Molecular conformations of a disaccharide investigated using NMR spectroscopy

Landersjö, Clas; Stevensson, Baltzar; Eklund, Robert; Östervall, Jennie; Söderman, Peter; Widmalm, Göran; Maliniak, Arnold

doi:10.1007/s10858-006-9006-0

Cited by 26 publications

(20 citation statements)

References 36 publications

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“…In the isotropic liquid only the J-couplings are observable, whereas the direct dipolar interactions are averaged (by the rapid molecular tumbling) to zero. [44][45][46][47][48][49][50][51] We have used trajectories generated in the MD simulations carried out in the previous study 5 for interpretation of experimental herein acquired NMR parameters and analyses of the membrane-TRH interactions. In principle, there are two NMR spectroscopy techniques to study anisotropic dipolar interactions: a) conventional high-resolution NMR where a weakly ordered solvent [37][38][39] is used, and b) solid-state NMR.…”

Section: Introductionmentioning

confidence: 99%

Molecular dynamics simulations and NMR spectroscopy studies of trehalose–lipid bilayer systems

Kapla

Engström

Stevensson

et al. 2015

Phys. Chem. Chem. Phys.

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The disaccharide trehalose (TRH) strongly affects the physical properties of lipid bilayers. We investigate interactions between lipid membranes formed by 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and TRH using NMR spectroscopy and molecular dynamics (MD) computer simulations. We compare dipolar couplings derived from DMPC/TRH trajectories with those determined (i) experimentally in TRH using conventional high-resolution NMR in a weakly ordered solvent (bicelles), and (ii) by solid-state NMR in multilamellar vesicles (MLV) formed by DMPC. Analysis of the experimental and MD-derived couplings in DMPC indicated that the force field used in the simulations reasonably well describes the experimental results with the exception for the glycerol fragment that exhibits significant deviations. The signs of dipolar couplings, not available from the experiments on highly ordered systems, were determined from the trajectory analysis. The crucial step in the analysis of residual dipolar couplings (RDCs) in TRH determined in a bicelle-environment was access to the conformational distributions derived from the MD trajectory. Furthermore, the conformational behavior of TRH, investigated by J-couplings, in the ordered and isotropic phases is essentially identical, indicating that the general assumptions in the analyses of RDCs are well founded.

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Section: Introductionmentioning

confidence: 99%

Molecular dynamics simulations and NMR spectroscopy studies of trehalose–lipid bilayer systems

Kapla

Engström

Stevensson

et al. 2015

Phys. Chem. Chem. Phys.

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“…conformational maps) using a particular level of theory, [7][8][9][10][11][12][13][14][15][16][17][18] NMR-NOE based maps, [19][20][21][22] and MD scatter plots, [23][24][25][26][27] there has been little effort at creating generalized carb-Rama plots. In 1999 and 2002, Wormald and coworkers surveyed available NMR and X-ray data of oligosaccharides and glycopeptides.…”

Section: Introductionmentioning

confidence: 99%

Ramachandran‐type plots for glycosidic linkages: Examples from molecular dynamic simulations using the Glycam06 force field

et al. 2008

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The goals of this article are to (1) provide further validation of the Glycam06 force field, specifically for its use in implicit solvent molecular dynamic (MD) simulations, and (2) to present the extension of G.N. Ramachandran's idea of plotting amino acid phi and psi angles to the glycosidic phi, psi, and omega angles formed between carbohydrates. As in traditional Ramachandran plots, these carbohydrate Ramachandran-type (carb-Rama) plots reveal the coupling between the glycosidic angles by displaying the allowed and disallowed conformational space. Considering two-bond glycosidic linkages, there are 18 possible conformational regions that can be defined by (alpha, phi, psi) and (beta, phi, psi), whereas for three-bond linkages, there are 54 possible regions that can be defined by (alpha, phi, psi, omega) and (beta, phi, psi, omega). Illustrating these ideas are molecular dynamic simulations on an implicitly hydrated oligosaccharide (700 ns) and its eight constituent disaccharides (50 ns/disaccharide). For each linkage, we compare and contrast the oligosaccharide and respective disaccharide carb-Rama plots, validate the simulations and the Glycam06 force field through comparison to experimental data, and discuss the general trends observed in the plots.

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“…4) and 2D NMR (HSQC, HMBC) spectra (Fig. 5) and by further comparison with those of lactulose and to the literatures (Landersjo et al, 2006;Taubert, Konschin, & Sundholm, 2005).…”

Section: Resultsmentioning

confidence: 79%

Enzymatic synthesis and identification of oligosaccharides obtained by transgalactosylation of lactose in the presence of fructose using β-galactosidase from Kluyveromyces lactis

et al. 2012

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Molecular conformations of a disaccharide investigated using NMR spectroscopy

Cited by 26 publications

References 36 publications

Molecular dynamics simulations and NMR spectroscopy studies of trehalose–lipid bilayer systems

Molecular dynamics simulations and NMR spectroscopy studies of trehalose–lipid bilayer systems

Ramachandran‐type plots for glycosidic linkages: Examples from molecular dynamic simulations using the Glycam06 force field

Enzymatic synthesis and identification of oligosaccharides obtained by transgalactosylation of lactose in the presence of fructose using β-galactosidase from Kluyveromyces lactis

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