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Water and Protein Dynamics in Biological Systems Studied by Magnetic Relaxation Dispersion

Persson Sunde, Erik LU (2009)
Abstract (Swedish)
Popular Abstract in Swedish

Allt liv på jorden har utvecklats i en vattenbaserad miljö. Proteiner och andra biomolekyler har därigenom anpassats i sin struktur och funktion till vattnets speciella egenskaper. För att kunna förstå biologiska processer måste vi studera hur biomolekyler växelverkar med det omgivande vattnet under fysiologiska betingelser. Detta är särkilt viktigt eftersom det flesta biologiska processer sker i gränsytan mellan proteinet och vatten. Men vatten finns inte bara på proteinets yta, enskilda vattenmolekyler finns även inneslutna inuti proteinet. Subtila förändringar i proteinets struktur avgör om dessa inneslutna vattenmolekyler tränger in eller ut ur proteinet. Dessa strukturella förändringar kan... (More)
Popular Abstract in Swedish

Allt liv på jorden har utvecklats i en vattenbaserad miljö. Proteiner och andra biomolekyler har därigenom anpassats i sin struktur och funktion till vattnets speciella egenskaper. För att kunna förstå biologiska processer måste vi studera hur biomolekyler växelverkar med det omgivande vattnet under fysiologiska betingelser. Detta är särkilt viktigt eftersom det flesta biologiska processer sker i gränsytan mellan proteinet och vatten. Men vatten finns inte bara på proteinets yta, enskilda vattenmolekyler finns även inneslutna inuti proteinet. Subtila förändringar i proteinets struktur avgör om dessa inneslutna vattenmolekyler tränger in eller ut ur proteinet. Dessa strukturella förändringar kan visa sig vara viktiga för proteinets funktion och det är således viktigt att kunna mäta dessa. I artiklar I –III utvecklar vi en metod för att kunna karakterisera just dessa strukturella förändringar på en tidskala som inte varit tillgänglig tidigare. Detta gör vi genom att mäta den kärnmagnetiska relaxationen av vattenmolekylerna i olika proteingeler.



En vanlig bakterie består till 30% av proteiner och andra biomolekyler. Detta medför att vattenmolekylerna inuti celler beter sig annorlunda än i ett provrör. Hur stor denna skillnad är råder det fortfarande delade meningar om. Men med hjälp av kärnmagnetiska relaxation visar vi i artikel IV att cellvatten till största delen är lika lättflytande som kranvatten. Detta har stor betydelse för de processer som sker i cellen. I artikel V visar vi att detta är sant även för bakteriella sporer trotts att vissa forskare påstår att sporernas exceptionella överlevnadsförmåga kommer från vattenmolekylernas glasliknande karaktär.



Bildgivande magnetresonans (MR), har blivit en allt viktigare teknik inom diagnostisk medicin. I MR baseras kontrasten på specifika molekylära detaljer i vattenmolekylernas växelverkan med proteiner i kroppen. I artikel III & VI klarlägger vi vilka olika molekylära mekanismer som ger upphov till en viss typ av MR kontrast. Denna nya förståelse kan förbättra MR-teknikens kliniska potential. (Less)
Abstract
The results presented in this thesis demonstrate that the magnetic relaxation dispersion (MRD) technique can provide information of relevance to protein biophysics, magnetic resonance imaging and cell biology.



By immobilizing proteins with covalent cross-links, intermittent protein dynamics on the previously inaccessible ns-µs time scale could be probed with MRD via the exchange of water molecules between internal cavities and the surrounding bulk solvent phase. Persistent side-chain dynamics on the same time scale could also be probed via labile hydrogens that exchange with bulk water.



A critical test of two physically distinct mechanisms that are used to interpret 1H MRD profiles from immobilized... (More)
The results presented in this thesis demonstrate that the magnetic relaxation dispersion (MRD) technique can provide information of relevance to protein biophysics, magnetic resonance imaging and cell biology.



By immobilizing proteins with covalent cross-links, intermittent protein dynamics on the previously inaccessible ns-µs time scale could be probed with MRD via the exchange of water molecules between internal cavities and the surrounding bulk solvent phase. Persistent side-chain dynamics on the same time scale could also be probed via labile hydrogens that exchange with bulk water.



A critical test of two physically distinct mechanisms that are used to interpret 1H MRD profiles from immobilized proteins was performed. A quantitative analysis of the 1H profiles from protonated and partially deuterated ubiquitin resolved the long-standing controversy over the molecular basis of water-1H relaxation in systems containing immobilized macromolecules, including biological tissue. The molecular mechanisms behind the 1H-14N magnetization transfer, the so called quadrupolar peaks, observed in immobilized systems was also investigated.



The state of water in living cells is of fundamental biological importance, but previous attempts to characterize cell water have been inconclusive. MRD experiments on deuterated cell water are reported that, for the first time, quantify the slowing down of all intracellular water and rule out the idea of a highly perturbed cytoplasm. Water 2H and 17O MRD was also used to address a related problem of both fundamental and practical importance: the molecular mechanism behind the exceptional heat resistance and dormancy of bacterial spores. The dehydrated core region is thought to play a key role but little is known about the physical state of water in the different spore compartments or about the rate of water transport among them. These questions could be answered by monitoring the water dynamics in the different compartments of B. subtilis spores. (Less)
Please use this url to cite or link to this publication:
author
supervisor
opponent
  • Prof. Navon, Gil, Tel Aviv University, Tel Aviv, Israel
organization
publishing date
type
Thesis
publication status
published
subject
keywords
protein dynamics, ubiquitin, BPTI, Escherichia coli, Haloarcula marismortui, nuclear magnetic resonance, protein hydration, magnetic relaxation dispersion, water dynamics, cell water
pages
224 pages
defense location
Sal K:A, Kemicentrum, Getingevägen 60, Lund University Faculty of Engineering
defense date
2009-11-27 13:15
ISBN
978-91-628-7895-5
language
English
LU publication?
yes
id
10314a70-9993-4d33-82a3-7a2ae131f22e (old id 1496549)
date added to LUP
2009-11-03 12:00:35
date last changed
2016-09-19 08:45:16
@phdthesis{10314a70-9993-4d33-82a3-7a2ae131f22e,
  abstract     = {The results presented in this thesis demonstrate that the magnetic relaxation dispersion (MRD) technique can provide information of relevance to protein biophysics, magnetic resonance imaging and cell biology.<br/><br>
<br/><br>
By immobilizing proteins with covalent cross-links, intermittent protein dynamics on the previously inaccessible ns-µs time scale could be probed with MRD via the exchange of water molecules between internal cavities and the surrounding bulk solvent phase. Persistent side-chain dynamics on the same time scale could also be probed via labile hydrogens that exchange with bulk water. <br/><br>
<br/><br>
A critical test of two physically distinct mechanisms that are used to interpret 1H MRD profiles from immobilized proteins was performed. A quantitative analysis of the 1H profiles from protonated and partially deuterated ubiquitin resolved the long-standing controversy over the molecular basis of water-1H relaxation in systems containing immobilized macromolecules, including biological tissue. The molecular mechanisms behind the 1H-14N magnetization transfer, the so called quadrupolar peaks, observed in immobilized systems was also investigated.<br/><br>
 <br/><br>
The state of water in living cells is of fundamental biological importance, but previous attempts to characterize cell water have been inconclusive. MRD experiments on deuterated cell water are reported that, for the first time, quantify the slowing down of all intracellular water and rule out the idea of a highly perturbed cytoplasm. Water 2H and 17O MRD was also used to address a related problem of both fundamental and practical importance: the molecular mechanism behind the exceptional heat resistance and dormancy of bacterial spores. The dehydrated core region is thought to play a key role but little is known about the physical state of water in the different spore compartments or about the rate of water transport among them. These questions could be answered by monitoring the water dynamics in the different compartments of B. subtilis spores.},
  author       = {Persson Sunde, Erik},
  isbn         = {978-91-628-7895-5},
  keyword      = {protein dynamics,ubiquitin,BPTI,Escherichia coli,Haloarcula marismortui,nuclear magnetic resonance,protein hydration,magnetic relaxation dispersion,water dynamics,cell water},
  language     = {eng},
  pages        = {224},
  school       = {Lund University},
  title        = {Water and Protein Dynamics in Biological Systems Studied by Magnetic Relaxation Dispersion},
  year         = {2009},
}