The conformational free-energy map for solvated neocarrabiose

Potential of mean force conformational energy maps for disaccharide linkages of the Burkholderia multivorans exopolysaccharide C1576 in aqueous solution

Potential of Mean Force Ramachandran energy maps in aqueous solution have been prepared for all of the glycosidic linkages found in the C1576 exopolysaccharide from the biofilms of the bacterial species Burkholderia multivorans, a member of the Burkholderia cepacian complex that was isolated from a cystic fibrosis patient. C1576 is a rhamnomannan with a tetrasaccharide repeat unit. In general, for the four linkage types in this polymer, hydration did not produce dramatic changes in the Ramachandran energy surfaces, with the 3-methyl-α-d-rhamnopyranose-(1→3)-α-d-rhamnopyranose case exhibiting the greatest hydration change, with the global minimum energy conformation shifting by more than 80° in ψ. However, hydration did reduce the rigidity of all the linkages, increasing the overall flexibility of this polysaccharide.

Molecular dynamics simulations of two double-helical hexamer fragments of iota-carrageenan in aqueous solution

The gelation of anionic carrageenans is known to occur through a coil-to-helix transition followed by further aggregation or association on which positive counterions play a significant role. In the present work, molecular dynamics (MD) simulations were performed on two double-helical iota-carrageenan hexamer fragments along with their sodium counterions using the Carbohydrate Solution Force Field (CSFF) in an aqueous (TIP4P) solution with the GROMACS molecular dynamics package. Results showed a counterion condensation between the two double helices and that the subsequent forces of interaction between them were predominantly attractive. By varying the distance separating the two double helices, the effect of distance on the counterion distribution and the forces of attraction was also investigated. In the presence of counterions, an increase in the forces of attraction was observed as the distance between the two double helices decreases which can be attributed to the greater counterion density between the two like-charged oligosaccharides.

Marine polysaccharides in microencapsulation and application to aquaculture: "from sea to sea"

This review's main objective is to discuss some physico-chemical features of polysaccharides as intrinsic determinants for the supramolecular structures that can efficiently provide encapsulation of drugs and other biological entities. Thus, the general characteristics of some basic polysaccharides are outlined in terms of their conformational, dynamic and thermodynamic properties. The analysis of some polysaccharide gelling properties is also provided, including the peculiarity of the charged polysaccharides. Then, the way the basic physical chemistry of polymer self-assembly is made in practice through the laboratory methods is highlighted. A description of the several literature procedures used to influence molecular interactions into the macroscopic goal of the encapsulation is given with an attempt at classification. Finally, a practical case study of specific interest, the use of marine polysaccharide matrices for encapsulation of vaccines in aquaculture, is reported.

NMR study on hydroxy protons of κ- and κ/μ-hybrid carrageenan oligosaccharides: experimental evidence of hydrogen bonding and chemical exchange interactions in κ/μ oligosaccharides

The hydroxy protons of κ- and κ/μ-hybrid carrageenan oligosaccharides have been studied by NMR spectroscopy in 85% H(2)O/15% acetone-d(6). Hydration and hydrogen bonding interactions in di- (κ), tetra- (κκ), hexa (κκκ), and octa- (κκκκ) κ-oligosaccharides and hexa- (κμκ), octa- (κμμκ), and deca- (κμμμκ) κ/μ-oligosaccharides have been investigated by measuring the chemical shifts, temperature coefficients, and chemical exchange of the hydroxy protons. These NMR parameters indicate that no strong and persistent intramolecular hydrogen bonds involving hydroxy protons stabilize the structure of κ-carrageenan oligosaccharides in aqueous solution. In the κ/μ-oligosaccharides, the presence of chemical exchange between OH3 of α-d-Gal-6-sulfate (D6S) and OH2 of β-d-Gal-4-sulfate (G4S) across the β-d-Gal-4-S-(1→4)-α-d-Gal-6-S linkage reveals the existence of a weak hydrogen bond interaction between the two hydroxyl groups. The smaller temperature coefficients of OH2_D6S and OH3_D6S indicate reduced hydration, interpreted as spatial proximity to the 4-sulfate group and O5 ring oxygen of the neighboring G4S residues, respectively. These first experimental results on the conformation of κ/μ-carrageenan oligosaccharides shine light on the potential role of "kinks" in the properties of the three-dimensional carrageenan gel network.

Osmolyte-induced perturbations of hydrogen bonding between hydration layer waters: correlation with protein conformational changes

Gadolinium vibronic sideband luminescence spectroscopy (GVSBLS) is used to probe osmolyte-induced changes in the hydrogen bond strength between first and second shell waters on the surface of free Gd(3+) and Gd(3+) coordinated to EDTA and to structured calcium binding peptides in solution. In parallel, Raman is used to probe the corresponding impact of the same set of osmolytes on hydrogen bonding among waters in the bulk phase. Increasing concentration of added urea is observed to progressively weaken the hydrogen bonding within the hydration layer but has minimal observed impact on bulk water. In contrast, polyols are observed to enhance hydrogen bonding in both the hydration layer and the bulk with the amplitude being polyol dependent with trehalose being more effective than sucrose, glucose, or glycerol. The observed patterns indicate that the size and properties of the osmolyte as well as the local architecture of the specific surface site of hydration impact preferential exclusion effects and local hydrogen bond strength. Correlation of the vibronic spectra with CD measurements on the peptides as a function of added osmolytes shows an increase in secondary structure with added polyols and that the progressive weakening of the hydrogen bonding upon addition of urea first increases water occupancy within the peptide and only subsequently does the peptide unfold. The results support models in which the initial steps in the unfolding process involve osmolyte-induced enhancement of water occupancy within the interior of the protein.

Additive effects in the modeling of oligosaccharides with MM3 at high dielectric constants: an approach to the 'multiple minimum problem'

The production of an adiabatic map for a di- or trisaccharide requires the generation of many relaxed maps, ideally 59,049 for a disaccharide or 4,782,969 for a trisaccharide composed by hexose residues, due to a combination of exocyclic angle torsions. As the production of this amount of maps is usually ruled out for time considerations, different approaches were exploited. When working at low dielectric constants, starting points originated in cooperative hydrogen bonds through the rings are usually sufficient to produce an adiabatic map, but at higher dielectric constants those circuits are meaningless, and many low-energy conformers appear in each energy well. Herein, different conformations of four disaccharides (beta-4-linked mannobiose, and three galactobioses, linked alpha-(1-->3), alpha-(1-->4), and beta-(1-->4)) and one trisaccharide (beta-4-linked mannotriose) were minimized using mm3 at epsilon = 80, and the difference in energy produced by changes in torsional angles was recorded. A remarkable additive effect was found to occur when the exocyclics were gathered in groupings of two or three neighboring angles. Thus, in most cases, each grouping can be studied separately, and the minimum energy conformers can be predicted without the need of resorting to thousands of calculations. In some cases where two protons of different groups show steric interactions in some specific conformations, small deviations of the additivity were encountered. Anyway, a complex system with many variables can be transformed in one with many fewer variables, thus simplifying further studies. An attempt to calculate the same effect at epsilon = 3 shows that hydrogen bonding and electrostatic interactions make impossible to find those additive effects, thus precluding its utilization at such low dielectric constants.

The disordered conformation of κ-carrageenan in solution as determined by NMR experiments and molecular modeling

The conformation of kappa-carrageenan in solution was studied combining 1H and 13C NMR with molecular mechanics. The experimental conditions were chosen to characterize the disordered conformation of the polymer. Particular attention has been given to explore a wide range of experimental conditions as to the dependence on solvent (water and Me2SO), polymer concentration, temperature, pH, presence of a denaturing agent (guanidinium chloride), and of ions otherwise able to induce conformational order of the carrageenan chains, either in solution (I-) or in the gel state (Rb+). Two-dimensional NOE experiments were analyzed to obtain information on internuclear distances, and molecular mechanics provided the range of energetically accessible conformations. Two inter-residue topological constraints were clearly identified: their combination is rather restricting for the chain and suggests that the disordered conformation of kappa-carrageenan is characterized by an intrinsic stiffness with high values of persistent length and characteristic ratio. They also rule out any postulated interchain hydrogen bonds. In contrast, experiments on the temperature dependence of the chemical shift in Me2SO reveal the existence of two inter-residue intramolecular H-bonds which might contribute positively to the rigidity of the polymer chain. The overall picture emerging from the present results is that of a locally elongated 'loose single helix'.

Hyaluronan chain conformation and dynamics

An overview of the present state of research in the field of hyaluronan chain conformational aspects is presented. The relationship between structure and dynamics are illustrated for a series of hyaluronan oligomers. Conformational characteristics of hyaluronan chains are discussed, together with the dynamic chain patterns, evaluated by using a theoretical approach to diffusive polymer dynamics. The dependence of correlation times and NMR relaxation parameters from the chain dimension are investigated. Topological features and dimensional properties are related to the structural determinants by using classical computational methods of molecular mechanics and Monte Carlo simulation.