Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Structure, dynamics and interactions of biomolecules: Investigations by NMR spectroscopy and computational methods
Stockholm University, Faculty of Science, Department of Organic Chemistry. (Bioorganisk kemi)
2009 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

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.

Place, publisher, year, edition, pages
Stockholm: Department of Organic Chemistry, Stockholm University , 2009. , 82 p.
Keyword [en]
NMR spectroscopy, MD simulation, carbohydrate synthesis, protein-ligand interaction, glycosyltransferase
National Category
Chemical Sciences
Research subject
Organic Chemistry
Identifiers
URN: urn:nbn:se:su:diva-30120ISBN: 978-91-7155-953-1 (print)OAI: oai:DiVA.org:su-30120DiVA: diva2:245906
Public defence
2009-11-13, 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 3: Submitted. Paper 4: Submitted. Paper 5: In progress. Paper 6: In progress. Paper 7: Manuscript.Available from: 2009-10-22 Created: 2009-10-04 Last updated: 2011-11-23Bibliographically approved
List of papers
1. Interaction of a Salmonella enteritidis O-antigen octasaccharide with the phage P22 tailspike protein by NMR spectroscopy and docking studies
Open this publication in new window or tab >>Interaction of a Salmonella enteritidis O-antigen octasaccharide with the phage P22 tailspike protein by NMR spectroscopy and docking studies
Show others...
2008 (English)In: Glycoconjugate Journal, ISSN 0282-0080, E-ISSN 1573-4986, Vol. 25, no 2, 137-143 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-13154 (URN)10.1007/s10719-007-9065-9 (DOI)000252991800005 ()
Available from: 2008-12-03 Created: 2008-12-03 Last updated: 2017-12-13Bibliographically approved
2. Synthesis of and molecular dynamics simulations on a tetrasaccharide corresponding to the repeating unit of the capsular polysaccharide from Salmonella enteritidis
Open this publication in new window or tab >>Synthesis of and molecular dynamics simulations on a tetrasaccharide corresponding to the repeating unit of the capsular polysaccharide from Salmonella enteritidis
Show others...
2009 (English)In: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 7, no 8, 1612-1618 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-28937 (URN)10.1039/b823428k (DOI)000265195100014 ()
Available from: 2009-07-22 Created: 2009-07-22 Last updated: 2017-12-13Bibliographically approved
3. Transient hydrogen bonding in uniformly 13C,  15N labeled carbohydrates in water
Open this publication in new window or tab >>Transient hydrogen bonding in uniformly 13C,  15N labeled carbohydrates in water
Show others...
2012 (English)In: Biopolymers, ISSN 0006-3525, E-ISSN 1097-0282, Vol. 97, no 3, 145-154 p.Article in journal (Refereed) Published
Abstract [en]

We report NMR studies of transient hydrogen bonding in a polysaccharide (PS) dissolved in water without cosolvent at ambient temperature. The PS portion of the Escherichia coli O142 lipopolysaccharide is comprised of repeating pentasaccharide units of GalNAc (N-acetyl galactosamine), GlcNAc (N-acetyl glucosamine), and rhamnose in a 3:1:1 ratio, respectively. A 105-ns molecular dynamics (MD) simulation on one pentasaccharide repeat unit predicts transient inter-residue hydrogen bonds from the GalNAc NH groups in the PS. To investigate these predictions experimentally, the PS was uniformly 13C,15N enriched and the NH, carbonyl, C2, C4, and methyl resonances of the GalNAc and GlcNAc residues assigned using through-bond triple-resonance NMR experiments. Temperature dependence of amide NH chemical shifts and one-bond NH J couplings support that NH groups on two of the GalNAc residues are donors in transient hydrogen bonds. The remaining GalNAc and GlcNAc NHs do not appear to be donors from either temperature-dependent chemical shifts or one-bond NH J couplings. These results substantiate the presence of weak or partial hydrogen bonds in carbohydrates, and that MD simulations of repeating units in PSs provide insight into overall PS structure and dynamics.

Place, publisher, year, edition, pages
Wiley Periodicals, Inc., 2012
Keyword
polysaccharides, carbohydrate NMR, oligosaccharide, isotopic labeling, molecular dynamics simulations, radial distribution function, hydrogen bonding
National Category
Organic Chemistry
Identifiers
urn:nbn:se:su:diva-30113 (URN)10.1002/bip.21710 (DOI)000298480400001 ()21858784 (PubMedID)
Available from: 2009-10-04 Created: 2009-10-04 Last updated: 2017-12-13Bibliographically approved
4. Glycan flexibility: Insights into nanosecond dynamics from a microsecond molecular dynamics simulation explaining an unusual nuclear Overhauser effect
Open this publication in new window or tab >>Glycan flexibility: Insights into nanosecond dynamics from a microsecond molecular dynamics simulation explaining an unusual nuclear Overhauser effect
(English)Manuscript (preprint) (Other academic)
Identifiers
urn:nbn:se:su:diva-30114 (URN)
Available from: 2009-10-04 Created: 2009-10-04 Last updated: 2010-01-25Bibliographically approved
5. NMR-based exploration of the acceptor binding site of human blood group B galactosyltransferase with molecular fragments
Open this publication in new window or tab >>NMR-based exploration of the acceptor binding site of human blood group B galactosyltransferase with molecular fragments
Show others...
2010 (English)In: Glycoconjugate Journal, ISSN 0282-0080, E-ISSN 1573-4986, Vol. 27, no 3, 349-358 p.Article in journal (Refereed) Published
Abstract [en]

A substantial body of work has been devoted to the design and synthesis of glycosyltransferase inhibitors. A major obstacle has always been the demanding chemistry. Therefore, only few potent and selective inhibitors are known to date. Glycosyltransferases possess two distinct binding sites, one for the donor substrate, and one for the acceptor substrate. In many cases binding to the donor site is well defined but data for acceptor binding is sparse. In particular, acceptor binding sites are often shallow, and in many cases the dimensions of the binding pocket are not well defined. One approach to glycosyltransferase inhibitors is to chemically link donor site and acceptor site ligands to generate high affinity binders. Here, we describe a novel approach to identify acceptor site ligands from a fragment library. We have chosen human blood group B galactosyltransferase (GTB) as a biologically important model target. The approach utilizes a combination of STD NMR, spin-lock filtered NMR experiments and surface plasmon resonance measurements. Following this route we have identified molecular fragments from a fragment library that bind to the acceptor site of GTB with affinities of the order of a natural acceptor substrate. Unlike natural substrates these fragments allow for straightforward chemical modifications and, therefore will serve as scaffolds for potent GTB inhibitors. In general, the approach described is applicable to any glycosyltransferase and may assist in the development of novel glycosyltransferase inhibitors.

Place, publisher, year, edition, pages
Springer, 2010
National Category
Organic Chemistry
Identifiers
urn:nbn:se:su:diva-38507 (URN)10.1007/s10719-010-9282-5 (DOI)000276168200005 ()
Available from: 2010-04-15 Created: 2010-04-15 Last updated: 2017-12-12Bibliographically approved
6. Exploration of the molecular recognition and dynamic properties of WaaG glycosyltransferase
Open this publication in new window or tab >>Exploration of the molecular recognition and dynamic properties of WaaG glycosyltransferase
Show others...
(English)Manuscript (preprint) (Other academic)
National Category
Organic Chemistry
Research subject
Organic Chemistry
Identifiers
urn:nbn:se:su:diva-30118 (URN)
Available from: 2009-10-04 Created: 2009-10-04 Last updated: 2011-04-19Bibliographically approved
7. Combining WAC, NMR and computer simulations in Lysozyme interaction studies
Open this publication in new window or tab >>Combining WAC, NMR and computer simulations in Lysozyme interaction studies
Show others...
(English)Manuscript (preprint) (Other academic)
Identifiers
urn:nbn:se:su:diva-30119 (URN)
Available from: 2009-10-04 Created: 2009-10-04 Last updated: 2010-01-25Bibliographically approved

Open Access in DiVA

No full text

Search in DiVA

By author/editor
Landström, Jens
By organisation
Department of Organic Chemistry
Chemical Sciences

Search outside of DiVA

GoogleGoogle Scholar

isbn
urn-nbn

Altmetric score

isbn
urn-nbn
Total: 235 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf