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NMR studies of host-pathogen interactions
Umeå University, Faculty of Medicine, Medical Biochemistry and Biophsyics. (Prof. Schleucher)
2009 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

This thesis describes the use of Nuclear Magnetic Resonance (NMR) for characterizing two host-pathogen interactions: The behavior of a regulatory RNA of the Hepatitis B virus (HBV) and the attachment of Helicobacter pylori (H. pylori) to the gastric mucosa. NMR is a powerful tool in biomedicine, because molecules ranging from small ligands to biomacromolecules can be studied with atomic resolution. Different NMR experiments are designed to determine structures, or to monitor interactions, folding, stability or motion.

Paper I describes the analysis of the motions of a regulatory RNA of HBV. The NMR structure of the RNA had revealed before that several well-conserved nucleotides adopt multiple conformations. Therefore an analysis of possible underlying motions was undertaken using two different NMR techniques, one of which (off-resonance ROESY) was applied to nucleic acids for the first time. The observed motions suggest an explanation why the structurally poorly defined nucleotides are highly conserved.

In paper II we improved the ROESY NMR experiment, which is used to measure internuclear distances for structure determination of medium-sized molecules. Using a small protein and an organometallic complex as examples, we demonstrated that the new EASY ROESY experiment yields clean spectra that can directly be integrated to derive interatomic distances.

H. pylori, the bacterium involved in peptic ulcer disease and gastric cancer, survives in the harsh acidic environment of the stomach. It possesses many membrane proteins which mediate adherence, raising the question, if their activity is related to membrane composition. In paper III & IV we analyzed therefore the phospholipid composition of H. pylori membranes.

In paper III, an advanced method for the analysis of the phospholipid composition of biological membranes was developed. The two-dimensional semi-constant-time 31P,1H-COSY experiment combines information from phosphorus and hydrogen atoms of phospholipids for their unambiguous identification. Furthermore, the high resolution of the two-dimensional experiment allows the quantification of phospholipids where conventional methods fail.

In paper IV we applied the new experiment to analyze the lipid composition of whole H. pylori cells, their inner and outer membranes, and of vesicles shed by the bacterium. The goal of this study was to characterize the vesicles which are suggested to play a role in the inflammation process. We established that the outer membrane and the vesicles have similar phospholipid compositions, suggesting that the vesicles are largely derived from the outer membrane.

The NMR results presented here elucidate details of molecular systems engaged in pathogenicity, as basis for therapeutic strategies against these pathogens.

Place, publisher, year, edition, pages
Umeå, 2009. , 48 p.
Series
Umeå University medical dissertations, ISSN 0346-6612 ; 1275
Keyword [en]
NMR, regulatory RNA, HBV, H.pylori, phospholipids, ROESY
National Category
Biophysics
Research subject
Biochemistry
Identifiers
URN: urn:nbn:se:umu:diva-25710ISBN: 978-91-7264-816-6 (print)OAI: oai:DiVA.org:umu-25710DiVA: diva2:233439
Distributor:
Medicinsk kemi och biofysik, 901 85, Umeå
Public defence
2009-09-26, KB3A9, plan 3, KBC-huset, Umeå Universität, Umeå, 10:00 (English)
Opponent
Supervisors
Available from: 2009-09-08 Created: 2009-08-31 Last updated: 2009-09-22Bibliographically approved
List of papers
1. Conserved nucleotides in an RNA essential for hepatitis B virus replication show distinct mobility patterns
Open this publication in new window or tab >>Conserved nucleotides in an RNA essential for hepatitis B virus replication show distinct mobility patterns
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2007 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 35, no 20, 6854-6861 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:umu:diva-6539 (URN)10.1093/nar/gkm774 (DOI)17933777 (PubMedID)
Available from: 2007-12-13 Created: 2007-12-13 Last updated: 2010-04-09Bibliographically approved
2. EASY ROESY: reliable cross-peak integration in adiabatic symmetrized ROESY
Open this publication in new window or tab >>EASY ROESY: reliable cross-peak integration in adiabatic symmetrized ROESY
2009 (English)In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 15, no 3, 585-588 p.Article in journal (Refereed) Published
Abstract [en]

Estimates of intramolecular distances are essential for structure determination. For medium-sized molecules, ROESY NMR is the method of choice for obtaining distances. However, the integration of ROESY cross-peaks is problematic due to the offset dependence of theintegrals and/or TOCSY artefacts. We here present EASY ROESY (rEliable Adiabatic SYmmetrized ROESY), which yields reliable intramolecular distances without sample-specific setup.

National Category
Chemical Sciences
Identifiers
urn:nbn:se:umu:diva-25735 (URN)10.1002/chem.200802027 (DOI)
Available from: 2009-09-01 Created: 2009-09-01 Last updated: 2012-08-10Bibliographically approved
3. Semiconstant-Time P,H-COSY NMR: Analysis of Complex Mixtures of Phospholipids Originating from Helicobacter pylori
Open this publication in new window or tab >>Semiconstant-Time P,H-COSY NMR: Analysis of Complex Mixtures of Phospholipids Originating from Helicobacter pylori
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2009 (English)In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 131, no 40, 14150-1 p.Article in journal (Refereed) Published
Abstract [en]

Lipids play a central role in numerous biological events, ranging from normal physiological processes to host−pathogen interactions. The proposed semiconstant-time 31P,1H−COSY NMR experiment provides identification of known and structural characterization of unknown phospholipids in complex membrane extracts with high sensitivity, based on the combination of their 1H and 31P chemical shifts and coupling patterns. Furthermore, the spectra allow quantification of phospholipid composition. Analysis of the phospholipid composition of Helicobacter pylori, the causative agent of peptic ulcer disease, showed the presence of uncommon phospholipids. This novel NMR approach allows the study of changes in membrane composition in response to biological stimuli and opens up the possibility of identifying soluble phosphorus species in a number of research fields.

Place, publisher, year, edition, pages
ACS Publications ASAP, 2009
Identifiers
urn:nbn:se:umu:diva-26035 (URN)10.1021/ja905282h (DOI)
Note
Publication Date (Web): September 17, 2009Available from: 2009-09-21 Created: 2009-09-21 Last updated: 2013-04-26Bibliographically approved
4. Characterization of Helicobacter pylori vesicles and their cognate properties for intimate host interactions
Open this publication in new window or tab >>Characterization of Helicobacter pylori vesicles and their cognate properties for intimate host interactions
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(English)Manuscript (preprint) (Other academic)
National Category
Cell and Molecular Biology Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
urn:nbn:se:umu:diva-25737 (URN)
Available from: 2009-09-01 Created: 2009-09-01 Last updated: 2017-05-22Bibliographically approved

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Petzold, Katja

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