Nuclear magnetic resonance and molecular modeling studies on O-β-D-galactopyranosyl-(1→4)-O-β-D-xylopyranosyl-(1→0)-L-serine, a carbohydrate-protein linkage region fragment from connective tissue proteoglycans

Academic Article


  • The solution conformation of O-β-D-galactopyranosyl-(1→4)-O-β-D-xylopyranosyl-(1→0)-L-serine (GXS), a carbohydrate-protein linkage region fragment from connective tissue proteoglycans, was investigated by two-dimensional NMR spectroscopy and molecular modeling calculations. Specifically, the 1H and 13C resonances were assigned by 2D-COSY and by 1H-13C heteronuclear correlation spectroscopy methods. 2D-NOESY was used to generate distance constraints between the galactose and xylose and between the xylose and serine residues. The 1H vicinal coupling constants for the sugars and the serine were also determined. A general molecular modeling methodology suitable for complex carbohydrates was developed. This methodology employed molecular dynamics and energy minimization procedures together with the application of inter-residue spatial constraints across the linkages derived from 2D-NOESY. The first step in this methodology is the generation of a wide variety of starting conformations that span the (φ, ψ) space for each linkage. In the present study, nine such conformations were constructed for each linkage using the torsion angles φ and ψ corresponding to the gauche+, gauche-, and trans configurations across each of the two bonds constituting the linkage. These conformations were subjected to a combined molecular dynamics/energy minimization refinement using the NOESY derived constraints as pseudoenergy functions. Families of conformations for the whole molecule were then constructed from the structures derived for each linkage. Characterization of GXS using this methodology identified a single family of conformations that are consistent with the solution phase NMR data on this molecule.
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    Author List

  • Krishna NR; Choe BY; Prabhakaran M; Ekborg GC; Roden L; Harvey SC
  • Start Page

  • 18256
  • End Page

  • 18262
  • Volume

  • 265
  • Issue

  • 30