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Exploring the Molecular Behavior of Carbohydrates by NMR Spectroscopy: Shapes, motions and interactions
Stockholm University, Faculty of Science, Department of Organic Chemistry. (Göran Widmalm)
2015 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Carbohydrates are essential biomolecules that decorate cell membranes and proteins in organisms. They are important both as structural elements and as identification markers. Many biological and pathogenic processes rely on the identification of carbohydrates by proteins, thereby making them attractive as molecular blueprints for drugs. This thesis describes how NMR spectroscopy can be utilized to study carbohydrates in solution at a molecular level. This versatile technique facilitates for investigations of (i) shapes, (ii) motions and (iii) interactions.

A conformational study of an E. coli O-antigen was performed by calculating atomic distances from NMR NOESY experiments. The acquired data was utilized to validate MD simulations of the LPS embedded in a membrane. The agreement between experimental and calculated data was good and deviations were proven to arise from spin-diffusion. In another study presented herein, both the conformation and the dynamic behavior of amide side-chains linked to derivatives of D-Fucp3N, a sugar found in the O-antigen of bacteria, were investigated. J-couplings facilitated a conformational analysis and 13C saturation transfer NMR experiments were utilized to measure rate constants of amide cis-trans isomerizations.

13C NMR relaxation and 1H PFG diffusion measurements were carried out to explore and describe the molecular motion of mannofullerenes. The dominating motions of the mannofullerene spectral density were found to be related to pulsating motions of the linkers rather than global rotational diffusion. The promising inhibition of Ebola viruses identified for a larger mannofullerene can thus be explained by an efficient rebinding mechanism that arises from the observed flexibility in the linker.

Molecular interactions between sugars and caffeine in water were studied by monitoring chemical shift displacements in titrations. The magnitude of the chemical shift displacements indicate that the binding occurs by a face to face stacking of the aromatic plane of caffeine to the ring plane of the sugar, and that the interaction is at least partly driven by solvation effects. Also, the binding of a Shigella flexneri serotype Y octasaccharide to a bacteriophage Sf6 tail spike protein was investigated. This interaction was studied by 1H STD NMR and trNOESY experiments. A quantitative analysis of the STD data was performed employing a newly developed method, CORCEMA-ST-CSD, that is able to simulate STD data more accurately since the line broadening of protein resonances are accounted for in the calculations.

Place, publisher, year, edition, pages
Stockholm: Department of Organic Chemistry, Stockholm University , 2015.
Keyword [en]
NMR spectroscopy, NMR relaxation, DNMR, CORCEMA-ST, carbohydrates, caffeine, O-antigen, glycofullerenes
National Category
Organic Chemistry
Research subject
Organic Chemistry
Identifiers
URN: urn:nbn:se:su:diva-116037ISBN: 978-91-7649-140-9 (print)OAI: oai:DiVA.org:su-116037DiVA: diva2:801496
Public defence
2015-05-22, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 10:00 (English)
Opponent
Supervisors
Funder
Swedish Research Council
Note

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 4: Manuscript. Paper 5: Manuscript.

Available from: 2015-04-29 Created: 2015-04-09 Last updated: 2017-02-20Bibliographically approved
List of papers
1. Caffeine and Sugars Interact in Aqueous Solutions: A Simulation and NMR Study
Open this publication in new window or tab >>Caffeine and Sugars Interact in Aqueous Solutions: A Simulation and NMR Study
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2012 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, no 38, 11701-11711 p.Article in journal (Refereed) Published
Abstract [en]

Molecular dynamics simulations were carried out on several systems of caffeine interacting with simple sugars. These included a single caffeine molecule in a 3 in solution of alpha-D-glucopyranose, at a caffeine concentration of 0.083 m, a single caffeine in a 3 in solution of beta-D-glucopyranose, and a single caffeine molecule in a 1.08 m solution of sucrose (table sugar). Parallel nuclear magnetic resonance titration experiments were carried out on the same solutions under similar conditions. Consistent with previous thermodynamic experiments, the sugars were found to have an affinity for the caffeine molecules in both the simulations and experiments, and the binding in these complexes occurs by face-to-face stacking of the hydrophobic triad of protons of the pyranose rings against the caffeine face, rather than by hydrogen bonding. For the disaccharide, the binding occurs via stacking of the glucose ring against the caffeine, with a lesser affinity for the fructose observed. These findings are consistent with the association being driven by hydrophobic hydration and are similar to the previously observed binding of glucose rings to various other planar molecules, including indole, serotonin, and phenol.

National Category
Physical Chemistry
Research subject
Organic Chemistry
Identifiers
urn:nbn:se:su:diva-82102 (URN)10.1021/jp303910u (DOI)000309150000016 ()
Funder
Swedish Research CouncilKnut and Alice Wallenberg Foundation
Note

AuthorCount:8;

Available from: 2012-11-09 Created: 2012-11-08 Last updated: 2017-12-07Bibliographically approved
2. Probing the conformational space of Shigella flexneri O‑antigen bound to the tailspike protein of bacteriophage Sf6 by X-ray crystallography, NMR, and Molecular Dynamics
Open this publication in new window or tab >>Probing the conformational space of Shigella flexneri O‑antigen bound to the tailspike protein of bacteriophage Sf6 by X-ray crystallography, NMR, and Molecular Dynamics
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(English)Manuscript (preprint) (Other academic)
Keyword
Shigella flexneri O antigen, protein-carbohydrate interaction, X-ray crystallography, molecular dynamics, STD-NMR, tailspike
National Category
Organic Chemistry
Research subject
Organic Chemistry
Identifiers
urn:nbn:se:su:diva-116016 (URN)
Funder
Swedish Research CouncilKnut and Alice Wallenberg Foundation
Available from: 2015-04-09 Created: 2015-04-09 Last updated: 2016-01-29Bibliographically approved
3. Molecular Dynamics and NMR Spectroscopy Studies of E. coli Lipopolysaccharide Structure and Dynamics
Open this publication in new window or tab >>Molecular Dynamics and NMR Spectroscopy Studies of E. coli Lipopolysaccharide Structure and Dynamics
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2013 (English)In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 105, no 6, 1444-1455 p.Article in journal (Refereed) Published
Abstract [en]

Lipopolysaccharide (LPS), a component of Gram-negative bacterial outer membranes, comprises three regions: lipid A, core oligosaccharide, and O-antigen polysaccharide. Using the CHARMM36 lipid and carbohydrate force fields, we have constructed a model of an Escherichia coil R1 (core) 06 (antigen) LPS molecule. Several all-atom bilayers are built and simulated with lipid A only (LIPA) and varying lengths of 0 (LPS0), 5 (LPS5), and 10 (LPS10) O6 antigen repeating units; a single unit of 06 antigen contains five sugar residues. From H-1,H-1-NOESY experiments, cross-relaxation rates are obtained from an O-antigen polysaccharide sample. Although some experimental deviations are due to spin-diffusion, the remaining effective proton-proton distances show generally very good agreement between NMR experiments and molecular dynamics simulations. The simulation results show that increasing the LPS molecular length has an impact on LPS structure and dynamics and also on LPS bilayer properties. Terminal residues in a LPS bilayer are more flexible and extended along the membrane normal. As the core and O-antigen are added, per-lipid area increases and lipid bilayer order decreases. In addition, results from mixed LPS0/5 and LPS0/10 bilayer simulation's show that the LPS O-antigen conformations at a higher concentration of LPS5 and LPS10 are more orthogonal to the membrane and less flexible. The O-antigen concentration of mixed LPS bilayers does not have a significant effect on per-lipid area and hydrophobic thickness. Analysis of ion and water penetration shows that water molecules can penetrate inside the inner core region, and hydration is critical to maintain the integrity of the bilayer structure.

National Category
Biophysics
Research subject
Organic Chemistry
Identifiers
urn:nbn:se:su:diva-95430 (URN)10.1016/j.bpj.2013.08.002 (DOI)000324606300020 ()
Funder
Swedish Research CouncilKnut and Alice Wallenberg Foundation
Note

AuthorCount:8;

Available from: 2013-10-31 Created: 2013-10-28 Last updated: 2017-12-06Bibliographically approved
4. Conformational dynamics and exchange kinetics of N-formyl and N-acetyl groups substituting 3-amino-3,6-dideoxy-α-D-galactopyranose, a sugar found in bacterial O-antigen polysaccharides
Open this publication in new window or tab >>Conformational dynamics and exchange kinetics of N-formyl and N-acetyl groups substituting 3-amino-3,6-dideoxy-α-D-galactopyranose, a sugar found in bacterial O-antigen polysaccharides
(English)Manuscript (preprint) (Other academic)
Keyword
DNMR, carbohydrates, energy barriers, line-shape analysis, Eyring plot, DFT calculations, Karplus equation
National Category
Organic Chemistry
Research subject
Organic Chemistry
Identifiers
urn:nbn:se:su:diva-116030 (URN)
Funder
Knut and Alice Wallenberg FoundationSwedish Research Council
Available from: 2015-04-09 Created: 2015-04-09 Last updated: 2016-01-29Bibliographically approved
5. Investigation of glycofullerene dynamics by NMR spectroscopy
Open this publication in new window or tab >>Investigation of glycofullerene dynamics by NMR spectroscopy
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2015 (English)In: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 13, no 32, 8750-8755 p.Article in journal (Refereed) Published
Abstract [en]

Glycofullerenes, in which carbohydrate molecules are attached via a linker to a [60]fullerene core, facilitate spherical presentation of glyco-based epitopes. We herein investigate the dynamics of two glycofullerenes, having 12 and 36 mannose residues at their periphery, by NMR translational diffusion and quantitative C-13 relaxation studies employing a model-free approach for their interpretation. The sugar residues are shown to be highly flexible entities with S-2 < 0.2 in both compounds. Notably, the larger glycofullerene with longer linkers shows faster internal dynamics and higher flexibility than its smaller counterpart. The dynamics and flexibility as well as the slower translational diffusion of the larger glycofullerene, thereby favoring rebinding to a receptor, may together with its spatial extension explain why it is better than the smaller one at blocking the DC-SIGN receptor and inhibiting the infection by pseudotyped Ebola virus particles.

National Category
Organic Chemistry
Research subject
Organic Chemistry
Identifiers
urn:nbn:se:su:diva-120486 (URN)10.1039/c5ob00929d (DOI)000359134700020 ()
Funder
Swedish Research CouncilKnut and Alice Wallenberg Foundation
Available from: 2015-09-11 Created: 2015-09-10 Last updated: 2017-12-04Bibliographically approved

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