Comparison of aqueous molecular dynamics with NMR relaxation and residual dipolar couplings favors internal motion in a mannose oligosaccharide

Andrew Almond, J. Bunkenborg, Thomas Franch, Charlotte Held Gotfredsen, Jens Øllgaard Duus

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

An investigation has been performed to assess how aqueous dynamical simulations of flexible molecules can be compared against NMR data. The methodology compares state-of-the-art NMR data (residual dipolar coupling, NOESY, and C-13 relaxation) to molecular dynamics simulations in water over several nanoseconds. In contrast to many previous applications of residual dipolar coupling in structure investigations of biomolecules, the approach described here uses molecular dynamics simulations to provide a dynamic representation of the molecule. A mannose pentasaccharide, alpha -D-Manp-(1 -->3)-alpha -D-Manp-(1 -->3)-alpha -D-Manp(1 -->3)-alpha -D-Manp-(1 -->2)-D-Manp, was chosen as the model compound for this study. The presence of a-linked mannan is common to many glycopeptides, and therefore an understanding of the structure and the dynamics of this molecule is of both chemical and biological importance. This paper sets out to address the following questions. (1) Are the single structures which have been used to interpret residual dipolar couplings a useful representation of this molecule? (2) If dynamic flexibility is included in a representation of the molecule, can relaxation and residual dipolar coupling data then be simultaneously satisfied? (3) Do aqueous molecular dynamics simulations provide a reasonable representation of the dynamics present in the molecule and its interaction with water? In summary, two aqueous molecular dynamics simulations, each of 20 ns, were computed. They were started from two distant conformations and both converged to one flexible ensemble. The measured residual dipolar couplings were in agreement with predictions made by averaging the whole ensemble and from a specific single structure selected from the ensemble. However, the inclusion of internal motion was necessary to rationalize the relaxation data. Therefore, it is proposed that although residual dipolar couplings can be interpreted as a single-structure, this may not be a correct interpretation of molecular conformation in light of other experimental data. Second, the methodology described here shows that the ensembles from aqueous molecular dynamics can be effectively tested against experimental data sets. In the simulation, significant conformational motion was observed at each of the linkages, and no evidence for intramolecular hydrogen bonds at either alpha (1 -->) or alpha (1 -->3) linkages was found. This is in contrast to simulations of other linkages, such as beta (1 -->4), which are often predicted to maintain intramolecular hydrogen bonds and are coincidentally predicted to have less conformational freedom in solution.
Original languageEnglish
JournalJournal of the American Chemical Society
Volume123
Issue number20
Pages (from-to)4792-4802
ISSN0002-7863
DOIs
Publication statusPublished - 2001
Externally publishedYes

Keywords

  • Carbohydrate Sequence
  • Chemistry, Physical
  • Crystallography, X-Ray
  • Magnetic Resonance Spectroscopy
  • Mannose
  • Models, Molecular
  • Molecular Sequence Data
  • Oligosaccharides
  • Physicochemical Phenomena
  • Pichia
  • Solutions
  • PHA4727WTP Mannose
  • Computer simulation
  • Conformations
  • Hydrogen bonds
  • Nuclear magnetic resonance
  • Water
  • Molecular dynamics
  • glycopeptide
  • mannan
  • mannose
  • oligosaccharide
  • pentasaccharide
  • article
  • chemical analysis
  • chemical structure
  • hydrogen bond
  • molecular dynamics
  • nuclear magnetic resonance
  • nuclear Overhauser effect
  • simulation
  • Dynamic flexibility
  • T
  • X
  • CHEMISTRY,
  • NUCLEAR-MAGNETIC-RESONANCE
  • E.COSY-TYPE MEASUREMENT
  • STATE-SELECTIVE EXCITATION
  • LIQUID-CRYSTALLINE MEDIUM
  • RAY FIBER DIFFRACTION
  • HOLSTII NRRL Y-2448
  • EXTRACELLULAR POLYSACCHARIDE
  • CONFORMATIONAL-ANALYSIS
  • SIMULATIONS
  • CONSTANTS

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