Change search
ReferencesLink to record
Permanent link

Direct link
Conformations of Flexible Oligosaccharides: Molecular Simulations and NMR spectroscopy
Stockholm University, Faculty of Science, Department of Organic Chemistry. (Göran Widmalm)
2013 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The conformational preferences of several oligosaccharides are investigated herein using a combination of NMR spectroscopy and molecular dynamics (MD) simulations, focusing on the torsion angles associated with the glycosidic linkages.

Strategies for obtaining usable J-HMBC spectra for carbons with an adjacent 13C label are described. By employing a selective pulse or a constant time modification, spectra free from interferences are obtained for site-specifically 13C labeled oligosaccharides.

Intermolecular hydrogen bonding in sucrose is investigated using MD simulations performed at different concentrations. One of the most frequent intermolecular hydrogen bonds in the simulations, O3f∙∙∙HO3g, was detected using the HSQC-TOCSY NMR experiment.

Based on MD simulations and NMR spectroscopy, the conformational ensemble for a trisaccharide segment of the LeaLex hexasaccharide is proposed to feature conformational exchange between conformations with positive and negative values for the ψ3 torsion angle in the β-D-GlcpNAc-(1→3)-β-D-Galp linkage.

Using MD simulations, the conformation of the N-acetyl group is shown to influence the glycosidic conformation at a nearby linkage in two oligosaccharides.

Short (1→6)-linked oligosaccharides are shown to exhibit conformational exchange at the ω and ψ torsion angles. Notably, the former torsion angle populates states with ψ ≈ ±90°. Conformationally sensitive homo- and heteronuclear coupling constants are determined using various NMR experiments. The experimental data, including effective distances from NOESY obtained for two of the compounds, is used to improve the representation of the ω torsion angle in the CHARMM36 force field.

Place, publisher, year, edition, pages
Stockholm: Department of Organic Chemistry, Stockholm University , 2013. , 78 p.
Keyword [en]
Carbohydrates, Oligosaccharide, Conformation, NMR spectroscopy, MD simulations
National Category
Organic Chemistry
Research subject
Organic Chemistry
Identifiers
URN: urn:nbn:se:su:diva-95480ISBN: 978-91-7447-808-2OAI: oai:DiVA.org:su-95480DiVA: diva2:661098
Public defence
2013-12-13, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 10:00 (English)
Opponent
Supervisors
Note

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 1: Manuscript. Paper 5: Accepted. Paper 6: Manuscript.

Available from: 2013-11-21 Created: 2013-10-29 Last updated: 2015-10-06Bibliographically approved
List of papers
1. Suppressing one-bond homonuclear 13C,13C scalar couplings in the J-HMBC NMR experiment: application to 13C site-specifically labeled oligosaccharides
Open this publication in new window or tab >>Suppressing one-bond homonuclear 13C,13C scalar couplings in the J-HMBC NMR experiment: application to 13C site-specifically labeled oligosaccharides
2014 (English)In: Magnetic Resonance in Chemistry, ISSN 0749-1581, E-ISSN 1097-458X, Vol. 52, no 3, 82-86 p.Article in journal (Refereed) Published
Abstract [en]

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.

Keyword
NMR, 1H, 13C, J-HMBC, oligosaccharide, heteronuclear long-range coupling constants, site-specific labeling
National Category
Chemical Sciences Physical Chemistry Organic Chemistry
Identifiers
urn:nbn:se:su:diva-101733 (URN)10.1002/mrc.4038 (DOI)000330951600003 ()
Funder
Swedish Research CouncilKnut and Alice Wallenberg Foundation
Note

AuthorCount:3;

Available from: 2014-03-17 Created: 2014-03-14 Last updated: 2015-10-21Bibliographically approved
2. Direct Evidence for Hydrogen Bonding in Glycans: A Combined NMR and Molecular Dynamics Study
Open this publication in new window or tab >>Direct Evidence for Hydrogen Bonding in Glycans: A Combined NMR and Molecular Dynamics Study
2013 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, no 17, 4860-4869 p.Article in journal (Refereed) Published
Abstract [en]

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.

National Category
Physical Chemistry Organic Chemistry
Research subject
Organic Chemistry
Identifiers
urn:nbn:se:su:diva-91041 (URN)10.1021/jp400402b (DOI)000318536700015 ()
Funder
Swedish Research Council
Note

AuthorCount:4;

Available from: 2013-06-19 Created: 2013-06-18 Last updated: 2016-10-03Bibliographically approved
3. Conformational Dynamics of a Central Trisaccharide Fragment of the LeaLex Tumor Associated Antigen Studied by NMR Spectroscopy and Molecular Dynamics Simulations
Open this publication in new window or tab >>Conformational Dynamics of a Central Trisaccharide Fragment of the LeaLex Tumor Associated Antigen Studied by NMR Spectroscopy and Molecular Dynamics Simulations
Show others...
2012 (English)In: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, no 25, 4705-4715 p.Article in journal (Refereed) Published
Abstract [en]

Certain carbohydrate structures are recognized as cancer antigens, and identification of these and relevant epitopes are essential in fighting the disease. The trisaccharide beta-D-GlcpNAc-(1?3)-beta-D-Galp-(1?4)-beta-D-GlcpNAc-OMe represents a model for the central region of the LeaLex hexasaccharide and it has herein been investigated by 1D 1H,1H-NOESY experiments to obtain effective interresidue protonproton distances as well as by 2D J-HMBC experiments to determine transglycosidic 3JCH coupling constants. Molecular dynamics (MD) simulations using explicit water as solvent and three different carbohydrate force fields, namely, GLYCAM06, PARM22/SU01, and CHARMM2011, were employed for the interpretation of experimental data. Overall, the force field based MD simulations are able to reproduce the experimental data and the ? torsion angle at the beta-(1?3)-linkage is concluded to be flexible. In addition, different minor states were present for the three force fields with either anti-? or non-exo-anomeric conformations. Transitions between the exo-anomeric and the non-exo-anomeric conformations for the f torsion angle at the beta-(1?4)-linkage in one of the MD simulations were analyzed in detail. It was found that hydrogen-bonding water molecules, interresidue hydrogen bonds and the transitions between antiperiplanar and synperiplanar conformations for the tH torsion angle of an N-acetyl group were all essential in the description of the glycosidic transition process. In particular, the transition of tH may be a general way of regulating other transitions into less populated but biologically important conformational regions.

Keyword
Carbohydrates, Conformation analysis, NMR spectroscopy, Molecular dynamics
National Category
Organic Chemistry
Research subject
Organic Chemistry
Identifiers
urn:nbn:se:su:diva-81235 (URN)10.1002/ejoc.201200569 (DOI)000307937800008 ()
Funder
Swedish Research CouncilKnut and Alice Wallenberg Foundation
Note

AuthorCount:6;

Available from: 2012-10-18 Created: 2012-10-15 Last updated: 2013-11-18Bibliographically approved
4. Glycan synthesis, structure, and dynamics: A selection
Open this publication in new window or tab >>Glycan synthesis, structure, and dynamics: A selection
2013 (English)In: Pure and Applied Chemistry, ISSN 0033-4545, E-ISSN 1365-3075, Vol. 85, no 9, 1759-1770 p.Article in journal (Refereed) Published
Abstract [en]

Glycan structural information is a prerequisite for elucidation of carbohydrate function in biological systems. To this end we employ a tripod approach for investigation of carbo hydrate 3D structure and dynamics based on organic synthesis; different experimental spectroscopy techniques, NMR being of prime importance; and molecular simulations using, in particular, molecular dynamics (MD) simulations. The synthesis of oligosaccharides in the form of glucosyl fluorides is described, and their use as substrates for the Lam16A E115S glucosyl synthase is exemplified as well as a conformational analysis of a cyclic beta-(1 -> 3)-heptaglucan based on molecular simulations. The flexibility of the N-acetyl group of aminosugars is by MD simulations indicated to function as a gatekeeper for transitions of glycosidic torsion angles to other regions of conformational space. A novel approach to visualize glycoprotein (GP) structures is presented in which the protein is shown by, for example, ribbons, but instead of stick or space-filling models for the carbohydrate portion it is visualized by the colored geometrical figures known as CFG representation in a 3D way, which we denote 3D-CFG, thereby effectively highlighting the sugar residues of the glycan part of the GP and the position(s) on the protein.

Keyword
carbohydrates, glycosynthase, molecular dynamics, structure, synthesis
National Category
Organic Chemistry
Research subject
Organic Chemistry
Identifiers
urn:nbn:se:su:diva-94061 (URN)10.1351/PAC-CON-12-10-17 (DOI)000323700200002 ()
Note

AuthorCount:3;

Available from: 2013-09-24 Created: 2013-09-24 Last updated: 2013-11-18Bibliographically approved
5. Conformation and Dynamics at a Flexible Glycosidic Linkage Revealed by NMR Spectroscopy and Molecular Dynamics Simulations: Analysis of β-ʟ-Fucp-(1→6)-α-ᴅ-Glcp-OMe in Water Solution
Open this publication in new window or tab >>Conformation and Dynamics at a Flexible Glycosidic Linkage Revealed by NMR Spectroscopy and Molecular Dynamics Simulations: Analysis of β-ʟ-Fucp-(1→6)-α-ᴅ-Glcp-OMe in Water Solution
2013 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, no 47, 14709-14722 p.Article in journal (Refereed) Published
Abstract [en]

The intrinsic flexibility of carbohydrates facilitates different 3D structures in response to altered environments. At glycosidic (1 -> 46)-linkages, three torsion angles are variable, and herein the conformation and dynamics of beta-1.-Fucp-(1 -> 6)-alpha-D-Glcp-OMe are investigated using a combination of NMR spectroscopy and molecular dynamics (MD) simulations. The disaccharide shows evidence of conformational averaging for the psi and co torsion angles, best explained by a four-state conformational distribution. Notably, there is a significant population of conformations having psi = 85 degrees (clinal) in addition to those having psi = 180 degrees (anfiperiplanar). Moderate differences in C-13 R-1 relaxation rates are found to be best explained by axially symmetric tumbling in combination with minor differences in librational motion for the two residues, whereas the isomerization motions are occurring too slowly to significantly to the observed relaxation rates. The MD simulation was found to give a reasonably good agreement with experiment, especially with respect to diffusive properties, among which the rotational anisotropy, D parallel to/D parallel to, is found to be 2.35. The force field employed showed too narrow omega torsion angles in the gauche trans and gauche gauche states as well as overestimating the population of the gauche trans conformer. This information can subsequently be used in directing parameter developments and emphasizes the need for refinement of force fields for (1 -> 6)-linked carbohydrates.

National Category
Organic Chemistry
Research subject
Organic Chemistry
Identifiers
urn:nbn:se:su:diva-100876 (URN)10.1021/jp409985h (DOI)000330160100013 ()
Funder
Swedish Research CouncilKnut and Alice Wallenberg Foundation
Note

AuthorCount:3;

Available from: 2014-02-18 Created: 2014-02-17 Last updated: 2016-10-03Bibliographically approved
6. Conformational Properties of alpha- or beta-(1 -> 6)-Linked Oligosaccharides: Hamiltonian Replica Exchange MD Simulations and NMR Experiments
Open this publication in new window or tab >>Conformational Properties of alpha- or beta-(1 -> 6)-Linked Oligosaccharides: Hamiltonian Replica Exchange MD Simulations and NMR Experiments
Show others...
2014 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, no 11, 2851-2871 p.Article in journal (Refereed) Published
Abstract [en]

Conformational sampling for a set of 10 alpha- or beta-(1 -> 6)-linked oligosaccharides has been studied using explicit solvent Hamiltonian replica exchange (HREX) simulations and NMR spectroscopy techniques. Validation of the force field and simulation methodology is done by comparing calculated transglycosidic J coupling constants and proton-proton distances with the corresponding NMR data. Initial calculations showed poor agreement, for example, with >3 Hz deviation of the calculated (3)J(H5,H6R) values from the experimental data, prompting optimization of the omega torsion angle parameters associated with (1 -> 6)-linkages. The resulting force field is in overall good agreement (i.e., within similar to 0.5 Hz deviation) from experimental (3)J(H5,H6R) values, although some small limitations are evident. Detailed hydrogen bonding analysis indicates that most of the compounds lack direct intramolecular H-bonds between the two monosaccharides; however, minor sampling of the O6 center dot center dot center dot HO2' hydrogen bond is present in three compounds. The results verify the role of the gauche effect between O5 and O6 atoms in gluco- and manno-configured pyranosides causing the omega torsion angle to sample an equilibrium between the gt and gg rotamers. Conversely, galacto-configured pyranosides sample a population distribution in equilibrium between gt and tg rotamers, while the gg rotamer populations are minor. Water radial distribution functions suggest decreased accessibility to the O6 atom in the (1 -> 6)-linkage as compared to the O6' atom in the nonreducing sugar. The role of bridging water molecules between two sugar moieties on the distributions of omega torsion angles in oligosaccharides is also explored.

National Category
Organic Chemistry
Research subject
Organic Chemistry
Identifiers
urn:nbn:se:su:diva-102956 (URN)10.1021/jp412051v (DOI)000333381800008 ()
Funder
NIH (National Institute of Health)Knut and Alice Wallenberg FoundationSwedish Research Council
Note

AuthorCount:5;

Available from: 2014-04-29 Created: 2014-04-25 Last updated: 2015-10-06Bibliographically approved

Open Access in DiVA

fulltext(3797 kB)413 downloads
File information
File name FULLTEXT01.pdfFile size 3797 kBChecksum SHA-512
38c552d0cc11fc56fef532a5c6a01ace25fac803a424458b2ddcfe491ec467f9af043cf73cada0a3fd71e4833b1db9f17bfe29fa797d6b66e441712822cbfdd4
Type fulltextMimetype application/pdf

Search in DiVA

By author/editor
Pendrill, Robert
By organisation
Department of Organic Chemistry
Organic Chemistry

Search outside of DiVA

GoogleGoogle Scholar
Total: 413 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Total: 330 hits
ReferencesLink to record
Permanent link

Direct link