A FRET-based method to study the activity of electron or oxygen transfer proteins and redox enzymes
Zauner, G.
Citation
Zauner, G. (2008, October 23). A FRET-based method to study the activity of electron or oxygen transfer proteins and redox enzymes. Retrieved from https://hdl.handle.net/1887/13201
Version: Corrected Publisher’s Version
License: Licence agreement concerning inclusion of doctoral thesis in the Institutional Repository of the University of Leiden
Downloaded from: https://hdl.handle.net/1887/13201
Note: To cite this publication please use the final published version (if applicable).
Appendices
Abbreviations List of Publications
Curriculum Vitae
Acknowledgements
Appendices
List of Abbreviations
A Acceptor or absorption
Stretching parameter
BM(PEO)3 1,11-bis-maleimidotriethyleneglycol
BSA Bovine serum albumin
CT Charge transfer
d Distance
D Donor
DMSO Dimethylsulfoxide
DTT Dithiotreitol
E Efficiency of energy transfer
Extinction coefficient
ESI Electrospray ionization
ET Electron transfer
F Fluorescence
FAD Flavin adenine dinucleotide
FMN Flavin mononucleotide
FRET Förster Resonance Energy Transfer
G Fluorescence intensity autocorrelation function GFP Green fluorescence protein
Hc Hemocyanin
I Integral of the Poissonian distribution
J Spectral overlap integral between donor emission and acceptor absorption.
k Rate constant
N2 Orientation factor in Resonance Energy Transfer
Kd Dissociation constant
Km Michaelis constant
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MALDI Matrix assisted laser desorption ionization MPTS 3-mercaptopropyl-trimethoxysilane
MV Methylviologen
n Refractive index
NHS N-hydroxyl succinimidyl
NADH Nicotine adenine dinucleotide
NiR Nitrite reductase
NMR Nuclear Magnetic Resonance
oxy Oxygenated
oxi Oxidized
P Relative occurrence of a certain state
PES Phenazine ethosulfate
Fluorescence quantum yield
R Donor-acceptor distance in Resonance Energy Transfer
R0 Förster distance in Resonance Energy Transfer rmsd Root mean square difference
RT Room temperature
RZ Reinheitszahl
SR Switching ratio
W Decay time
TES Triethoxysilane
TMOS Alkoxide TetraMethOxySilane
Trp Tryptophan
Tyr Tyrosinase
UV-Vis Ultraviolet and visible spectrum Vmax Maximum velocity of a reaction
WT Wild type
XRD X-ray diffraction
Appendices
List of Publications
Gerhild Zauner, Yating Wang, Manuel Lavesa-Curto, Andrew MacDonald , Andrew G. Mayes , Richard P. Bowater and Julea N.Butt
‘Tethered DNA hairpins facilitate electrochemical detection of DNA ligation.’ Analyst, 2005, 130 (3), 345 – 349.
S.Kuznetsova, G.Zauner, R.Schmauder, O.A.Mayboroda, A.M.Deelder, T.J.Aartsma, G.W.Canters
‘A FRET-based method for fluorescence detection of the protein redox state.’ Anal.
Biochem., 2006, 350, 52-60.
J. J. Davis, H. Burgess, G. Zauner, S. Kuznetsova, J. Salverda, T. Aartsma, and G.
W. Canters
‘Monitoring interfacial bioelectrochemistry using a FRET switch.’ J. Phys. Chem. B, 110 (41), 20649 -20654, 2006.
Zauner G, Lonardi E, Bubacco L, Aartsma TJ, Canters GW, Tepper AWJW
‘Tryptophan-to-dye fluorescence energy transfer applied to oxygen sensing by using type-3 copper proteins.’ Chemistry 2007; 13:7085-90.
Zauner G, Strianese M, Bubacco L, Aartsma TJ, Tepper AWJW, Canters GW
‘ Type-3 copper proteins as biocompatible and reusable oxygen sensors.’ Inorganica Chimica Acta, 2008, 361,1116-1121.
Sofya Kuznetsova, Gerhild Zauner, Thijs Aartsma, Hans Engelkamp, Nikos Hatzakis, Alan E. Rowan, Roeland J.M. Nolte, Jan C. Maan and Gerard W.
Canters
‘The enzyme mechanism of nitrite reductase studied at single-molecule level.’ PNAS, 2008, vol. 105, no. 9, 3250-3255.
Maria Strianese, Gerhild Zauner, Luigi Bubacco, Armand W.J.W. Tepper, Thijs J. Aartsma, Gerard W. Canters and Leandro C. Tabares.
‘A protein-based oxygen biosensor for high-throughput monitoring of cell growth and cell viability.’
Submitted.
Zauner G. et al. ‘Sensitive fluorescence method to detect substrate binding to P450cam.’
(manuscript in preparation).
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Curriculum Vitae
Gerhild Zauner was born on the 8th of September 1979 in Leoben/Austria. She received her ‘Matura’ at the Neues Gymnasium Leoben in Austria in 1998, whereafter she started her studies of Pharmaceutical Sciences at the Karl Franzens University of Graz/Austria. There she earned her MSc degree in June 2004. The research towards her Master thesis she performed at the University of East Anglia (UEA) in Norwich/UK under the supervision of Dr. Julea Butt. The project concerned the development of a novel electrochemical based assay for DNA ligases.
In July 2004 she joined the Metalloprotein Group (now Protein Chemistry) at the University of Leiden/The Netherlands under the supervision of Prof.G.W.Canters and Prof.T.J.Aartsma as a PhD student. Her project has been funded by the ‘Stichting voor Fundamenteel Onderzoek der Materie’ (FOM). The work conducted mainly focused on the development of a fluorescence based technique for redox and electron transfer proteins and enzymes. Several collaborations with other research groups could be established during her PhD period, including that of Dr. J.J.Davis at the University of Oxford/UK, of Dr. Peter Christianen, Prof. R.Nolte and Prof. A.Rowan at the University of Nijmegen/The Netherlands, of Prof. L.Bubacco at the University of Padua/Italy, of Prof. A.M.Deelder at the Leiden University Medical Center (LUMC)/The Netherlands and the group of Prof.Mazumdar at the Tata Institute in Mumbai/India.
Parts of the research were presented at several international conferences as the EuroBiC in Aveiro/Portugal in 2006, the Bioscope Symposium in 2007 in Copenhagen/Denmark, the ICBiC in Vienna/Austria (2007), the EuroBiC in Wroclaw/Poland in 2008.
Appendices
She also presented her work at the annual meetings of the Dutch Biophysical, the Chemical and the Protein-Chemistry Society as well as the Royal Netherlands Academy of Arts and Sciences (KNAW). As the groups of Prof. Canters and Prof.
Aartsma are part of the ‘EdRox’ research consortium (a Marie Curie Research Training Network consisting of 7 academic institutions and 2 industry partners), she also presented her work at meetings in Newcastle, Leiden and Torino.
Her contribution at the EuroBiC in Aveiro in 2006 was awarded the prize for best oral presentation and in 2007 she won a poster prize at the Chemistry meeting in Lunteren/The Netherlands.
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Acknowledgements
First of all I would like to thank all the collaborators and collegues that cooperated to the work presented in this thesis here.
I start with the people from the Randboud University in Nijmegen, where I had a great time during my PhD working on their single molecule set-up: Dr. Nikos Hatzakis, Dr. Hans Engelkamp, Viktor Claessen, Dr. Peter Christianen, Prof. Roland Nolte and Prof. Alan Rowan. Thank you for giving me the opportunity to get introduced to the world of single molecule fluorescence!
Then, I am also very grateful to Dr. Oleg A. Mayboroda and Prof. Andre M. Deelder at the Leiden University Medical Center (LUMC) for the analysis of our dye labelled protein samples.
Marc Stampraad and Prof. Simon de Vries from the Delft Technical University for their help with measuring the NiR activity by NO formation.
A special thanks to Prof. Luigi Bubacco at the University of Padua (Italy) for providing us with all the hemocyanin samples used in this study.
I am also greatful to Prof. Shyamalava Mazumdar at the Tata Institute in Mumbai (India) and his group to give me the opportunity to work in his lab. It was a wonderful experience!
Thank you also to people in the Biophysics group in Leiden for measuring with me and also for all the coffees we had together.
Appendices
People from our group in Leiden, some of them already moved on working in other places...
Dr. Sonya Kuznetsova, “my PostDoc”, she took care of me when I joined the project.
She helped me getting started and gave me constant scientific and moral support!
Thank you so much.
Dr. Ralf Schmauder, who introduced me to the world of ‘how to label a protein’.
Dr. Hein Wijma I would like to thank for sharing his knowledge about nitrite reductase with us.
Dr. Mariella Strianese, it was great to work with you in the lab. Thank you for your help and friendship.
Dr. Leandro Tabares, Dr. Marsia Gustiananda and Alessio Andreoni for daily support and in the lab.
Emanuela Lonardi for all the hours we spent together and your tyrosinase samples.
Hanna Lindfors is thanked for a quality Dutch translation of the summary.
Virginie, Hanna, Rinske, Monica for everything (you know those special moments I am referring to).
And the one person that is the major driving force in our lab, Dr. Armand Tepper. I believe he is one of most inspiring persons in science I know. Armand without you this would not have been possible.
All the people from the protein chemistry group in Leiden I would like to thank for those wonderful years in the lab. I learned so much and enjoyed it at the same time,
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because all of you have been helping me with scientific problems or you have been great friends. Thank you so much, it has been a pleasure working with you.
I would also like to acknowledge two friends I met here during my stay in the Netherlands: Barbara and Madeleine. Thank you for listening to all the ‘protein stories’ during going on a ride with the horses…
Zum Schluß, die Menschen die mir persönlich am Nähesten stehen:
Meinen Eltern und meiner Schwester Heidrun danke ich fürs Zuhören und die Unterstützung.
Bernhard, Du hast mich motiviert dieses Projekt zu beginnen und es zu beenden.
Danke für Deinen Glauben in mich und meine Fähigkeiten!
