Uncovering the reactive nature of 4-deoxy-l-erythro-5-hexoseulose uronate for the utilization of alginate, a promising marine biopolymer

Alginate is a linear polyuronate in brown macroalgae. It is also a promising marine biopolymer that can be degraded by exo-type alginate lyase into an unsaturated uronate that is non-enzymatically or enzymatically converted to 4-deoxy-l-erythro-5-hexoseulose uronate (DEH). In a bioengineered yeast Saccharomyces cerevisiae (DEH++) strain that utilizes DEH, DEH is not only an important physiological metabolite but also a promising carbon source for biorefinery systems. In this study, we uncovered the essential chemical nature of DEH. In particular, we showed that DEH non-enzymatically reacts with specific amino groups in Tris, ammonium salts [(NH4)2SO4 and NH4Cl], and certain amino acids (e.g., Gly, Ser, Gln, Thr, and Lys) at 30 °C and forms other compounds, one of which we tentatively named DEH-related product-1 (DRP-1). In contrast, Asn, Met, Glu, and Arg were almost inert and Ala, Pro, Leu, Ile, Phe, Val, and Asp, as well as sodium nitrate (NaNO3), were inert in the presence of DEH. Some of the above amino acids (Asn, Glu, Ala, Pro, Phe, and Asp) were suitable nitrogen sources for the DEH++ yeast strain, whereas ammonium salts and Ser, Gln, and Thr were poor nitrogen sources owing to their high reactivity to DEH. Nutrient-rich YP medium with 1% (w/v) Yeast extract and 2% (w/v) Tryptone, as well as 10-fold diluted YP medium, could also be effectively used as nitrogen sources. Finally, we identified DRP-1 as a 2-furancarboxylic acid and showed that it has a growth-inhibitory effect on the DEH++ yeast strain. These results show the reactive nature of DEH and suggest a basis for selecting nitrogen sources for use with DEH and alginate in biorefineries. Our results also provide insight into the physiological utilization of DEH. The environmental source of 2-furancarboxylic acid is also discussed.

Extension and validation of the GLYCAM force field parameters for modeling glycosaminoglycans

Glycosaminoglycans (GAGs) are an important class of carbohydrates that serve critical roles in blood clotting, tissue repair, cell migration and adhesion, and lubrication. The variable sulfation pattern and iduronate ring conformations in GAGs influence their polymeric structure and nature of interaction. This study characterizes several heparin-like GAG disaccharides and tetrasaccharides using NMR and molecular dynamics simulations to assist in the development of parameters for GAGs within the GLYCAM06 force field. The force field additions include parameters and charges for a transferable sulfate group for O- and N-sulfation, neutral (COOH) forms of iduronic and glucuronic acid, and Δ4,5-unsaturated uronate (ΔUA) residues. ΔUA residues frequently arise from the enzymatic digestion of heparin and heparin sulfate. Simulations of disaccharides containing ΔUA reveal that the presence of sulfation on this residue alters the relative populations of 1H2 and 2H1 ring conformations. Simulations of heparin tetrasaccharides containing N-sulfation in place of N-acetylation on glucosamine residues influence the ring conformations of adjacent iduronate residues.

Chondroitinase ABC digestion of dermatan sulphate. N.m.r. spectroscopic characterization of the oligo- and poly-saccharides

Dermatan sulphates, in which iduronate was the predominant uronate constituent, were partially digested by chondroitinase ABC to produce oligosaccharides of the following structure: delta UA-[GalNAc(4SO3)-IdoA]mGalNAc(4SO3) [where m = 0-5, delta UA represents beta-D-gluco-4-enepyranosyluronate, IdoA represents alpha-L-iduronate and GalNAc(4SO3) represents 2-acetamido-2-deoxy-beta-D-galactose 4-O-sulphate], which were fractionated by gel-permeation chromatography and examined by 100 MHz 13C-n.m.r. and 400/500 MHz 1H-n.m.r. spectroscopy. Experimental conditions were established for the removal of non-reducing terminal unsaturated uronate residues by treatment with HgCL2, and reducing terminal N-acetylgalactosamine residues of the oligosaccharides were reduced with alkaline borohydride. These modifications were shown by 13C-n.m.r. spectroscopy to have proceeded to completion. Assignments of both 13C-n.m.r. and 1H-n.m.r. resonances are reported for the GalNAc(4SO3)-IdoA repeat sequence in the oligosaccharides as well as for the terminal residues resulting from enzyme digestion and subsequent modifications. A full analysis of a trisaccharide derived from dermatan sulphate led to the amendment of published 13C-n.m.r. chemical-shift assignments for the polymer.