNF-2 and LND-1 produce simulated spectra agreeing within experimental error to the data. Conformational energy calculations reveal that each of these conformations is also one of minimum energy. It is concluded that the Lewis(a) and Lewis(b) oligosaccharides adopt relatively compact rigid structures in solution, as shown by the observation of cross peaks between protons in nonadjacent residues. Like the blood group A and H oligosaccharides, there exists only a small dependence of the conformation for Lewis(a) and Lewis(b) oligosaccharides on solvent. The apparent lack of dependence of conformation of these oligosaccharides on DMSO in D2O suggests that modification of solvent viscosity with mixtures of DMSO:D2O may provide a useful general strategy of NOESY studies of oligosaccharides.  相似文献   

4.
The conformational behavior of the synthetic hexa- and heptasaccharide methyl beta-glycosides alpha-D-Manp-(1 --> 6)-[alpha-D-Manp-(1 --> 3)-][beta-D-Xylp-(1 --> 2)-]beta-D-Manp-(1 --> 4)-beta-D-GlcpNAc-(1 --> 4)-beta-D-GlcpNAc-(1 --> OMe and alpha-D-Manp-(1 --> 6)-[alpha-D-Manp-(1 --> 3)-][beta-D-Xylp-(1 --> 2)-]beta-D-Manp-(1 --> 4)-beta-D-GlcpNAc-(1 --> 4)-[alpha-L-Fucp-(1 --> 6)-]beta-D-GlcpNAc-(1 --> OMe, representing the xylosylated and the xylosylated alpha-(1 --> 6)-fucosylated core structures of N-glycans in alpha(D)-hemocyanin of the snail Helix pomatia, respectively, were investigated by 1H NMR spectroscopy in combination with molecular dynamics (MD) simulations in water. 1H and 13C chemical shifts of the oligosaccharides were assigned using 1H-(1)H COSY, TOCSY, and NOESY, and 1H-(13)C HMQC techniques. Experimental 2D 1H cross-peak intensities from one series of NOESY and one series of ROESY experiments of the two oligosaccharides were compared with calculated values derived from MD trajectories using the CROSREL program, yielding information about the conformation of each glycosidic linkage of the methyl glycosides. The flexibility of the linkages was described by generalized order parameters and internal rotation correlation times. Analysis of the data indicated that several conformations are likely to exist for the alpha-D-Man-(1 --> 6)-beta-D-Man, the alpha-L-Fuc-(1 --> 6)-beta-D-GlcNAc, and the alpha-D-Man-(1 --> 3)-beta-D-Man linkage, whereas the beta-D-Xyl-(1 --> 2)-beta-D-Man-(1 --> 4)-beta-D-GlcNAc-(1 --> 4)-beta-D-GlcNAc fragment occurs in one rigid conformation. No significant differences were found between the corresponding structural elements in both methyl glycosides. NOESY and ROESY experiments proved to be suitable for providing the experimental data required, however, due to more overlap within the ROESY spectra, reducing the accuracy of the analysis, NOESY spectral analysis is preferred.  相似文献   

5.
Three-bond heteronuclear coupling constants (3JCH) are extremelyuseful in describing flexible models for oligosaccharides. Weshow that antiphase methods for measuring 3JCH in oligosaccharideshave limited reliability but that the coupling constants canbe reliably measured in natural abundance by quantitative J-correlationmethods. Interpretation of 3JCH data for a pentasaccharide (lacto-N-fuco-pentaose2) from human milk are consistent with a rigid model for theLewisa trisaccharide epitope but for an antigenic tetrasaccharidefragment from the cell wall polysaccharide of viridans streptococci,3JCH data imply a considerably more flexible model. NuclearOverhauser effect (NOE) data are reported for a heptasacchariderepeating unit isolated from the cell wall polysaccharide ofStreptococcus gordonii 38. The results for a tetrasaccharidefragment are similar to data reported for the same fragmentin the cell wall polysaccharide from S.mitis 322. This resultimplies a similar conformation for the tetrasaccharide fragmentin the polysaccharide and in the heptasaccharide and also impliesthat anisotropy of motion is not significant in the interpretationof the nuclear Overhauser effects in the polysaccharide. Interpretationof the NOE results for the tetrasaccharide fragment, like the3JCH data, implies a flexible model with three conformationsin fast exchange. The results of the two experimental techniquesare combined with molecular modeling results including moleculardynamics simulation to provide a clear delineation between flexibleand rigid oligosaccharide epitopes. The blood group Lewisa trisaccharideantigenic determinant is highly restricted in its motions bysteric interactions while the antigenic tetrasaccharide fragmentof the S.gordonii 38 heptasaccharide is considerably more mobile.We propose that some branched oligosaccharides are relativelyrigid and some are flexible depending on subtle details of thelinkages. oligosaccharide conformation molecular dynamics  相似文献   

6.
The conformations of heparin in aqueous solution in the presence of sodium, potassium, magnesium and calcium cations were studied using circular dichroism, optical rotation, nuclear magnetic resonance and equilibrium dialysis. Potassium and magnesium cations, when added to sodium heparinate solutions, cause small chiroptical changes. Binding of calcium ions gives rise to large changes in both optical rotation and circular dichroism. This is indicative of a major change in chain conformation, which is also manifest in 13C and 1H n.m.r.4Equilibrium dialysis suggests one mole of calcium bound per mole of tetrasaccharide, which n.m.r. indicates to be appropriately sulphated iduronateglucosamine-iduronate-glucosamine. The calcium is chelated by two iduronate carboxyl groups. Proton-proton coupling constants, determined by convolution difference spectroscopy and Carr-Purcell sequences, indicate that, over the temperature range 285 to 353 K, the iduronate ring is best described as 1C4(l) and the glucosamine residue as 4C1(d) for both sodium and calcium forms.The conformational change induced by calcium is ascribed to rotation around the glycosidic linkages. The binding process is co-operative and the binding constant of 103 to 104m?1 is biologically significant. The findings are consistent with intramolecular binding. Hence, this study represents the first report of a polysaccharide undergoing a cation-induced intramolecular disorder-order process. The authors postulate that a function of the post-polymerization epimerization of d-glucuronate to l-iduronate is the attainment of the precise geometry required for co-operative calcium binding with consequent modulation of the flexibility of the tetrasaccharide units.  相似文献   

7.
The O-specific polysaccharide obtained by mild-acid degradation of lipopolysaccharide of Aeromonas bestiarum P1S was studied by sugar and methylation analyses along with 1H and 13C NMR spectroscopy. The sequence of the sugar residues was determined using 1H,1H NOESY and 1H,13C HMBC experiments. The O-specific polysaccharide was found to be a high-molecular-mass polysaccharide composed of tetrasaccharide repeating units of the structureSince small amounts of a terminal Quip3N residue were identified in methylation analysis, it was assumed that the elucidated structure also represented the biological repeating unit of the O-specific polysaccharide.  相似文献   

8.
By use of heteronuclear (13c, 1H) NMR methods, the threedimensionalstructure and dynamia of the glycoconjugate estrone-3-glucuronide(E3G) uniformly 13c enriched in the glucuronic acid moiety hasbeen probed both in free solution and in association with ananti-E3G antibody singlechain Fv fragment. The glycan is foundto exist in multiple conformations in free solution, with particularlylarge torsional fluctuations about the glycosidic linkage .Resonance assignments and distance restraints for the glycococonjugatein the bound state were obtained from heteronuclear protonarbon-carbon-proton-COSYand isotopeedited NOESY techniques, respectively. Quantitationof the NOE data with a full-relaxation matrix approach showedthat the antibody selects a conformation from the solution repertoirewhich does not correspond with either of the two lowest energyconformations of the free glycan, and the internal energy ofthe glycan in the bound state is estimated to be at most 15kcal/mol higher than the global minimum energy conformation.The glucuronide moiety undergoes a stacking interaction withan aromatic ring in the binding site, and both ring-currentshifts and nuclear Overhauser effects computed from the predictedboundstate conformation are in good agreement with experiment.The bound-state conformation is also in goad agreement withpreliminary x-ray data on a related complex. NMR estrone antibody ring current shifts  相似文献   

9.
P Cagas  C A Bush 《Biopolymers》1992,32(3):277-292
To probe differences in conformation of the type 1 and type 2 linkages in blood group oligosaccharides, two-dimensional nuclear Overhauser effect spectroscopy (2D-NOESY) and 1H T1 data were obtained for two blood group A oligosaccharide alditols containing the type 1 and type 2 linkage. The NOE data were interpreted using a complete relaxation matrix approach. Simulations of NOE and T1 values were made using disaccharide and tetrasaccharide model conformations generated by a systemic variation of the glycosidic dihedral angles phi and psi. NOEs from the amide protons of GlcNAc and GalNAc in the type 1 pentasaccharide alditol were obtained, and simulated in a manner similar to those from carbon-bound protons. In addition to providing data for determining the conformation of the type 1 linkage from amide proton NOEs of GlcNAc and GalNAc to neighboring residues, amide proton NOEs also yield information on the orientation of the acetamido side chains. The amide NOE data indicated subtle differences in the orientation of the amide side chain of GlcNAc among the A type 1 pentasaccharide alditol and two previously studied blood group oligosaccharides, lacto-N-difucohexaose 1 and lacto-N-fucopentaose 1. From the NOE and 1H T1 data, and from simple rigid geometry energy calculations, it is concluded that the type 1 and type 2 linkages in the oligosaccharides studied have different conformations and that these conformations are relatively rigid in solution.  相似文献   

10.
A newly reported strain of Vibrio cholerae, known as strain O139 Bengal, is the first instance of an encapsulated strain that has caused epidemic cholera. The O-antigenic capsule is the critical antigen for protective immunity. Since mapping of the antigenic epitopes will assist in the development of a protein conjugate vaccine based on the capsular polysaccharide, we have undertaken a study of the three-dimensional conformation of the polysaccharide. It contains six residues in the repeating subunit with the unusual feature of a 4,6 cyclic phosphate on a beta-galactopyranoside. A structural epitope composed of four of the residues is somewhat similar to the Lewis(b) blood group tetrasaccharide. Polysaccharide samples enriched in (13)C have been prepared by growth of the bacteria in (13)C-enriched medium. Multidimensional heteronuclear NMR and molecular modeling studies are reported, which show that the O139 tetrasaccharide adopts a compact and tightly folded conformation that is relatively rigid and similar to the Le(b) conformation. The cyclic phosphate on the beta-galactopyranoside residue is in contact with the colitose residue linked to the beta-GlcNAc.  相似文献   

11.
The O-specific polysaccharide (OPS) of Vibrio cholerae 08 was isolated by mild acid degradation of the lipopolysaccharide and studied by two-dimensional NMR spectroscopy, including NOESY and heteronuclear multiple-bond correlation (HMBC) experiments. The OPS was found to have a tetrasaccharide repeating unit with the following structure: --> 4)-beta-D-Glcp NAc3NAcylAN-(1 --> 4)-beta-D-Manp NAc3NAcAN-(1 --> 4)-alpha-L-Gulp NAc3NAcA-(1 --> 3) -beta-D-QuipNAc4NAc-(1 --> where QuiNAc4NAc is 2,4-diacetamido-2,4,6-trideoxyglucose, GlcNAc3NAcylAN is 2-acetamido-3-(N-formyl-L-alanyl)amino-2,3-dideoxyglucuronamide, ManNAc3NAcAN is 2,3-diacetamido-2,3-dideoxymannuronamide, and GulNAc3NAcA is 2,3-diacetamido-2,3-dideoxyguluronic acid. The OPS was stable towards acid hydrolysis and solvolysis with anhydrous hydrogen fluoride, but could be cleaved selectively with trifluoromethanesulfonic (triflic) acid by the glycosidic linkages of beta-QuiNAc4NAc and alpha-GulNAc3NAcA. The structures of the oligosaccharides obtained that were elucidated by electrospray ionization (ESI) MS and NMR spectroscopy, confirmed the OPS structure.  相似文献   

12.
The capsular polysaccharide from Klebsiella type K54, containing both O-formyl and O-acetyl groups, has been investigated by using the techniques of methylation analysis (by gas-liquid chromatography), periodate oxidation-Smith degradation, and both 1H- and 13C-n.m.r. spectroscopy. Degradation of the native polysaccharide with a bacteriophage-induced glucosidase generated a formylated, as well as a formylated and acetylated, tetrasaccharide, whereas similar depolymerization of the deacetylated polysaccharide yielded a single tetrasaccharide; the corresponding, O-acylated octasaccharides were also isolated and characterized. These oligosaccharides, utilized in chemical and spectroscopic studies in order to determine the location of the O-acyl substituents in the repeating sequence, indicated formylation at O-4 of each lateral d-glucosyl group and acetylation at O-2 of alternate l-fucosyl residues. A new structure for the repeating unit in the polysaccharide is proposed.  相似文献   

13.
A 2-D 1H NMR study (NOESY, COSY, HOHAHA and ROESY experiments) of the antifungal peptide stendomycin is presented. The variation of the NOESY cross peak intensities is measured as a function of temperature in order to discriminate between constant and fluctuating interproton distances. It is shown that among 71 NOESY cross peaks, only 12 correspond to well defined interproton distances and their correlation time is determined. The other cross peaks cannot be translated accurately in terms of distances owing to internal molecular motions. 1H}–13C nOe measurements confirm the internal mobility of the molecule. Finally a flexibility map of stendomycin can be established. Offprint requests to: J. P. Simorre  相似文献   

14.
The structure of the capsular polysaccharide from Klebsiella type 55 has been investigated by using the techniques of methylation, Smith periodate oxidation, and partial, acid hydrolysis. The anomeric configurations of the glycosidic linkages were determined by performing 1H-n.m.r. and 13C-n.m.r.spectroscopy on the polysaccharide and derived poly- and oligo-saccharides obtained through degradative procedures. The position of the O-acetyl group was located by devising an improved method for its replacement by a methyl ether group. The structure was shown to consist of the following tetrasaccharide repeating unit.  相似文献   

15.
In this study, a set of nuclear magnetic resonance experiments, some of them commonly used in the study of 13C-labeled proteins and/or nucleic acids, is applied for the structure determination of uniformly 13C-enriched carbohydrates. Two model substances were employed: one compound of low molecular weight [(UL-13C)-sucrose, 342 Da] and one compound of medium molecular weight (13C-enriched O-antigenic polysaccharide isolated from Escherichia coli O142, ~10 kDa). The first step in this approach involves the assignment of the carbon resonances in each monosaccharide spin system using the anomeric carbon signal as the starting point. The 13C resonances are traced using 13C–13C correlations from homonuclear experiments, such as (H)CC–CT–COSY, (H)CC–NOESY, CC–CT–TOCSY and/or virtually decoupled (H)CC–TOCSY. Based on the assignment of the 13C resonances, the 1H chemical shifts are derived in a straightforward manner using one-bond 1H–13C correlations from heteronuclear experiments (HC–CT–HSQC). In order to avoid the 1 J CC splitting of the 13C resonances and to improve the resolution, either constant-time (CT) in the indirect dimension or virtual decoupling in the direct dimension were used. The monosaccharide sequence and linkage positions in oligosaccharides were determined using either 13C or 1H detected experiments, namely CC–CT–COSY, band-selective (H)CC–TOCSY, HC–CT–HSQC–NOESY or long-range HC–CT–HSQC. However, due to the short T2 relaxation time associated with larger polysaccharides, the sequential information in the O-antigen polysaccharide from E. coli O142 could only be elucidated using the 1H-detected experiments. Exchanging protons of hydroxyl groups and N-acetyl amides in the 13C-enriched polysaccharide were assigned by using HC–H2BC spectra. The assignment of the N-acetyl groups with 15N at natural abundance was completed by using HN–SOFAST–HMQC, HNCA, HNCO and 13C-detected (H)CACO spectra.  相似文献   

16.
N-linked oligosaccharides often act as ligands for receptor proteins in a variety of cell recognition processes. Knowledge of the solution conformations, as well as protein-bound conformations, of these oligosaccharides is required to understand these important interactions. In this paper we present a model for the solution conformations sampled by a simple trimannoside, methyl 3, 6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranoside, which contains two of the most commonly found glycosidic linkages in N-linked oligosaccharides. This model was derived from simulated annealing protocols incorporating distance restraints extracted from NOESY spectra along with torsional restraints computed from three-bond (1)H-(13)C coupling constants measured across the glycosidic bonds. The model was refined in light of unrestrained molecular dynamics simulations conducted in the presence of solvent water. The resulting model depicts a molecule undergoing conformational averaging in solution, adopting four major and two minor conformations. The four major conformations arise from a pair of two-state transitions, one each at the alpha(1-->3) and alpha(1-->6) linkages, whereas the minor conformations result from an additional transition of the alpha(1-->6) linkage. Our data also suggest that the alpha(1-->3) transition is fast and changes the molecular shape slightly, whereas the alpha(1-->6) is much slower and alters the molecular shape dramatically.  相似文献   

17.
The heptasaccharide isolated from the cell wall polysaccharide of Streptococcus mitis J22 serves as an important model for the dynamics and conformation of complex polysaccharides, illustrating the nature of flexibility with rigid epitopes joined by flexible hinges. One-bond C-H residual dipolar couplings (1DCH) and long-range H-H residual dipolar couplings (nDHH) were measured for the heptasaccharide in a cetylpyridinium chloride/hexanol/brine lamellar liquid crystal medium. A method is proposed to determine the nDHH in natural abundance based on a 13C resolved 1H TOCSY pulse sequence previously published to determine the homonuclear scalar couplings. Different methods for interpretation of the 1DCH and the nDHH residual dipolar coupling data obtained were compared and combined with the NOE and long-range H,C and C,C scalar couplings available for this heptasaccharide. A flexible model of the heptasaccharide was determined in which two structurally well-defined regions involving four and two sugar residues, respectively are joined by a flexible hinge which involves two 16 glycosidic linkages.  相似文献   

18.
Complex carbohydrates have critical roles in a wide variety of biological processes. An understanding of the molecular mechanisms that underlie these processes is essential in the development of novel oligosaccharide-based therapeutic strategies. Unfortunately, obtaining detailed structural information for larger oligosaccharides (>10 residues) can be exceedingly difficult, especially where the amount of sample available is limited. Here we demonstrate the application of 13 C O-acetylation in combination with novel NMR experiments to obtain much of the information required to characterize the primary structure of oligosaccharides. (H)CMeCOH-HEHAHA and H(CMe)COH-HEHAHA experiments are presented that use heteronuclear Hartmann–Hahn transfer to correlate the acetyl groups with sugar ring protons in peracetylated oligosaccharides. The in-phase, pure absorption nature of the correlation peaks in these experiments allows measurement of both chemical shifts and, importantly, 1H-1H coupling constants that are used to define the stereochemistry of the sugar ring. The (HCMe)COH and (HCMe)COH-RELAY experiments provide additional methods for obtaining chemical shift assignments for larger oligosaccharides to define the sites of glycosidic linkages from the patterns of acetylation.  相似文献   

19.
The structural and electronic properties of 4′-epiadriamycin, adriamycin, and daunomycin have been studied using density functional theory (DFT) employing B3LYP exchange correlation. The chemical shifts of 1H and 13C resonances in nuclear magnetic resonance spectra have been calculated using Gauge-Invariant Atomic Orbital (GIAO) method as implemented in Gaussian 98 and compared with experimental spectra recorded at 500 MHz. 13C resonances of drugs have been assigned for the first time. A restrained molecular dynamics approach was used to get the optimized solution structure of drugs using inter-proton distance constraints obtained from 2D NOESY spectra. The glycosidic angle C7-O7-C1′-C2′ is found to show considerable flexibility by adopting 156°-161° (I), 142°-143° (II), and 38°-78° (III) conformations, of which the biological relevant structure appears to be the conformer II. The observed different conformations of the three drugs are correlated to the differential anticancer activity and the available biochemical evidence exhibited by these drugs.  相似文献   

20.
The coaggregation of Streptococcus mitis strain J22 in the early stages of dental plaque formation has been shown to result from interaction of cell wall polysaccharides with lectins on the surface of other oral bacterial species. This bacterium was grown in a medium containing 13C as the sole carbon source. We have isolated the lectin receptor polysaccharide from this strain with full enrichment in 13C and have determined a number of two-bond and three-bond 13C-1H coupling constants from measurements of the offsets in two-dimensional homonuclear nmr spectra [exclusive correlated spectroscopy (E-COSY) method]. A scheme for reliable extraction of these coupling constants from homonuclear Hartmann-Hahn and nuclear Overhauser effect spectroscopy spectra is tested in model compounds. We interpret the three-bond coupling across the glycosidic linkage in terms of dihedral angles in order to provide conformational information to supplement molecular modeling and nuclear Overhauser effect data. We show that the E-COSY method works well even for coupling constants smaller than the nmr line width and that a number of the 3JCH across the glycosidic linkage are in the range of 1–2 Hz, which is much smaller than many previously reported values. © 1994 John Wiley & Sons, Inc.  相似文献   

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