Research Collection Doctoral Thesis Small molecule diselenides as probes of oxidative protein folding Author(s): Beld, Joris Publication Date: 2009 Permanent Link: https://doi.org/10.3929/ethz-a-005950993 Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library Diss. ETH No. 18510 Small molecule diselenides as probes of oxidative protein folding. A dissertation submitted to ETH Zürich For the degree of Doctor of Sciences Presented by Joris Beld MSc. University of Twente, Enschede Born February 15, 1978 Citizen of the Netherlands Accepted on the recommendation of Prof. Dr. Donald Hilvert, examiner Prof. Dr. Bernhard Jaun, co‐examiner Zürich 2009 How to work better. Do one thing at a time Know the problem Learn to listen Learn to ask questions Distinguish sense from nonsense Accept change as inevitable Admit mistakes Say it simple Be calm Smile Peter Fischli and David Weiss, 1991 To my family. Publications Parts of this thesis have been published. Beld, J., Woycechowsky, K.J., and Hilvert, D. Small molecule diselenides catalyze oxidative protein folding in vivo, submitted (2009) Beld, J., Woycechowsky, K.J., and Hilvert, D. Diselenide resins for oxidative protein folding, patent application EP09013216 (2009) Beld, J., Woycechowsky, K. J., and Hilvert, D. Catalysis of oxidative protein folding by small‐ molecule diselenides, Biochemistry 47, 6985‐6987 (2008) Beld, J., Woycechowsky, K.J., and Hilvert, D. Selenocysteine as a probe of oxidative protein folding, Oxidative folding of Proteins and Peptides, edited by J. Buchner and L. Moroder, Royal Society of Chemistry, 253‐273 (2008) Beld, J., Woycechowsky, K. J., and Hilvert, D. Selenoglutathione: Efficient oxidative protein folding by a diselenide, Biochemistry 46, 5382‐5390 (2007) Published results not part of this thesis. Coquiere, D., Bos, J., Beld, J. and Roelfes, G. Enantioselective artificial metalloenzymes based on a bPP scaffold, Angewandte Chemie International Edition, 121, 6894‐6897 (2009) Steinmann, D., Nauser, T., Beld, J., Tanner, M., Günther, D., Bounds, P.L., Koppenol, W.H. Kinetics of tyrosyl radical reduction by selenocysteine, Biochemistry 47, 9602‐9607 (2008) iv Acknowledgements Acknowledgements I would like to thank my PhD advisor Professor Donald Hilvert for giving me the opportunity to pursue my doctoral studies in his laboratory. Don, I have learned a lot from you. I thank Professor Bernhard Jaun for being my co‐examiner. I am very grateful to Professor Kenneth J. Woycechowsky. Without his “Friday‐ afternoon” idea to synthesize selenoglutathione and do oxidative protein folding, this thesis would not have been possible. I would like to thank my students Gisela Fontaine (selenazolidines) and Sandro Tonazzi (telluroglutathione and selenotrypanothione) for pleasant times in and out of the lab. I am grateful to Professor David Reinhoudt without whom I would never have gotten the opportunity to do my PhD studies in Don’s laboratory. I am very grateful to Dr. Mercedes Crego ‐ Calama and Professor Peter Timmerman for being my supervisors during my undergraduate studies, as well as writing numerous letters of recommendations when I was applying for post doctoral positions. I would like to thank Professor Gerard Roelfes for a fruitfull collaboration. Before I came to Zürich, he warned me not to take the BPTI project. I should have listened. Also, I would like to thank Professor Wim Koppenol for a short but productive collaboration. Without proteins, E. coli strains, S. cerevisae strains and plasmids from Roche, Roche‐ Diagnostics, Carlsberg (Anders Brandt), Bayer, Professor Rudi Glockshuber, Professor Chris Kaiser and Professor Luise Krauth‐Siegel, this project would have been impossible. Without assistance of Peter Kast, René Fischer, Regula Grüninger, the “Schalter”, the mass‐spectrometry service and the NMR service, doing research would be very difficult here on the Hönggerberg. Although we often do not realize and appreciate, our secretaries Elisabetha Halter, Nathalie Rudatis, Antonella Toth and Anita Luessi‐Meier keep the group running. Thanks! Many thanks go to my F322 labmates: Giulio Casi, Mike DeClue, Jörg Serafimov, Andreas Aemissegger, Thorsten Stafforst and Dennis Gillingham. Also, of course to all the students that passed through our lab. Selenium is an important element for a few people in the Hilvert group. Although our projects are very different we all work with the same smelly compound. Looking back, more synergy would have been beneficial but I would like to thank the little selenium subgroup: Giulio Casi, Maryam Edalat‐Hansson, Caroline Aldag, Alisa Davis and Norman Metanis. v Acknowledgements I would like to thank our regular Hilvert group climbing crew: Maren Butz, Dennis Gillingham, Irina Coserea, Thorsten Stafforst, Bigna Wörsdörfer, Andreas Kleeb and Irene Kleeb. Running is my therapeutic hour on the couch with a shrink, thanks to my frequent running partners Rebecca Blomberg, Amanda Stouffer, Christian Jäckel and Bigna Wörsdörfer. Although time‐consuming and challenging, teaching the lab course OCP1 was a wonderful experience. I would like to thank all my students: Isabelle, Alex, Xenia, Danielle, Felix, Adrian, Lorenz, Müge, Michael, Gabriel and Michael, Stephanie, Phillip, Sabina, Christine, Cristina, Mirjam, Katharina, Susanne and Miriam, Yanic, Sebastian, Sandra, Liliana, Christine, Mario, Anky, Nicole, Josiane. I would like to thank Lydia Bänziger and Rebecca Herbst for countless rejuvenating coffee breaks. Rebecca, I wish we would have parted on better terms. Spending so much time in the lab, the Hilvert family (Don, Moni, Alex and Beto) becomes part of your life. Apart from Don, I would like to thank Moni for help with my applications among other things. Beto, although you can be a bit much, you always manage to cheer us up. In 2008, we (Don, Caroline, Giulio and me) got invited to a conference in Osaka, Japan, by Professor Kikuchi. I would like to thank Don and Prof. Kikuchi for their generosity and this unique opportunity to visit Japan. You showed me the interesting restaurants in town and amazingly we have kept contact ever since. Thanks Yael. Anaida and later Yanela introduced me to Cuban food and salsa. Thanks for everything. Caroline, we had our good and bad times. I will always remember the Greek party after the European Championship soccer in 2004. For that any many other things I would like to thank Katherina Vamvaca. I would like to thank one of my F322 lab mates in particular: Giulio Casi. Thanks a lot for all the help with peptide synthesis and HPLCs. Also, thanks for introducing me to the Italian crowd. The dinners at your place and later at yours and Stefania’s are always memorable. I wish you both all the best. I will remember Andreas Kleeb running down a mountain while yodeling. Many thanks for organizing skiweekends, hiking trips and schmutzliparty (games). Also many thanks go out to Roger Müller and Bigna Wörsdörfer for organizing past skiweekends. Besides running, sushi is my shared passion with Rebecca Blomberg. Thanks for organizing many sushi dinners. vi Acknowledgements My three Luxemburgish musketeers, Josy, Françoise and Georges, showed me the way back into the climbing hall. I am very grateful for all the Sundays we went climbing and had dinner. I’m going to miss you guys. PhD students are solely responsible for computer administration within the laboratory of organic chemistry. Far from ideal but impossible without the expertise of Alexander Kienhöfer, Andreas Kleeb and Andreas Aemissegger. Deepblue and deepfreezer are the servers in the Hilvert group and I thank Andreas Aemissegger for countless questions regarding server and system administration. The analytical ultracentrifuge became my group job and without the help of Richard Thomas and Borries Demeler I would not have succeeded in understanding and using this technique. Once a year the PhD students of the LOC invite a speaker. The organizing Behringer Simon lecture committee consist of members from each group and a good platform for new PhD student initiated activities. Despite motivated members, we once more learned how viscous academic politics is. Our one o’clock lunch group was joined for a long time by Christine Crane and Martina Cacciarini from the Diederich group. Thanks! One of my friends from the Reinhoudt lab, Marta Reinoso, came to Zürich for postdoctoral studies. Thanks a lot for dragging me out of the lab to have dinner and drinks. Bigna Wörsdörfer, we have experienced a lot together and I think our friendship has grown over the years. I could not have imagined a better friend. I would like to thank the whole Hilvert lab for a very pleasant time. The group changes again and again in consistency but the atmosphere stays more‐or‐less the same. In analogy to ‘a dog is like its owner’, I believe that ‘a PhD student becomes like its Professor’. It is difficult to maintain contact with my friends in the Netherlands. However, throughout the years Rodrigo Helder, Lisette Smit, Roy van Putten, Arno Stassen and Jurriaan & Ikina Boon have been visiting Zürich and kept asking when I was about to finish. Last but not least, my family. I think my grandmother ‘Oma Lobith’ would have been very proud if she could have seen me finishing my PhD. I hope I can explain to my other grandmother, ‘Oma Tukkie’, what I have actually done here in Zürich. In any case, thanks for everything. Many many thanks go out to my parents. You kept believing in me, although my papers are hard to understand and read. I owe you so much. Finally, my brother Rogier. You vii Acknowledgements kept me sane by going on holidays every year. We are not so different as it may seem and I hope we can have many holidays together in the future. Thanks for everything. viii Table of contents Table of contents Summary ..................................................................................................................................