SWEET - WWW-based rapid 3D construction of oligo- and polysaccharides

Abstract

The current version of SWEET generates only one conformation out of a manifold. Several authors have analysed possible conformations of high-mannose N-linked glycans using a combination of NMR methods and computational approaches showing that such molecules are rather flexible populating normally several conformations for each glycosidic linkage. The displayed model exhibits for all glycosidic linkages a conformation which is in accordance with the reported variations of Phi, psi and omega values for specific linkage (see http://www.dkfz-heidelberg. de/spec/sweet2/doc/input/sba_example.html).

A Brief Review of Bioinformatics Tools for Glycosylation Analysis by Mass Spectrometry

“…13) "GlycoFragment" enables the easy generation of all theoretically possible A-, B-, C-, X-, Y-and Z-fragments of a de ned glycan structure according to the de nitions of Domon and Costello. 14) e algorithm uses the Sweet-II 15,16) program to interpret nomenclature and chooses suitable templates from a database according to linkage information. "GlycoSearchMS" imports a mass spectrum to a database search of theoretically calculated spectra and identi es the best candidate spectra.…”

Evidence for N-Glycan Shielding of Antigenic Sites during Evolution of Human Influenza A Virus Hemagglutinin

“…The three-dimensional (3D) structures for the variants of N-glycans were constructed using SWEET (5). The structures of sugar chains were inferred using formulae for N-glycans that were reported to be attached to the HA of A/H1N1 viruses (15) (see Table S1 in the supplemental material).…”

An improved expression system for the VC1 ligand binding domain of the receptor for advanced glycation end products in Pichia pastoris

“…Most ligands bind to the extracellular V or VC1 domains of the receptor. In this work, V and VC1 of 33 human RAGE were produced in the methylotrophic yeast Pichia pastoris and directed to the secretory 34 pathway. Fusions to a removable C-terminal His-tag evidenced proteolytic processing of the tag by extra- 35 cellular proteases and also intracellular degradation of the N-terminal portion of V-His.…”