| 1. |
- Pendrill, Robert, et al.
(author)
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Suppressing one-bond homonuclear 13C,13C scalar couplings in the J-HMBC NMR experiment : application to 13C site-specifically labeled oligosaccharides
- 2014
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In: Magnetic Resonance in Chemistry. - : Wiley. - 0749-1581 .- 1097-458X. ; 52:3, s. 82-86
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Journal article (peer-reviewed)abstract
- Site-specific C-13 isotope labeling is a useful approach that allows for the measurement of homonuclear C-13,C-13 coupling constants. For three site-specifically labeled oligosaccharides, it is demonstrated that using the J-HMBC experiment for measuring heteronuclear long-range coupling constants is problematical for the carbons adjacent to the spin label. By incorporating either a selective inversion pulse or a constant-time element in the pulse sequence, the interference from one-bond C-13,C-13 scalar couplings is suppressed, allowing the coupling constants of interest to be measured without complications. Experimental spectra are compared with spectra of a nonlabeled compound as well as with simulated spectra. The work extends the use of the J-HMBC experiments to site-specifically labeled molecules, thereby increasing the number of coupling constants that can be obtained from a single preparation of a molecule.
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| 2. |
- Landström, Jens, 1978-
(author)
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Structure, dynamics and interactions of biomolecules : Investigations by NMR spectroscopy and computational methods
- 2009
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Doctoral thesis (other academic/artistic)abstract
- In this thesis, the structure, dynamics and interactions of proteins and carbohydrates are investigated using mainly NMR spectroscopy and computer simulations. Oligosaccharides representing a Salmonella O-antigen have been synthesized and their dynamic behavior and interaction with the bacteriophage P22 tail-spike protein have been studied by NMR spectroscopy, MD and docking simulations. A binding mechanism between the protein and the O-antigen has been proposed. Transient hydrogen bonds have been defined and examined in an E. coli polysaccharide and in a pentasaccharide representing the repeating unit, using MD simulation and NMR spectroscopy. Conformational dynamics of a trisaccharide representing the repeating unit of an A. salmonicida O-antigen have been investigated by MD simulations. The simulation together with relaxation matrix calculations reveals a conformational exchange on a ns timescale and explains an unusual NOE. A fragment-based screening for inhibitors of the glycosyltransferase GTB acceptor site has been performed using NMR spectroscopy and SPR. IC50 values of the binding fragments are reported. Complex structures of the fragments and GTB have been proposed using docking simulations. A fragment-based screening for inhibitors of the WaaG glycosyltransferase donor site has been performed using NMR spectroscopy and three compounds were selected. Structures of the WaaG-fragment complexes have been suggested from docking simulations. Binding of natural substrates and activity has also been investigated by NMR spectroscopy. MD simulations have been carried out on WaaG with and without bound donor substrate. The simulation revealed a conformational change upon substrate binding. Interactions between HEWL and carbohydrate ligands have been investigated, using a combination of weak affinity chromatography, NMR spectroscopy and computer simulations. KDs of the ligands have been presented as well as the solution structures of two HEWL-disaccharide complexes.
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| 3. |
- Battistel, Marcos D., et al.
(author)
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Direct Evidence for Hydrogen Bonding in Glycans : A Combined NMR and Molecular Dynamics Study
- 2013
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In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 117:17, s. 4860-4869
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Journal article (peer-reviewed)abstract
- We introduce the abundant hydroxyl groups of glycans as NMR handle's and structural probes to expand the repertoire of tools for structure function studies on glycans in solution. To this end, we present the facile detection and assignment of hydroxyl groups in a Wide range of sample concentrations (0.5-1700 mM) and temperatures, ranging from -5 to 25 degrees C.,We then exploit this information to directly detect hydrogen bonds, well-known for their importance in molecular structural determination through NMR. Via HSQC-TOCSY, we were able to determine the directionality; of these hydrogen bonds in sucrose Furthermore, by means Of molecular dynamics simulations in conjunction with NMR, we establish that one Out of the three detected hydrogen bonds arises from intermolecular interactions. This finding may shed light on glycan glycan interactions and glycan recognition by proteins.
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| 4. |
- Kotsyubynskyy, Dmytro, et al.
(author)
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Stochastic Modeling of Flexible Biomolecules Applied to NMR Relaxation : 2. Interpretation of Complex Dynamics in Linear Oligosaccharides
- 2012
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In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 116:50, s. 14541-14555
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Journal article (peer-reviewed)abstract
- A computational stochastic approach is applied to the description of flexible molecules. By combining (i) molecular dynamics simulations, (ii) hydrodynamics approaches, and (iii) a multidimensional diffusive description for internal and global dynamics, it is possible to build an efficient integrated approach to the interpretation of relaxation processes in flexible systems. In particular, the model is applied to the interpretation of nuclear magnetic relaxation measurements of linear oligosaccharides, namely a mannose-containing trisaccharide and the pentasaccharide LNF-1. Experimental data are reproduced with sufficient accuracy without free model parameters.
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| 5. |
- Ruda, Alessandro, 1990-, et al.
(author)
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O-Methylation in Carbohydrates : An NMR and MD Simulation Study with Application to Methylcellulose
- 2021
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In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 125:43, s. 11967-11979
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Journal article (peer-reviewed)abstract
- Methylated carbohydrates are important from both biological and technical perspectives. Specifically, methylcellulose is an interesting cellulose derivative that has applications in foods, materials, cosmetics, and many other fields. While the molecular dynamics simulation technique has the potential for both advancing the fundamental understanding of this polymer and aiding in the development of specific applications, a general drawback is the lack of experimentally validated interaction potentials for the methylated moieties. In the present study, simulations using the GROMOS 56 carbohydrate force field are compared to NMR spin–spin coupling constants related to the conformation of the exocyclic torsion angle ω in d-glucopyranose and derivatives containing a 6-O-methyl substituent and a 13C-isotopologue thereof. A 3JCC Karplus-type relationship is proposed for the C5–C6–O6–CMe torsion angle. Moreover, solvation free energies are compared to experimental data for small model compounds. Alkylation in the form of 6-O-methylation affects exocyclic torsion only marginally. Computed solvation free energies between nonmethylated and methylated molecules were internally consistent, which validates the application of these interaction potentials for more specialized purposes.
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| 6. |
- Angles d'Ortoli, Thibault, et al.
(author)
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Temperature Dependence of Hydroxymethyl Group Rotamer Populations in Cellooligomers
- 2015
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In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 119:30, s. 9559-9570
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Journal article (peer-reviewed)abstract
- Empirical force fields for computer simulations of carbohydrates are often implicitly assumed to be valid also at temperatures different from room temperature for which they were optimited: Herein, the temperature dependence of the hydroxymethyl group rotamer populations in short oligogaccharides is invegtigated using Molecular dynamics simulations and NMR spectroscopy. Two oligosaccharides, methyl beta-cellobioside and beta-cellotetraose were simulated using three different carbohydrate force fields (CHARMM C35, GLYCAM06, and GROMOS 56A(carbo)) in combination with different water models (SPC, SPC/E, and TIP3P) using replica exchange molecular dynamics simulations. For comparison, hydroxymethyl group rotamer populations were investigated for methyl beta-cellobioside and cellopentaose based- on measured NMR (3)J(H5,H6) coupling constants, in the latter case by using a chemical shift selective NMR-filter. Molecular dynamics simulations in combination with NMR spectroscopy show that the temperature dependence of the hydroxymethyl rotamer population in these short cellooligomers, in the range 263-344 K, generally becomes exaggerated in simulations when compared to experimental data, but also that it is dependent on simulation conditions, and most notably properties of the water model.
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| 7. |
- Kapla, Jon, et al.
(author)
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Molecular Dynamics Simulations of Membrane-Sugar Interactions
- 2013
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In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 117:22, s. 6667-6673
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Journal article (peer-reviewed)abstract
- It is well documented that disaccharides in general and trehalose (TRH) in particular strongly affect physical properties and functionality of lipid bilayers. We investigate interactions between lipid membranes formed by 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and TRH by means of molecular dynamics (MD) computer simulations. Ten different TRH concentrations were studied in the range W-TRH = 0-0.20 (w/w). The potential of mean force (PMF) for DMPC bilayer TRH interactions was determined using two different force fields, and was subsequently used in a simple analytical model for description of sugar binding at the membrane interface. The MD results were in good agreement with the predictions of the model. The net affinities of TRH for the DMPC bilayer derived from the model and MD simulations were compared with experimental results. The area per lipid increases and the membrane becomes thinner with increased TRH concentration, which is interpreted as an intercalation effect of the TRH molecules into the polar part of the lipids, resulting in conformational changes in the chains. These results are consistent with recent experimental observations. The compressibility modulus related to the fluctuations of the membrane increases dramatically with increased TRH concentration, which indicates higher order and rigidity of the bilayer. This is also reflected in a decrease (by a factor of 15) of the lateral diffusion of the lipids. We interpret these observations as a formation of a glassy state at the interface of the membrane, which has been suggested in the literature as a hypothesis for the membrane sugar interactions.
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| 8. |
- Landström, Jens, et al.
(author)
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Combining weak affinity chromatography, NMR spectroscopy and molecular simulations in carbohydrate-lysozyme interaction studies
- 2012
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In: Organic and biomolecular chemistry. - : Royal Society of Chemistry (RSC). - 1477-0520 .- 1477-0539. ; 10:15, s. 3019-3032
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Journal article (peer-reviewed)abstract
- By examining the interactions between the protein hen egg-white lysozyme (HEWL) and commercially available and chemically synthesized carbohydrate ligands using a combination of weak affinity chromatography (WAC), NMR spectroscopy and molecular simulations, we report on new affinity data as well as a detailed binding model for the HEWL protein. The equilibrium dissociation constants of the ligands were obtained by WAC but also by NMR spectroscopy, which agreed well. The structures of two HEWL-disaccharide complexes in solution were deduced by NMR spectroscopy using H-1 saturation transfer difference (STD) effects and transferred H-1,H-1-NOESY experiments, relaxation-matrix calculations, molecular docking and molecular dynamics simulations. In solution the two disaccharides beta-D-Galp-(1 -> 4)-beta-D-GlcpNAc-OMe and beta-D-GlcpNAc-(1 -> 4)-beta-D-GlcpNAc-OMe bind to the B and C sites of HEWL in a syn-conformation at the glycosidic linkage between the two sugar residues. Intermolecular hydrogen bonding and CH/pi-interactions form the basis of the protein-ligand complexes in a way characteristic of carbohydrate-protein interactions. Molecular dynamics simulations with explicit water molecules of both the apo-form of the protein and a ligand-protein complex showed structural change compared to a crystal structure of the protein. The flexibility of HEWL as indicated by a residue-based root-mean-square deviation analysis indicated similarities overall, with some residue specific differences, inter alia, for Arg61 that is situated prior to a flexible loop. The Arg61 flexibility was notably larger in the ligand-complexed form of HEWL. N,N'-Diacetylchitobiose has previously been observed to bind to HEWL at the B and C sites in water solution based on H-1 NMR chemical shift changes in the protein whereas the disaccharide binds at either the B and C sites or the C and D sites in different crystal complexes. The present study thus highlights that protein-ligand complexes may vary notably between the solution and solid states, underscoring the importance of targeting the pertinent binding site(s) for inhibition of protein activity and the advantages of combining different techniques in a screening process.
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| 9. |
- Ali, Tara, 1980-
(author)
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Structural Studies of O-Polysaccharides from Diarrhoeal Escherichia coli
- 2007
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Doctoral thesis (other academic/artistic)abstract
- This thesis describes the structural analysis of O-polysaccharides from the Gram-negative bacterium Escherichia coli that is a diarrhoeal pathogen. The Escherichia coli serotypes investigated were O178, O171, O166 and O128. The methods used in these studies were nuclear magnetic resonance spectroscopy and component analysis.All analysed serotypes had pentasaccharide repeating units. E. coli strain O128 and O166 was shown to have the topology of four carbohydrate residues in the backbone while the 5-residue backbone is found in E. coli O178 and O171.The biological repeating units have been determined for the analysed polysaccharides and it was shown that all of the serotypes studied had a 3-substituted N-acetylgalactosamine residue at the reducing end. From this it was deduced that the terminal end of E. coli O171 and O128 have sialic acid and blood type antigens, respectively. This should make E. coli O171 and O128 less recognizable to the immune system as a foreign invader. This can result in that E. coli O171 and O128 may evade the immune system more easily.
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| 10. |
- Jonsson, Hanna, 1979-
(author)
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Exploring the structure of oligo- and polysaccharides : Synthesis and NMR spectroscopy studies
- 2010
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Doctoral thesis (other academic/artistic)abstract
- A deeper understanding of the diversity of carbohydrates and the many applications of oligo- and polysaccharides found in nature are of high interest. Many of the processes involving carbohydrates affect our everyday life. This thesis is based on six papers all contributing to an extended perspective of carbohydrate property and functionality. An introduction to carbohydrate chemistry together with a presentation of selected carbohydrate synthesis and analysis methods introduces the reader to the research field. The first paper is an NMR spectroscopy reinvestigation of the structures of the O-antigens from the lipopolysaccharides (LPS) of Shigella dysenteriae type 3 and Escherichia coli O124. The repeating units were concluded to be built of identical branched pentasaccharides now with the correct anomeric configurations. Paper II is a structural investigation of the O-antigen from the LPS of E. coli O74 which is built of branched tetrasaccharide repeating units including the uncommon monosaccharide d-Fuc3NAc. Paper III is a conformational study of a rhamnose derivative, using NMR spectroscopy and X-ray crystallography. The benzoyl ester group positioned at C4 prefers an “eclipsed” conformation in the crystal as well as in solution. The use of site-specifically 13C-labeled compounds in conformational studies is discussed in Papers IV and V. The disaccharide α-L-Rhap-(1→2)-α-L-Rhap-OMe was synthesized together with two 13C-isotopologues and studied with NMR spectroscopy to give seven J-couplings related to torsion angles φ and ψ. The trisaccharide α-L-Rhap-(1→2)[α-L-Rhap-(1→3)]-α-L-Rhap-OMe was synthesized with 13C-labeling at two positions which presented a solution to a problem of overlapping signals in the 1H NMR spectrum. The site-specific labeling also facilitated the measurement of two 3JCC and two 2JCH coupling constants. Finally, chapter 6 gives a short introduction to glycosynthase chemistry and discusses the synthesis of α-glycosyl fluorides. A novel cyclic heptasaccharide was synthesized from α-laminariheptaosyl fluoride using a mutant of the enzyme laminarase 16A and subsequently analyzed by NMR spectroscopy.
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