Molecular conformations in the pentasaccharide LNF-1 derived from NMR spectroscopy and molecular dynamics simulations
2011 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 115, no 21, 7109-7121 p.Article in journal (Refereed) Published
The conformational dynamics of the human milk oligosaccharide lacto-N-fucopentaose (LNF-1), α-l-Fucp-(1 → 2)-β-d-Galp-(1 → 3)-β-d-GlcpNAc-(1 → 3)-β-d-Galp-(1 → 4)-d-Glcp, has been analyzed using NMR spectroscopy and molecular dynamics (MD) computer simulations. Employing the Hadamard 13C-excitation technique and the J-HMBC experiment, 1H,13C trans-glycosidic J coupling constants were obtained, and from one- and two-dimensional 1H,1H T-ROESY experiments, proton–proton cross-relaxation rates were determined in isotropic D2O solution. In the lyotropic liquid-crystalline medium consisting of ditetradecylphosphatidylcholine, dihexylphosphatidylcholine, N-cetyl-N,N,N-trimethylammonium bromide, and D2O, 1H, 1H and one-bond 1H, 13C residual dipolar couplings (RDCs), as well as relative sign information on homonuclear RDCs, were determined for the pentasaccharide. Molecular dynamics simulations with explicit water were carried out from which the internal isomerization relaxation time constant, τN, was calculated for transitions at the ψ torsion angle of the β-(1 → 3) linkage to the lactosyl group in LNF-1. Compared to the global reorientation time, τM, of 0.6 ns determined experimentally in D2O solution, the time constant for the isomerization relaxation process, τN(scaled), is about one-third as large. The NMR parameters derived from the isotropic solution show very good agreement with those calculated from the MD simulations. The only notable difference occurs at the reducing end, which should be more flexible than observed by the molecular simulation, a conclusion in complete agreement with previous 13C NMR relaxation data. A hydrogen-bond analysis of the MD simulation revealed that inter-residue hydrogen bonds on the order of 30% were present across the glycosidic linkages to sugar ring oxygens. This finding highlights that intramolecular hydrogen bonds might be important in preserving well-defined structures in otherwise flexible molecules. An analysis including generalized order parameters obtained from nuclear spin relaxation experiments was performed and successfully shown to limit the conformational space accessible to the molecule when the number of experimental data are too scarce for a complete conformational analysis.
Place, publisher, year, edition, pages
2011. Vol. 115, no 21, 7109-7121 p.
Organic Chemistry Physical Chemistry
IdentifiersURN: urn:nbn:se:su:diva-58298DOI: 10.1021/jp2017105ISI: 000290914600032OAI: oai:DiVA.org:su-58298DiVA: diva2:421255
FunderSwedish Research CouncilKnut and Alice Wallenberg Foundation