Synthesis and X-ray crystallographic investigation of N-(α-d-arabinopyranosyl)alkanamides as N-glycoprotein linkage region analogs (original) (raw)

Crystal and molecular structures of benzyl 3-O-benzoyl-4-O-benzyl-2-O-(2,3,6-trideoxy-α-l-glycero-hex-2-enopyranosyl-4- ulose)-α-l-rhamnopyranoside

Carbohydrate Research, 1983

Benzyl 3-O-benzoyl-4-O-benzyl-2-0-(2,3,6-trideoxy-cu-L-g~ycera-hex-2-enopyranosyl-4-ulose)-a-L-rhamnopyranoside has been investigated by X-ray diffraction methods. The crystals obtained from aqueous ethanol are orthorhombic, space group P212121 with cell constants u = l&775(2), b = 10.857(2), and c = 25.774(3) A. A four-circle, automatic diffractometer was used for intensity-data collection. Out of 3370 reflection intensities, 2634 were of I > 20, and these were used for refinement. The structure was solved by direct methods, and the atomic parameters were then refined by the full-matrix, least-squares procedure. The unsaturated dihydropyranone ring adopts a deformed sofa conformation, whereas the rhamnopyranose ring adopts a chair conformation. The glycosidic linkage is characterised by torsion angles @33(2)" and ly -13( 1)". A new classification for the conformations of glycosidic linkages is suggested. 0008-6215/83/$03.00 0 1983 Elsevier Science Pubhshers B.V.

Conformational Preferences of the Aglycon Moiety in Models and Analogs of GlcNAc-Asn Linkage: Crystal Structures and ab Initio Quantum Chemical Calculations of N -(β- d -Glycopyranosyl)haloacetamides

Journal of The American Chemical Society, 2008

The biological addition of oligosaccharide structures to asparagine residues of N-glycoproteins influences the properties and bioactivities of these macromolecules. The linkage region constituents, 2-acetamino-2-deoxy--D-glucopyranose monosaccharide (GlcNAc) and L-asparagine amino acid (Asn), are conserved in the N-glycoproteins of all eukaryotes. In order to gain information about the structure and dynamics of glycosylated proteins, two chloroacetamido sugars, Glc NAcNHCOCH 2Cl and Man NHCOCH 2Cl, have been synthesized, and their crystal structures have been solved. Structural comparison with a series of other models and analogs gives insight about the influence of the N-acetyl group at position C2 on the conformation of the glycan-peptide linkage at C1. Interestingly, this N-acetyl group also influences the packing and network of hydrogen bonds with involvement in weak hydrogen bonds C-H · · · X that are of biological importance. DFT ab initio calculations performed on a series of models and analogs also confirm that the GlcNAc derivatives present different preferred conformation about the N-CO-CH 2-X ( 2) torsion angle of the glycan-peptide linkage, when compared to other monosaccharide derivatives. The energy profiles that have been obtained will be useful for parametrization of molecular mechanics force-field. The conjunction of crystallographic and computational chemistry studies provides arguments for the structural effect of the N-acetyl group at C2 in establishing an extended conformation that presents the oligosaccharide away from the protein surface. Cummings, R.; Esko, J.; Freeze, H.; Hart, G.; Marth, J.

Toward Fully Synthetic N-Linked Glycoproteins

Angewandte Chemie International Edition, 2003

Coordination polymer 2 was synthesized according to a published procedure. Elemental analysis (%) calcd for C 13 H 8 NO 4 Cu: C 51.06, H 2.62, N 4.58; found C 50.62, H 2.45, N 4.60. Gas adsorption measurements: Sorption isotherms were measured at 298 K on an FMS-BG (BEL inc.) automatic gravimetric adsorption measurement system with Rubotherm magnet coupling balance incorporated in a SUS steel pressure chamber. A known weight (200±300 mg) of the as-synthesized sample was placed in the aluminum sample cell in the chamber, and the sample was dried under high vacuum at 373 K for 5 h to remove the host water molecules. The adsorbate was dosed into the chamber, and the change in weight was monitored. After correction for buoyancy, the absorbed amount was determined.