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1.
Org Biomol Chem ; 19(33): 7190-7201, 2021 09 07.
Artigo em Inglês | MEDLINE | ID: mdl-34382051

RESUMO

d-Allosamine is a rare sugar in Nature but its pyranoid form has been found α-linked in the core region of the lipopolysaccharide from the Gram-negative bacterium Porphyromonas gingivalis and in the chitanase inhibitor allosamidin, then ß-linked and N-acetylated. In water solution the monosaccharide N-acetyl-d-allosamine (d-AllNAc) shows a significant presence of four tautomers arising from pyranoid and furanoid ring forms and anomeric configurations. The furanoid ring forms both showed 3JH1,H2≈ 4.85 Hz and to differentiate the anomeric configurations a series of chemical shift anisotropy/dipole-dipole cross-correlated relaxation NMR experiments was performed in which the α-anomeric form showed notable different relaxation rates for its components of the H1 doublet, thereby making it possible to elucidate the anomeric configuration of each of the furanoses. The conformational preferences of the different forms of d-AllNAc were investigated by 3JHH, 2JCH and 3JCH coupling constants from NMR experiments, molecular dynamics simulations and density functional theory calculations. The pyranose form resides in the 4C1 conformation and the furanose ring form has the majority of its conformers located on the South-East region of the pseudorotation wheel, with a small population in the Northern hemisphere. The tautomeric equilibrium was quite sensitive to changes in temperature, where the ß-anomer of the pyranoid ring form decreased upon a temperature increase while the other forms increased.

2.
Chembiochem ; 20(19): 2519-2528, 2019 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-31066963

RESUMO

Carbohydrates, also known as glycans in biological systems, are omnipresent in nature where they as glycoconjugates occur as oligo- and polysaccharides linked to lipids and proteins. Their three-dimensional structure is defined by two or three torsion angles at each glycosidic linkage. In addition, transglycosidic hydrogen bonding between sugar residues may be important. Herein we investigate the presence of these inter-residue interactions by NMR spectroscopy in D2 O/[D6 ]DMSO (70:30) or D2 O and by molecular dynamics (MD) simulations with explicit water as solvent for disaccharides with structural elements α-d-Manp-(1→2)-d-Manp, ß-d-GlcpNAc-(1→2)-d-Manp, and α-d-Glcp-(1→4)-ß-d-Glcp, all of which have been suggested to exhibit inter-residue hydrogen bonding. For the disaccharide ß-d-GlcpNAc-(1→2)-ß-d-Manp-OMe, the large extent of O5'⋅⋅⋅HO3 hydrogen bonding as seen from the MD simulation is implicitly supported by the 1 H NMR chemical shift and 3 JHO3,H3 value of the hydroxy proton. In the case of α-d-Glcp-(1→4)-ß-d-Glcp-OMe, the existence of a transglycosidic hydrogen bond O2'⋅⋅⋅HO3 was proven by the presence of a cross-peak in 1 H,13 C HSQC-TOCSY experiments as a result of direct TOCSY transfer between HO3 of the reducing end residue and H2' (detected at C2') of the terminal residue. The occurrence of inter-residue hydrogen bonding, albeit transient, is judged important for the stabilization of three-dimensional structures, which may be essential in maintaining a conformational state for carbohydrate-protein interactions of glycans to take place in biologically important environments.


Assuntos
Carboidratos/química , Dissacarídeos/química , Espectroscopia de Ressonância Magnética/métodos , Simulação de Dinâmica Molecular , Configuração de Carboidratos , Ligação de Hidrogênio , Modelos Moleculares , Termodinâmica
3.
Phys Chem Chem Phys ; 18(28): 18776-94, 2016 Jul 28.
Artigo em Inglês | MEDLINE | ID: mdl-27346493

RESUMO

The conformation of saccharides in solution is challenging to characterize in the context of a single well-defined three-dimensional structure. Instead, they are better represented by an ensemble of conformations associated with their structural diversity and flexibility. In this study, we delineate the conformational heterogeneity of five trisaccharides via a combination of experimental and computational techniques. Experimental NMR measurements target conformationally sensitive parameters, including J couplings and effective distances around the glycosidic linkages, while the computational simulations apply the well-calibrated additive CHARMM carbohydrate force field in combination with efficient enhanced sampling molecular dynamics simulation methods. Analysis of conformational heterogeneity is performed based on sampling of discreet states as defined by dihedral angles, on root-mean-square differences of Cartesian coordinates and on the extent of volume sampled. Conformational clustering, based on the glycosidic linkage dihedral angles, shows that accounting for the full range of sampled conformations is required to reproduce the experimental data, emphasizing the utility of the molecular simulations in obtaining an atomic detailed description of the conformational properties of the saccharides. Results show the presence of differential conformational preferences as a function of primary sequence and glycosidic linkage types. Significant differences in conformational ensembles associated with the anomeric configuration of a single glycosidic linkage reinforce the impact of such changes on the conformational properties of carbohydrates. The present structural insights of the studied trisaccharides represent a foundation for understanding the range of conformations adopted in larger oligosaccharides and how these molecules encode their conformational heterogeneity into the monosaccharide sequence.

4.
J Phys Chem B ; 117(47): 14709-22, 2013 Nov 27.
Artigo em Inglês | MEDLINE | ID: mdl-24175957

RESUMO

The intrinsic flexibility of carbohydrates facilitates different 3D structures in response to altered environments. At glycosidic (1→6)-linkages, three torsion angles are variable, and herein the conformation and dynamics of ß-L-Fucp-(1→6)-α-D-Glcp-OMe are investigated using a combination of NMR spectroscopy and molecular dynamics (MD) simulations. The disaccharide shows evidence of conformational averaging for the ψ and ω torsion angles, best explained by a four-state conformational distribution. Notably, there is a significant population of conformations having ψ = 85° (clinal) in addition to those having ψ = 180° (antiperiplanar). Moderate differences in (13)C R1 relaxation rates are found to be best explained by axially symmetric tumbling in combination with minor differences in librational motion for the two residues, whereas the isomerization motions are occurring too slowly to be contributing significantly to the observed relaxation rates. The MD simulation was found to give a reasonably good agreement with experiment, especially with respect to diffusive properties, among which the rotational anisotropy, D∥/D⊥, is found to be 2.35. The force field employed showed too narrow ω torsion angles in the gauche-trans and gauche-gauche states as well as overestimating the population of the gauche-trans conformer. This information can subsequently be used in directing parameter developments and emphasizes the need for refinement of force fields for (1→6)-linked carbohydrates.


Assuntos
Dissacarídeos/química , Água/química , Configuração de Carboidratos , Espectroscopia de Ressonância Magnética , Simulação de Dinâmica Molecular , Soluções
5.
Carbohydr Res ; 380: 156-66, 2013 Oct 18.
Artigo em Inglês | MEDLINE | ID: mdl-24036391

RESUMO

(1)H and (13)C NMR chemical shift data are used by the computer program CASPER to predict chemical shifts of oligo- and polysaccharides. Three types of data are used, namely, those from monosaccharides, disaccharides, and trisaccharides. To improve the accuracy of these predictions we have assigned the (1)H and (13)C NMR chemical shifts of eleven monosaccharides, eleven disaccharides, twenty trisaccharides, and one tetrasaccharide; in total 43 compounds. Five of the oligosaccharides gave two distinct sets of NMR resonances due to the α- and ß-anomeric forms resulting in 48 (1)H and (13)C NMR chemical shift data sets. In addition, the pyranose ring forms of Neu5Ac were assigned at two temperatures, due to chemical shift displacements as a function of temperature. The (1)H NMR chemical shifts were refined using total line-shape analysis with the PERCH NMR software. (1)H and (13)C NMR chemical shift predictions were subsequently carried out by the CASPER program (http://www.casper.organ.su.se/casper/) for three branched oligosaccharides having different functional groups at their reducing ends, namely, a mannose-containing pentasaccharide, and two fucose-containing heptasaccharides having N-acetyllactosamine residues in the backbone of their structures. Good to excellent agreement was observed between predicted and experimental (1)H and (13)C NMR chemical shifts showing the utility of the method for structural determination or confirmation of synthesized oligosaccharides.


Assuntos
Espectroscopia de Ressonância Magnética/métodos , Monossacarídeos/química , Oligossacarídeos/química , Software
6.
Org Biomol Chem ; 10(23): 4577-85, 2012 Jun 21.
Artigo em Inglês | MEDLINE | ID: mdl-22572908

RESUMO

Human milk oligosaccharides (HMOs) are important as prebiotics since they stimulate the growth of beneficial bacteria in the intestine and act as receptor analogues that can inhibit the binding of pathogens. The conformation and dynamics of the HMO Lacto-N-fucopentaose 2 (LNF-2), α-L-Fucp-(1 → 4)[ß-D-Galp-(1 → 3)]-ß-D-GlcpNAc-(1 → 3)-ß-D-Galp-(1 → 4)-D-Glcp, having a Lewis A epitope, has been investigated employing NMR spectroscopy and molecular dynamics (MD) computer simulations. 1D (1)H,(1)H-NOESY experiments were used to obtain proton-proton cross-relaxation rates from which effective distances were deduced and 2D J-HMBC and 1D long-range experiments were utilized to measure trans-glycosidic (3)J(CH) coupling constants. The MD simulations using the PARM22/SU01 force field for carbohydrates were carried out for 600 ns with explicit water as solvent which resulted in excellent sampling for flexible glycosidic torsion angles. In addition, in vacuo MD simulations were performed using an MM3-2000 force field, but the agreement was less satisfactory based on an analysis of heteronuclear trans-glycosidic coupling constants. LNF-2 has a conformationally well-defined region consisting of the terminal branched part of the pentasaccharide, i.e., the Lewis A epitope, and a flexible ß-D-GlcpNAc-(1 → 3)-ß-D-Galp-linkage towards the lactose unit, which is situated at the reducing end. For this ß-(1 → 3)-linkage a negative ψ torsion angle is favored, when experimental NMR data is combined with the MD simulation in the analysis. In addition, flexibility on a similar time scale, i.e., on the order of the global overall molecular reorientation, may also be present for the ϕ torsion angle of the ß-D-Galp-(1 → 4)-D-Glcp-linkage as suggested by the simulation. It was further observed from a temperature variation study that some (1)H NMR chemical shifts of LNF-2 were highly sensitive and this study indicates that Δδ/ΔT may be an additional tool for revealing conformational dynamics of oligosaccharides.


Assuntos
Oligossacarídeos/química , Simulação por Computador , Modelos Moleculares , Conformação Molecular , Ressonância Magnética Nuclear Biomolecular
7.
Org Biomol Chem ; 10(12): 2453-63, 2012 Mar 28.
Artigo em Inglês | MEDLINE | ID: mdl-22344369

RESUMO

Bacterial polysaccharides are comprised of a variety of monosaccharides, L-rhamnose (6-deoxy-L-mannose) being one of them. This sugar is often part of α-(1 → 2)- and/or α-(1 → 3)-linkages and we have therefore studied the disaccharide α-L-Rhap-(1 → 2)-α-L-Rhap-OMe to obtain information on conformational preferences at this glycosidic linkage. The target disaccharide was synthesized with (13)C site-specific labeling at C1' and at C2', i.e., in the terminal group. 2D (1)H,(13)C-HSQC-HECADE and (1)H,(13)C-J-HMBC NMR experiments, 1D (13)C and (1)H NMR spectra together with total line-shape analysis were used to extract conformationally dependent hetero- and homonuclear spin-spin coupling constants. This resulted in the determination of (2)J(C2',H1'), (3)J(C1',C1), (3)J(C1',C3), (3)J(C2',C2), (2)J(C1',C2), (1)J(C1',C2'), and (1)J(C1',H1'). These data together with previously determined J(CH) and (1)H,(1)H NOEs result in fourteen conformationally dependent NMR parameters that are available for analysis of glycosidic linkage flexibility and conformational preferences. A 100 ns molecular dynamics (MD) simulation of the disaccharide with explicit water molecules as solvent showed a major conformational state at φ(H)≈ 40° and ψ(H)≈-35°, consistent with experimental NMR data. In addition, MD simulations were carried out also for α-L-Rhap-(1 → 3)-α-L-Rhap-OMe and a rhamnan hexasaccharide. The gathered information on the oligosaccharides was used to address conformational preferences for a larger structure, a 2- and 3-linked nonasaccharide, with implications for the 3D structure of rhamnan polysaccharides, which should be regarded as flexible polymers.


Assuntos
Bactérias/química , Desoxiaçúcares/química , Mananas/química , Oligossacarídeos/química , Ramnose/química , Espectroscopia de Ressonância Magnética , Modelos Moleculares , Conformação Molecular
8.
Carbohydr Res ; 348: 99-103, 2012 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-22196926

RESUMO

The structure of the repeating unit of the O-antigenic polysaccharide from Plesiomonas shigelloides strain AM36565 has been determined. Component analysis and (1)H and (13)C NMR spectroscopy experiments were employed to elucidate the structure. Inter-residue correlations were determined by (1)H,(13)C heteronuclear multiple-bond correlation, (1)H,(1)H-NOESY, and (1)H,(13)C-HSQC-(1)H,(1)H-NOESY experiments. The O-antigen polysaccharide is composed of repeating units with the following structure: →3)-α-L-Rhap-(1→2)-α-L-Rhap-(1→4)[ß-D-GalpNAc-(1→3)]-α-D-GlcpNAc-(1→, in which the monosaccharide side-chain substitutes the backbone in half of the repeating units. A matrix-assisted laser desorption/ionization mass spectrometry experiment suggested that the polysaccharide consists of two regions, one with tetrasaccharide repeating units and one with trisaccharide repeating units.


Assuntos
Antígenos O/química , Plesiomonas/química , Sequência de Carboidratos , Espectroscopia de Ressonância Magnética , Antígenos O/isolamento & purificação , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz
9.
Carbohydr Res ; 346(11): 1311-9, 2011 Aug 16.
Artigo em Inglês | MEDLINE | ID: mdl-21621752

RESUMO

The computer program casper uses (1)H and (13)C NMR chemical shift data of mono- to trisaccharides for the prediction of chemical shifts of oligo- and polysaccharides. In order to improve the quality of these predictions the (1)H and (13)C, as well as (31)P when applicable, NMR chemical shifts of 30 mono-, di-, and trisaccharides were assigned. The reducing sugars gave two distinct sets of NMR resonances due to the α- and ß-anomeric forms. In total 35 (1)H and (13)C NMR chemical shift data sets were obtained from the oligosaccharides. One- and two-dimensional NMR experiments were used for the chemical shift assignments and special techniques were employed in some cases such as 2D (1)H,(13)C-HSQC Hadamard Transform methodology which was acquired approximately 45 times faster than a regular t(1) incremented (1)H,(13)C-HSQC experiment and a 1D (1)H,(1)H-CSSF-TOCSY experiment which was able to distinguish spin-systems in which the target protons were only 3.3Hz apart. The (1)H NMR chemical shifts were subsequently refined using total line-shape analysis with the PERCH NMR software. The acquired NMR data were then utilized in the casper program (http://www.casper.organ.su.se/casper/) for NMR chemical shift predictions of the O-antigen polysaccharides from Klebsiella O5, Shigella flexneri serotype X, and Salmonella arizonae O62. The data were compared to experimental data of the polysaccharides from the two former strains and the lipopolysaccharide of the latter strain showing excellent agreement between predicted and experimental (1)H and (13)C NMR chemical shifts.


Assuntos
Espectroscopia de Ressonância Magnética/métodos , Monossacarídeos/química , Oligossacarídeos/química , Polissacarídeos/química , Trissacarídeos/química , Lipopolissacarídeos/química
10.
J Phys Chem B ; 115(21): 7109-21, 2011 Jun 02.
Artigo em Inglês | MEDLINE | ID: mdl-21545157

RESUMO

The conformational dynamics of the human milk oligosaccharide lacto-N-fucopentaose (LNF-1), α-L-Fucp-(1 → 2)-ß-D-Galp-(1 → 3)-ß-D-GlcpNAc-(1 → 3)-ß-D-Galp-(1 → 4)-D-Glcp, has been analyzed using NMR spectroscopy and molecular dynamics (MD) computer simulations. Employing the Hadamard (13)C-excitation technique and the J-HMBC experiment, (1)H,(13)C trans-glycosidic J coupling constants were obtained, and from one- and two-dimensional (1)H,(1)H T-ROESY experiments, proton-proton cross-relaxation rates were determined in isotropic D(2)O solution. In the lyotropic liquid-crystalline medium consisting of ditetradecylphosphatidylcholine, dihexylphosphatidylcholine, N-cetyl-N,N,N-trimethylammonium bromide, and D(2)O, (1)H, (1)H and one-bond (1)H, (13)C residual dipolar couplings (RDCs), as well as relative sign information on homonuclear RDCs, were determined for the pentasaccharide. Molecular dynamics simulations with explicit water were carried out from which the internal isomerization relaxation time constant, τ(N), was calculated for transitions at the ψ torsion angle of the ß-(1 → 3) linkage to the lactosyl group in LNF-1. Compared to the global reorientation time, τ(M), of ∼0.6 ns determined experimentally in D(2)O solution, the time constant for the isomerization relaxation process, τ(N(scaled)), is about one-third as large. The NMR parameters derived from the isotropic solution show very good agreement with those calculated from the MD simulations. The only notable difference occurs at the reducing end, which should be more flexible than observed by the molecular simulation, a conclusion in complete agreement with previous (13)C NMR relaxation data. A hydrogen-bond analysis of the MD simulation revealed that inter-residue hydrogen bonds on the order of ∼30% were present across the glycosidic linkages to sugar ring oxygens. This finding highlights that intramolecular hydrogen bonds might be important in preserving well-defined structures in otherwise flexible molecules. An analysis including generalized order parameters obtained from nuclear spin relaxation experiments was performed and successfully shown to limit the conformational space accessible to the molecule when the number of experimental data are too scarce for a complete conformational analysis.


Assuntos
Simulação de Dinâmica Molecular , Oligossacarídeos/química , Configuração de Carboidratos , Humanos , Espectroscopia de Ressonância Magnética , Modelos Moleculares
11.
J Phys Chem B ; 115(3): 597-608, 2011 Jan 27.
Artigo em Inglês | MEDLINE | ID: mdl-21158455

RESUMO

An investigation of the conformational properties of methyl ß-maltoside, methyl α-cellobioside, and methyl ß-cellobioside disaccharides using NMR spectroscopy and molecular dynamics (MD) techniques, is presented. Emphasis is placed on validation of a recently presented force field for hexopyranose disaccharides followed by elucidation of the conformational properties of two different types of glycosidic linkages, α-(1 → 4) and ß-(1 → 4). Both gas-phase and aqueous-phase simulations are performed to gain insight into the effect of solvent on the conformational properties. A number of transglycosidic J-coupling constants and proton-proton distances are calculated from the simulations and are used to identify the percent sampling of the three glycosidic conformations (syn, anti-φ, and anti-ψ) and, in turn, describe the flexibility around the glycosidic linkage. The results show the force field to be in overall good agreement with experiment, although some very small limitations are evident. Subsequently, a thorough hydrogen bonding analysis is performed to obtain insights into the conformational properties of the disaccharides. In methyl ß-maltoside, competition between HO2'-O3 intramolecular hydrogen bonding and intermolecular hydrogen bonding of those groups with solvent leads to increased sampling of syn, anti-φ, and anti-ψ conformations and better agreement with NMR J-coupling constants. In methyl α- and ß-cellobioside, O5'-HO6 and HO2'-O3 hydrogen bonding interactions are in competition with intermolecular hydrogen bonding involving the solvent molecules. This competition leads to retention of the O5'-HO3 hydrogen bond and increased sampling of the syn region of the φ/ψ map. Moreover, glycosidic torsions are correlated to the intramolecular hydrogen bonding occurring in the molecules. The present results verify that in the ß-(1 → 4)-linkage intramolecular hydrogen bonding in the aqueous phase is due to the decreased ability of water to successfully compete for the O5' and HO3 hydrogen bonding moieties, in contrast to that occurring between the O5' and HO6 atoms in this α-(1 → 4)-linkage.


Assuntos
Configuração de Carboidratos , Dissacarídeos/química , Glucosídeos/química , Estrutura Molecular , Ligação de Hidrogênio , Espectroscopia de Ressonância Magnética , Modelos Moleculares , Simulação de Dinâmica Molecular
12.
Org Biomol Chem ; 8(16): 3684-95, 2010 Aug 21.
Artigo em Inglês | MEDLINE | ID: mdl-20574564

RESUMO

The conformational space available to the flexible molecule α-D-Manp-(1-->2)-α-D-Manp-OMe, a model for the α-(1-->2)-linked mannose disaccharide in N- or O-linked glycoproteins, is determined using experimental data and molecular simulation combined with a maximum entropy approach that leads to a converged population distribution utilizing different input information. A database survey of the Protein Data Bank where structures having the constituent disaccharide were retrieved resulted in an ensemble with >200 structures. Subsequent filtering removed erroneous structures and gave the database (DB) ensemble having three classes of mannose-containing compounds, viz., N- and O-linked structures, and ligands to proteins. A molecular dynamics (MD) simulation of the disaccharide revealed a two-state equilibrium with a major and a minor conformational state, i.e., the MD ensemble. These two different conformation ensembles of the disaccharide were compared to measured experimental spectroscopic data for the molecule in water solution. However, neither of the two populations were compatible with experimental data from optical rotation, NMR (1)H,(1)H cross-relaxation rates as well as homo- and heteronuclear (3)J couplings. The conformational distributions were subsequently used as background information to generate priors that were used in a maximum entropy analysis. The resulting posteriors, i.e., the population distributions after the application of the maximum entropy analysis, still showed notable deviations that were not anticipated based on the prior information. Therefore, reparameterization of homo- and heteronuclear Karplus relationships for the glycosidic torsion angles Φ and Ψ were carried out in which the importance of electronegative substituents on the coupling pathway was deemed essential resulting in four derived equations, two (3)J(COCC) and two (3)J(COCH) being different for the Φ and Ψ torsions, respectively. These Karplus relationships are denoted JCX/SU09. Reapplication of the maximum entropy analysis gave excellent agreement between the MD- and DB-posteriors. The information entropies show that the current reparametrization of the Karplus relationships constitutes a significant improvement. The Φ(H) torsion angle of the disaccharide is governed by the exo-anomeric effect and for the dominating conformation Φ(H) = -40 degrees and Ψ(H) = 33 degrees. The minor conformational state has a negative Ψ(H) torsion angle; the relative populations of the major and the minor states are approximately 3 : 1. It is anticipated that application of the methodology will be useful to flexible molecules ranging from small organic molecules to large biomolecules.


Assuntos
Dissacarídeos/química , Entropia , Glicoproteínas/química , Manose/química , Espectroscopia de Ressonância Magnética , Modelos Moleculares , Conformação Molecular , Estrutura Molecular
13.
Phys Chem Chem Phys ; 12(25): 6587-9, 2010 Jul 07.
Artigo em Inglês | MEDLINE | ID: mdl-20445946

RESUMO

The dynamics of GATG glycodendrimers have been investigated by NMR translational diffusion and quantitative (13)C relaxation studies (Lipari-Szabo model-free), allowing the determination of the correlation times describing the dendrimer segmental orientational mobility.


Assuntos
Dendrímeros/química , Espectroscopia de Ressonância Magnética , Nucleotídeos/química , Isótopos de Carbono/química , Difusão , Fucose/química
14.
J Biomol NMR ; 47(2): 125-34, 2010 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-20474086

RESUMO

The use of lactic acid bacteria in fermentation of milk results in favorable physical and rheological properties due to in situ exopolysaccharide (EPS) production. The EPS from S. thermophilus ST1 produces highly viscous aqueous solutions and its structure has been investigated by NMR spectroscopy. Notably, all aspects of the elucidation of its primary structure including component analysis and absolute configuration of the constituent monosaccharides were carried out by NMR spectroscopy. An array of techniques was utilized including, inter alia, PANSY and NOESY-HSQC TILT experiments. The EPS is composed of hexasaccharide repeating units with the following structure: --> 3)[alpha-D-Glcp-(1 --> 4)]-beta-D-Galp-(1 --> 4)-beta-D-Glcp-(1 --> 4)[beta-D-Galf-(1 --> 6)]-beta-D-Glcp-(1 --> 6)-beta-D-Glcp-(1 -->, in which the residues in square brackets are terminal groups substituting backbone sugar residues that consequently are branch-points in the repeating unit of the polymer. Thus, the EPS consists of a backbone of four sugar residues with two terminal sugar residues making up two side-chains of the repeating unit. The molecular mass of the polymer was determined using translational diffusion experiments which resulted in Mw = 62 kDa, corresponding to 64 repeating units in the EPS.


Assuntos
Ressonância Magnética Nuclear Biomolecular/métodos , Polissacarídeos Bacterianos/química , Streptococcus thermophilus/química , Isótopos de Carbono , Glicosilação , Conformação Molecular , Peso Molecular , Polissacarídeos Bacterianos/metabolismo , Streptococcus thermophilus/metabolismo
15.
Carbohydr Res ; 345(8): 984-93, 2010 May 27.
Artigo em Inglês | MEDLINE | ID: mdl-20347069

RESUMO

The synthesis of two novel carbasugar analogues of alpha-L-iduronic acid is described in which the ring-oxygen is replaced by a methylene group. In analogy with the conformational equilibrium described for alpha-L-IdopA, the conformation of the carbasugars was investigated by (1)H and (13)C NMR spectroscopy. Hadamard transform NMR experiments were utilised for rapid acquisition of (1)H,(13)C-HSQC spectra and efficient measurements of heteronuclear long-range coupling constants. Analysis of (1)H NMR chemical shifts and J(H,H) coupling constants extracted by a total-lineshape fitting procedure in conjunction with J(H,C) coupling constants obtained by three different 2D NMR experiments, viz., (1)H,(13)C-HSQC-HECADE, J-HMBC and IPAP-HSQC-TOCSY-HT, as well as effective proton-proton distances from 1D (1)H,(1)H T-ROE and NOE experiments showed that the conformational equilibrium [formula in text] is shifted towards (4)C(1) as the predominant or exclusive conformation. These carbasugar bioisosteres of alpha-l-iduronic acid do not as monomers show the inherent flexibility that is anticipated to be necessary for biological activity.


Assuntos
Glicosídeos/química , Glicosídeos/síntese química , Ácido Idurônico/análogos & derivados , Espectroscopia de Ressonância Magnética , Conformação Molecular , Estrutura Molecular
16.
Chemistry ; 15(35): 8886-94, 2009 Sep 07.
Artigo em Inglês | MEDLINE | ID: mdl-19637158

RESUMO

The conformational flexibility and dynamics of two (1-->6)-linked disaccharides that are related to the action of the glycosyl transferase GnT-V have been investigated. NMR NOE and T-ROE spectroscopy experiments, conformation-dependent coupling constants and molecular dynamics (MD) simulations were used in the analyses. To facilitate these studies, the compounds were synthesised as alpha-d-[6-(13)C]-Manp-OMe derivatives, which reduced the (1)H NMR spectral overlap and facilitated the determination of two- and three-bond (1)H,(1)H, (1)H,(13)C and (13)C,(13)C-coupling constants. The population distribution for the glycosidic omega torsion angle in alpha-d-Manp-(1-->6)-alpha-d-Manp-OMe for gt/gg/tg was equal to 45:50:5, whereas in alpha-d-Manp-OMe it was determined to be 56:36:8. The dynamic model that was generated for beta-d-GlcpNAc-(1-->6)-alpha-d-Manp-OMe by MD simulations employing the PARM22/SU01 CHARMM-based force field was in very good agreement with experimental observations. beta-d-GlcpNAc-(1-->6)-alpha-d-Manp-OMe is described by an equilibrium of populated states in which the phi torsion angle has the exo-anomeric conformation, the psi torsion angle an extended antiperiplanar conformation and the omega torsion angle a distribution of populations predominantly between the gauche-trans and the gauche-gauche conformational states (i.e., gt/gg/tg) is equal to 60:35:5, respectively. The use of site-specific (13)C labelling in these disaccharides leads to increased spectral dispersion, thereby making NMR spectroscopy based conformational analysis possible that otherwise might be difficult to attain.


Assuntos
Epitopos/química , Oligossacarídeos/química , Configuração de Carboidratos , Simulação por Computador , Espectroscopia de Ressonância Magnética
17.
Bioorg Med Chem ; 14(19): 6659-65, 2006 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-16782347

RESUMO

Two formally C-xylosylated analogs to 2-naphthyl beta-D-xylopyranoside, which is known to initiate priming of glucosaminoglycan chains, were synthesized by a position inversion of glucose (i.e., position 1 becomes position 5). The D-C-xyloside showed priming, while the L-C-xyloside did not initiate priming.


Assuntos
Glucose/química , Glicosídeos/química , Glicosídeos/síntese química , Células 3T3 , Animais , Sequência de Carboidratos , Cromatografia Líquida de Alta Pressão , Cromatografia em Camada Fina , Indicadores e Reagentes , Espectroscopia de Ressonância Magnética , Camundongos , Dados de Sequência Molecular
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