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Shining Light on the Photoactive Yellow Protein from Halorhodospira Halophila

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Shining Light on the Photoactive Yellow Protein from Halorhodospira Halophila UvA-DARE (Digital Academic Repository) Shining light on the photoactive yellow protein from halorhodospira halophila Hendriks, J.C. Publication date 2002 Document Version Final published version Link to publication Citation for published version (APA): Hendriks, J. C. (2002). Shining light on the photoactive yellow protein from halorhodospira halophila. General rights It is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons). Disclaimer/Complaints regulations If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible. UvA-DARE is a service provided by the library of the University of Amsterdam (https://dare.uva.nl) Download date:30 Sep 2021 Uitnodiging Shining light on light Shining Shining light on voor het bijwonen van de openbare verdediging van het proefschrift van the Photoactive Yellow Protein Yellow the Photoactive Johnny Hendriks op vrijdag the Photoactive Yellow Protein 6 December 2002 om 11:00 precies from Halorhodospira halophila in de Doelenzaal Over the past few years I have thoroughly enjoyed the van de Aula van de investigation of the Photoactive Yellow Protein from Halorhodospira halophila. Having shed light on important aspects Universiteit van of this protein by shining light on it, raising new and interesting Amsterdam questions in the process, it is with pain in my hart that I bid the Oude Lutherse Kerk study of this protein farewell (for the time being). The time has Singel 411 (hoek Spui) come to spread my wings and fly of to new adventures in science. from Halorhodospira halophila Halorhodospira from Amsterdam Meet you further on up the road. Johnny Receptie na afloop van de promotie Johnny Hendriks Huigenbos 621 1102 KA Amsterdam 020-6911715 Paranimfen Johnny Hendriks Henk Fitters [email protected] Levi Meulensteen [email protected] Johnny Hendriks Het Spui is goed bereikbaar met de tram (lijn 1,2,5 of 9) Shining light on the Photoactive Yellow Protein from Halorhodospira halophila ACADEMISCH PROEFSCHRIFT ter verkrijging van de graad van doctor aan de Universiteit van Amsterdam op gezag van de Rector Magnificus prof. mr. P.F. van der Heijden ten overstaan van een door het college voor promoties ingestelde commissie, in het openbaar te verdedigen in de Aula der Universiteit op vrijdag 6 december 2002, te 11:00 uur door Johnny Hendriks geboren te ‘s-Hertogenbosch Promotiecommissie Promotor : prof. dr. K.J. Hellingwerf Co-promotor : dr. W. Crielaard Overige leden : prof. dr. R. Boelens prof. dr. L. De Cola prof. dr. J.W. Verhoeven dr. I.H.M. van Stokkum dr. A. Xie Faculteit der Natuurwetenschappen, Wiskunde en Informatica The research presented in this thesis was carried out at the Laboratory for Microbiology, Swammerdam Institute for Life Sciences (SILS, formerly E.C. Slater Institute), BioCentrum, Faculty of Science, University of Amsterdam. The work was financially supported by the Netherlands Organization for Scientific Research (NWO), through the division for Chemical Sciences (CW). Printed by PrintPartners Ipskamp, Enschede Contents Preface iv List of publications v Chapter 1 Comprehensive Review 1 1 Introduction 2 1.1 The roots of the Photoactive Yellow Protein ...................................................2 1.2 Xanthopsins: the Photoactive Yellow Protein in other organisms...................3 1.3 Photoactive Yellow Protein: the prototypical PAS domain.............................3 2 Structure 5 2.1 Primary, secondary, and tertiary structure .......................................................5 2.2 Solution structure vs. crystal structure.............................................................9 2.3 The Xanthopsins compared ...........................................................................10 3 Photocycle: basics 13 3.1 How the photocycle is measured ...................................................................13 3.2 The basic photocycle .....................................................................................14 3.3 Photocycle nomenclature...............................................................................15 3.4 Experimental context .....................................................................................15 3.5 Mutants and hybrids ......................................................................................16 4 Photocycle: initial events 19 4.1 Fluorescence spectroscopy ............................................................................20 4.2 Absorption spectroscopy................................................................................22 4.3 Photoacoustic and photothermal methods......................................................23 4.4 Low temperature............................................................................................24 4.5 Structure.........................................................................................................26 4.6 Modeling........................................................................................................27 4.7 Summary........................................................................................................29 5 Photocycle: signaling state 30 5.1 The photocycle model....................................................................................30 5.2 Influence of experimental conditions.............................................................31 5.3 Structural relaxation of pR.............................................................................32 5.4 Protonation change upon pB’ formation........................................................33 5.5 Structural change upon pB formation ............................................................33 5.6 Recovery of the ground state .........................................................................37 5.7 Summary........................................................................................................38 6 Tuning 40 6.1 Ground state tuning........................................................................................40 6.2 Tuning in photocycle intermediates...............................................................41 7 Final remarks 43 i Contents Chapter 2 Structural change 45 1 Sample preparation 46 1.1 Overproduction..............................................................................................46 1.2 Purification of holoPYP.................................................................................47 1.3 Removal of the His-tag..................................................................................47 2 Proton uptake / release 48 2.1 Materials & Methods .....................................................................................49 2.2 Results ...........................................................................................................50 2.3 Discussion......................................................................................................54 2.4 Concluding remarks.......................................................................................56 3 Nile Red probe binding 57 3.1 Materials & Methods .....................................................................................57 3.2 Results ...........................................................................................................59 3.3 Discussion......................................................................................................64 4 Fourier Transform Infrared Spectroscopy 67 4.1 Materials & Methods .....................................................................................67 4.2 Results ...........................................................................................................68 4.3 Discussion......................................................................................................70 4.4 Concluding remarks.......................................................................................72 Chapter 3 Photocycle characterization 73 1 Laser-flash photolysis 74 1.1 The set-up ......................................................................................................74 1.2 CCD measurements .......................................................................................74 1.3 Photomultiplier measurements.......................................................................74 2 Branching reaction 75 2.1 Materials & Methods .....................................................................................75 2.2 Results ...........................................................................................................76 2.3 Discussion......................................................................................................79 2.4 Concluding remarks.......................................................................................80 3 Deuterium isotope effect 81 3.1 Materials & Methods .....................................................................................81
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