Serge Pérez

The double-helical nature of the crystalline part of A-starch.

A new three-dimensional structure of the crystalline part of A-starch is described in which the unit cell contains 12 glucose residues located in two left-handed, parallel-stranded double helices packed in a parallel fashion; four water molecules are located between these helices. Chains are crystallized in a monoclinic lattice with a = 2.124 nm, b = 1.172 nm, c = 1.069 nm and gamma = 123.5 degrees, the c axis being parallel to the helix axis. Systematic absences are consistent with the space group B2. The structure was derived from joint use of electron diffraction of single crystals, X-ray powder patterns decomposed into individual peaks and previously reported X-ray fibre diffraction data after adequate re-indexing. The repeating unit consists of a maltotriose moiety where the glucose residues have the 4C1 pyranose conformation and are alpha(1----4) linked. The conformation of the glycosidic linkage is characterized by torsion angles (phi, psi) which take the values (91.8, -153.2), (85.7, -145.3) and 91.8, -151.3); all the primary hydroxyl groups exist in a gauche-gauche conformation. There are no intramolecular hydrogen bonds. Within the double helix, interstrand stabilization is achieved without any steric conflict and through the occurrence of O(2)...O(6) type hydrogen bonds. The present structure is consistent with both physicochemical and biochemical aspects of the crystalline component of the cereal starch granules.

Structural basis for oligosaccharide-mediated adhesion of Pseudomonas aeruginosa in the lungs of cystic fibrosis patients

Pseudomonas aeruginosa galactose- and fucose-binding lectins (PA-IL and PA-IIL) contribute to the virulence of this pathogenic bacterium, which is a major cause of morbidity and mortality in cystic fibrosis patients. The crystal structure of PA-IIL in complex with fucose reveals a tetrameric structure. Each monomer displays a nine-stranded, antiparallel b-sandwich arrangement and contains two close calcium cations that mediate the binding of fucose in a recognition mode unique among carbohydrate–protein interactions. Experimental binding studies, together with theoretical docking of fucose-containing oligosaccharides, are consistent with the assumption that antigens of the Lewis a (Lea) series may be the preferred ligands of this lectin. Precise knowledge of the lectin-binding site should allow a better design of new antibacterial-adhesion prophylactics.

Symbol Nomenclature for Graphical Representations of Glycans

Author(s): Varki, Ajit; Cummings, Richard D; Aebi, Markus; Packer, Nicole H; Seeberger, Peter H; Esko, Jeffrey D; Stanley, Pamela; Hart, Gerald; Darvill, Alan; Kinoshita, Taroh; Prestegard, James J; Schnaar, Ronald L; Freeze, Hudson H; Marth, Jamey D; Bertozzi, Carolyn R; Etzler, Marilynn E; Frank, Martin; Vliegenthart, Johannes Fg; Lutteke, Thomas; Perez, Serge; Bolton, Evan; Rudd, Pauline; Paulson, James; Kanehisa, Minoru; Toukach, Philip; Aoki-Kinoshita, Kiyoko F; Dell, Anne; Narimatsu, Hisashi; York, William; Taniguchi, Naoyuki; Kornfeld, Stuart

A complex plant cell wall polysaccharide: rhamnogalacturonan II. A structure in quest of a function

Walls of growing plants are extremely complex and sophisticated composite materials incorporating a dynamic assembly of polysaccharides, proteins and phenolics. Among the polysaccharides, the pectins encompass a group of acidic heteropolysaccharides; they offer a repertoire of structural complexity associated with the occurrence of, at least, three specific domains. Whereas most of these domains are notable for their structural heterogeneity, one of these, the so-called rhamnogalacturonan II (RG-II) exhibits a remarkable conservation throughout the plant kingdom. RG-II is thought to be the most complex plant polysaccharide on Earth (MW 5-10 kDa); its occurrence and strong conservation may indicate that it plays a major role in the structure and growth of higher plants. The present paper examines the most recent findings related to the occurrence, the structures, biosynthesis, biological role and properties, functional properties and technological applications of RG-II. Particular emphasis is given on the description of the three-dimensional structures of RG-II, in its monomeric and dimeric form as elucidated from the concerted investigations throughout 800 MHz NMR spectroscopy, light scattering, atomic force microscopy along with molecular mechanics and dynamics. Some attempts of deciphering of the structural role that RG-II may play in the cell wall of growing plants are presented.

Solid-state and solution conformation of scleroglucan

Abstract Scleroglucan is a neutral polysaccharide composed of a linear chain of (1→3)-linked β- d -glucopyranosyl residues with (1→6)-linked β- d -glucopyranosyl groups attached to every third residue. The conformational behaviour of scleroglucan has been investigated in solution and in the solid state. Order-disorder transitions in aqueous solution were studied by measurement of intrinsic viscosity. The results indicate the occurrence of such a transition at a pH /gt; 12, whereas gel formation under 10° is observed. X-Ray diffraction experiments performed on oriented fibers indicate that the backbone conformation is similar to that previously observed for curdlan, i.e. , a triple helix. The pendant (1→6)-linked β- d -glucopyranosyl residues protrude from the outside of the triplex, causing an expansion of the base plane parameters of the unit cell and further hampering lateral packing of the scleroglucan chains. The observed behaviour can be rationalized on the basis of a conformational analysis involving molecular modelling. As for the gentiobiose residue, extreme conformational flexibility about the (1→6)-β-linkage is disclosed. This conformational freedom is not significantly altered for the rotations about the (1→6)-β-linkage in the scleroglucan repeating-unit. Combination of solution and solid-state investigations provides insight into the aqueous gel-forming characteristics of scleroglucan.

CONFORMATIONAL AND CONFIGURATIONAL FEATURES OF ACIDIC POLYSACCHARIDES AND THEIR INTERACTIONS WITH CALCIUM IONS : A MOLECULAR MODELING INVESTIGATION

Modeling simulations have been performed on the four regular glycuronans: alpha-D-(1--->4) polygalacturonic, alpha-L-(1--->4) polyguluronic, beta-D-(1--->4) polymannuronic, and beta-D-(1--->4) polyglucuronic acids. The goal of this study was to characterize the similarities and differences in conformational and configurational behavior as well as in calcium binding in order to progress in the understanding of the physicochemical properties of the parent polysaccharides of industrial interest, namely pectin, alginate and glucuronan. This required the evaluation of the accessible conformational space for the disaccharide subunits of the four homopolymers, using the flexible residue protocol of the MM3 molecular mechanics procedure. The results were used to access the configurational statistics of representative polysaccharide chains, as well as for the determination of the regular polysaccharide helices and their conformational transitions. The surfaces of all regular helices likely to occur for each polyuronide were explored for cation binding using the GRID procedure. Both alpha-D-(1--->4) polygalacturonate and alpha-L-(1--->4) polyguluronate chains exhibit a high specificity for calcium binding, and have well-defined chelation sites. In contrast, beta-D-(1--->4) polymannuronate and beta-D-(1--->4) polyglucuronate chains do not display any stereospecificity for calcium binding. The results gathered from molecular modeling lead to a clear understanding of the different structural features that are displayed by the four ionic polymers.

Structural Basis of Calcium and Galactose Recognition by the Lectin Pa-Il of Pseudomonas Aeruginosa

The structure of the tetrameric Pseudomonas aeruginosa lectin I (PA‐IL) in complex with galactose and calcium was determined at 1.6 Å resolution, and the native protein was solved at 2.4 Å resolution. Each monomer adopts a β‐sandwich fold with ligand binding site at the apex. All galactose hydroxyl groups, except O1, are involved in a hydrogen bond network with the protein and O3 and O4 also participate in the co‐ordination of the calcium ion. The stereochemistry of calcium galactose binding is reminiscent of that observed in some animal C‐type lectins. The structure of the complex provides a framework for future design of anti‐bacterial compounds.

Negatively Charged Glyconanoparticles Modulate and Stabilize the Secondary Structures of a gp120 V3 Loop Peptide: Toward Fully Synthetic HIV Vaccine Candidates

The third variable region (V3 peptide) of the HIV-1 gp120 is a major immunogenic domain of HIV-1. Controlling the formation of the immunologically active conformation is a crucial step to the rational design of fully synthetic candidate vaccines. Herein, we present the modulation and stabilization of either the α-helix or β-strand conformation of the V3 peptide by conjugation to negatively charged gold glyconanoparticles (GNPs). The formation of the secondary structure can be triggered by the variation of the buffer concentration and/or pH as indicated by circular dichoism. The peptide on the GNPs shows increased stability toward peptidase degradation as compared to the free peptide. Moreover, only the V3β-GNPs bind to the anti-V3 human broadly neutralizing mAb 447-52D as demonstrated by surface plasmon resonance (SPR). The strong binding of V3β-GNPs to the 447-52D mAb was the starting point to address its study as immunogen. V3β-GNPs elicit antibodies in rabbits that recognize a recombinant gp120 and the serum displayed low but consistent neutralizing activity. These results open up the way for the design of new fully synthetic HIV vaccine candidates.

Computer simulation of histo-blood group oligosaccharides: energy maps of all constituting disaccharides and potential energy surfaces of 14 ABH and Lewis carbohydrate antigens

The three-dimensional structures of fourteen histo-blood groups carbohydrate antigens have been established through a combination of molecular mechanics and conformational searching methods. The conformational space available for each disaccharide, constituents of these determinants, has been throroughly characterized. The results have been organized in a data bank fashion. Larger relatives, i.e. 14 tri- and tetrasaccharides of histo-blood group antigens, have been modelled using a different method for exploring the complex potential energy surface. This approach is aimed at establishing all the possible families of conformations, along with the conformational pathways. Different conformational behaviours are exhibited by these oligosaccharides. Some of them, i.e. LeX and LeY tri and tetrasaccharides, are very rigid; 99% of their populations belong to the same conformational family. Others, like H type 1, H type 2 or H type 6 oligosaccharides, are essentially rigid, but a secondary conformational family, corresponding to 3–4% of the total population, can arise. Finally, the H types 3 and 4 trisaccharides, and the A type 1 and A type 2 tetrasaccharides are predicted to behave rather flexibly. The information gathered in the present investigation has been used to analyse the body of experimental evidence, either physical or biological, available for this series of carbohydrate antigens. Of special interest are the several different alignments that can be proposed for these molecules. They yield a realistic definition of the three-dimensional features of the epitopes thereby providing essential information about how carbohydrate antigens are recognized by proteins.

Conformational-energy calculations for oligosaccharides: a comparison of methods and a strategy of calculation

Abstract A theoretical conformational analysis of dimethoxymethane, 2-methoxytetrahydropyran, cellobiose, and maltose has been performed. The validity of several commonly used classical approaches to conformational energy, assuming non-bonded interactions, torsional terms, and the exo-anomeric contribution, and the MM2CARB method (a modified version of the MM2 force-field program using the Jeffrey-Taylor parameters) was tested against available experimental data or previous quantum-chemical calculations. The MM2CARB method correctly reproduces the energies and the variations in bond lengths and bond angles for conformers of dimethoxymethane and 2-methoxytetrahydropyran. Prediction of the observed conformers with simple potential functions appears to be less satisfactory. In particular, calculations that take into account non-bonded interactions and the exo-anomeric contribution based on dimethoxymethane give predicted energy differences that are 2–3 times higher than the experimental values. The general shapes of the ( Φ , Ψ ) potential-energy surfaces for cellobiose and maltose provided by potential-function calculations suggest the presence of several minima whose energies depend, to a great extent, on the choice of molecular geometry. The MM2CARB-calculated structures of seven cellobiose and five maltose conformers demonstrate clearly the variation of disaccharide geometry with change of conformation around the glycosidic linkage. The relative energies calculated by simple methods differ from MM2CARB energies and indicate that the simple potential-functions methods give only a qualitative estimate of oligosaccharide conformers. Based on these results, we propose a general strategy and two different approaches for the investigation of conformational properties of oligosaccharides.