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Solution structure of a pentasaccharide representing the repeating unit of the O‐antigen polysaccharide from Escherichia coli O142: NMR spectroscopy and molecular simulation studies
Author(s) -
Landersjö Clas,
Widmalm Göran
Publication year - 2002
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.10188
Subject(s) - chemistry , glycosidic bond , homonuclear molecule , nuclear magnetic resonance spectroscopy , hydrogen bond , nuclear overhauser effect , branching (polymer chemistry) , molecular dynamics , crystallography , oligomer , molecule , stereochemistry , computational chemistry , polymer chemistry , organic chemistry , enzyme
Abstract Conformational studies have been performed of a pentasaccharide derived from the O‐polysaccharide from Escherichia coli O142. The polymer was selectively degraded by anhydrous hydrogen fluoride and reduced to yield an oligosaccharide model of its repeating unit, which in the branching region consists of four aminosugars. A comparison of 1 H and 13 C chemical shifts between the pentasaccharide and the polymer showed only minor differences, except where the cleavage had taken place, indicating that the oligomer is a good model of the repeating unit. Langevin dynamics and molecular dynamics simulations with explicit water molecules were carried out to sample the conformational space of the pentasaccharide. For the glycosidic linkages between the hexopyranoside residues, small but significant changes were observed between the simulation techniques. One‐dimensional (1D) 1 H, 1 H double pulsed field gradient spin echo (DPFGSE) transverse rotating‐frame Overhauser effect spectroscopy (T‐ROESY) experiments were performed, and homonuclear cross‐relaxation rates were obtained. Subsequently, a comparison of interproton distances from NMR experiment and the two simulation approaches showed that in all cases the use of explicit water in the simulations resulted in better agreement. Hydrogen‐bond analysis of the trajectories from the molecular dynamics simulation revealed interresidue interactions to be important as a cluster of different hydrogen bonds and as a distinct highly populated hydrogen bond. NMR data are consistent with the presence of hydrogen bonding within the model of the repeating unit. © 2002 Wiley Periodicals, Inc. Biopolymers 64: 283–291, 2002