Showing papers by "Serge Pérez published in 1999"

The Relationship Between Internal Chain Length of Amylopectin and Crystallinity in Starch

Abstract: Molecular models of amylopectin were created and investigated by computer simulation. First, single and double helices of various lengths were constructed. The 1 --> 6 branching in double and single helices of amylopectin was studied. Subunits of single helices, double helices, and branch points were used as building blocks of larger systems. The possible makeup of amylopectin unit clusters was investigated via a series of models, including single-single, double-single, and double-double helix systems. The lengths of the single helix section that linked two branch points (internal chains) was systematically varied between values of 0-10 glucose residues. It was found that certain internal chain lengths lead to parallel double helices. Thus, it was postulated that the length of internal chains may determine the degree of local crystallinity. Furthermore, it was noted that some of the low-energy arrangement of double helices could be superimposed on either the two adjacent and nonadjacent double helices of crystalline A and B starch polymorphs. In other cases, the distance between the double helices is so large that it may in fact be a model for branching between two amylopectin crystals or unit clusters. Results obtained through this work were corroborated, where possible, with information available from crystallographic, branching, and enzymatic studies.

An NMR solution study of the mega-oligosaccharide, rhamnogalacturonan II.

Abstract: Rhamnogalacturonan II (RG-II) is a structurally complex pectic mega-oligosaccharide that is released enzymatically from the primary cell wall of higher plants. It contains roughly 30 monosaccharide units (MW ∼5 kDa) including very unusual residues such as Kdo, Dha, aceric acid and apiose. Previous studies have demonstrated that these monomers are arranged into four structurally well-defined oligosaccharide side chains (A–D), linked to a homogalacturonan mainchain, but the specific attachment sites of these branches on the pectic backbone have not yet been elucidated. In the present work, fairly complete assignments of the 750 MHz 1 H NMR spectra and partial assignments of the 13 C NMR spectra of the sodium-borohydride-reduced RG-II monomer were obtained for a 5 mM sample isolated from red wine. On the whole, these data corroborate the primary structures of the sidechains previously established by methylation analysis, partial hydrolysis and FAB-MS spectrometry but some heterogeneity has been demonstrated (partial substitution at B5, B6, and A5). The preferred orientations of the majority of the sidechain glycosidic linkages in the RG-II monomer have been determined from the sequential nOe data and the solution structure is generally in good agreement with the stable conformers previously obtained by molecular modeling (MM3) of the disaccharide and sidechain oligosaccharide building blocks. All of a two-residue, a three-residue, and a four-residue segment of the backbone have been tentatively identified from long range interactions between sidechain protons as well as in the mainchain. Taking into account the length of the 9-mer galacturonan mainchain described in prior work, these building blocks constitute almost the complete structure of RG-II (Scheme 2).

Stereochemical analysis of d-glucopyranosyl-sulfoxides via a combined NMR, molecular modeling and X-ray crystallographic approach

Abstract: ( S )-α-Methoxyphenylacetic acid (MPAA) was used as an NMR shift reagent in combination with molecular modeling to predict the absolute configuration of a representative epimeric pair of glucopyranosyl sulfoxides. The correctness of this assignment was confirmed by X-ray crystallographic examination of one of the epimers, 3a1 . The crystal structure of ethyl 2,3-di- O -acetyl-4,6- O -benzylidene-1-thio-β- d -glucopyranoside S -oxide monohydrate 3a1 was solved by direct methods and was shown to bear the ( R )-configuration at the sulfinyl center in accordance with our prediction. Furthermore, the conformation of 3a1 in the solid state was found to be remarkably similar to that predicted by molecular mechanics calculations.

Shapes and interactions of polysaccharide chains

Abstract: Polysaccharides form the most abundant and diverse family of biopolymers. With several hundreds of known examples they offer a great diversity of chemical structures, ranging from simple linear homopolymers to branched heteropolymers, having repeating units of up to octasaccharides. Simple polysaccharides, with a repeating structure composed of monosaccharides, are used to store energy, as in starch, glycogen, locust bean gum and guar gum. Carbohydrate functions are not limited to the storage or production of energy. Cellulose, a simple polymer of glucose, is an essential constituent of plant cell walls. It generates hard and solid elements in the form of tough fibers. The plasticity of the cell wall is further regulated via hydrated cross-linked three-dimensional networks where polysaccharides such as pectins play a key function. In marine species, carbohydrate polymers such as agar, alginates and carrageenans play a similar role. Other polysaccharides create viscous extracellular layers around bacteria. In the animal kingdom, the family of glycosaminoglycans (hyaluronate, chondroitin sulfate, derma-tan sulfate etc.) plays a key role in governing the solution properties of some physiological fluids as well as participating in the structural buildup of the intercellular matrix.

The Crystal and Molecular Structure of a Diglycosylamine: The N-Analogue of Peracetylated α,β-Trehalose.

Abstract: Crystals of the disaccharide, (2,3,4,6-tetra- O -acetyl- α - d -glucopyranosyl) (2,3,4,6–tetra- O -acetyl- β - d -glucopyranosyl)amine belong to the space group P2 1 with a =14.848(2), b =21.838(3), c =11.534(2) A, and β =113.72(4)° and Z=4. The crystal structure was solved by direct methods and refined by the full-matrix least squares procedure to an R value of 0.049 ( Rw =0.46) for 4262 observed reflections. This work provides the first crystalline features in the diglycosylamine series and this molecule can be considered as a N -analogue of peracetylated α , β -trehalose. The conformational features of the two independent diglycosylamine molecules do not display any major significant differences. The d –glucopyranose residues have the usual 4 C 1 chair conformations, whereas all the primary and secondary acetate groups display usual orientations. In the crystal structure the hydrogen atom covalently linked to the nitrogen at the glycosidic linkage could be located; its configuration is ( R ) providing the priority is given to the ( R ) carbon neighbor (C-1 β ). The torsional angles at the glycosidic linkages Φα (O-5–C-1 α –N-1–C-1 β ), Φβ (C-1 α –N-1–C-1 β –O-5) of the two molecules have values of (57.6°,−78.8°) and (59.8°,−85.9°), respectively, slightly different from the conformation found in α , β -trehalose monohydrate. These conformations have been rationalized through the use of molecular mechanics calculations. The packing mode is highly anisotropic, with the existence of chains of molecules along the c axis, stabilized by numerous van der Waals contacts and by a strong hydrogen bond, involving the NH group of the glycosidic linkage and the carbonyl group of one acetate.