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Characterization of Cpi and Cpii [Fefe]-Hydrogenases Reveals

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Characterization of Cpi and Cpii [Fefe]-Hydrogenases Reveals CHARACTERIZATION OF CPI AND CPII [FEFE]-HYDROGENASES REVEALS PROPERTIES CONTRIBUTING TO CATALYTIC BIAS by Jacob Hansen Artz A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biochemistry MONTANA STATE UNIVERSITY Bozeman, Montana November 2016 ©COPYRIGHT by Jacob, Hansen, Artz 2016 All Rights Reserved ii ACKNOWLEDGEMENTS Many people have contributed to this thesis in a significant manner and are deserving of acknowledgements. First, Dr. John Peters for his ongoing mentorship and scientific insights, as well as the rest of my committee, Dr. Brian Bothner, Dr. Joan Broderick, Dr. Jen DuBois, and Dr. Paul King, for their role in this developing science. I would also like to thank past lab members, in particular Dr. Swanson for his careful instruction in anaerobic protein expression. The entire BETCy team has greatly contributed to my scientific understanding, particularly Dr. David Mulder, and Mike Ratzloff of the NREL group, who have graciously hosted numerous experiments. Special thanks to Garret Williams and Dr. Anne K. Jones for collecting and interpreting electrochemistry data, and Saroj Poudel and Dr. Eric Boyd for help with bioinformatics. Many lab members have contributed greatly, including Dr. Zadvornyy, Dr. Mus, and the future Drs. Partovi, Prussia, Keable, Pence, and Alleman. This work has also been furthered by the excellent help of my undergraduate research assistant, Axl LeVan. Thanks also to Kim, Teresa, and Jane. My friends, family, and community have also played a critical role in the development of this these. Finally, I would like to thank the Air Force and DOE for ongoing funding. iii TABLE OF CONTENTS 1. INTRODUCTION ...........................................................................................................1 Introduction to Hydrogenases ..........................................................................................1 Taxonomic and Functional Diversity of Hyd ..................................................................5 Hydrogenase Mechanism ...............................................................................................11 [Fe-Fe]-hydrogenase Maturation ...................................................................................13 HydF ......................................................................................................................14 HydG ......................................................................................................................15 HydE ......................................................................................................................16 Future Directions ...........................................................................................................17 References ......................................................................................................................19 2. [FEFE]-HYDROGENASE OXYGEN INACTIVATION IS INITIATED BY THE MODIFICATION AND DEGRADATION OF THE H-CLUSTER 2FE SUBCLUSTER ..............................................................25 Contribution of Authors and Co-Authors ....................................................................25 Manuscript Information ...............................................................................................27 Abstract ........................................................................................................................28 Introduction ..................................................................................................................29 Methods........................................................................................................................32 Protein Preparation ................................................................................................32 Preparation of O2 Treated CrHydA1 .....................................................................34 FTIR Spectroscopy ................................................................................................36 Ultraviolet Visible Spectroscopy ...........................................................................36 Activity Assays ......................................................................................................37 Mass Spectrometry ................................................................................................37 Crystallization and Structure Determination .........................................................38 In vitro Activation of O2 Inactivated CrHydA1 .....................................................39 Results ..........................................................................................................................39 FTIR Analysis and Comparison of Hox, Hred-NaDT, Hred-H2, and Hox-CO ..............................................................................................39 FTIR Time Series of O2 Exposed Hox CrHydA1 ...................................................43 UVvis of O2 Exposed Hox CrHydA1 .....................................................................48 In vitro Activation of O2 Inactivated CrHydA1 ....................................................50 Discussion ....................................................................................................................52 Conclusion ...................................................................................................................55 Acknowledgements ......................................................................................................56 References ....................................................................................................................58 iv TABLE OF CONTENTS – CONTINUED 3. THE PHYSIOLOGICAL FUNCTIONS AND STRUCTURAL DETERMINANTS OF CATALYTIC BIAS IN THE [FEFE]-HYDROGENASES OF CLOSTRIDIUM PASTEURIANUM STRAIN W5 ..................................................................................62 Contribution of Authors and Co-Authors ....................................................................62 Manuscript Information ...............................................................................................64 Abstract ........................................................................................................................66 Background ............................................................................................................66 Results ....................................................................................................................66 Conclusions ............................................................................................................67 Background ..................................................................................................................68 Results and Discussion ................................................................................................70 Genome ..................................................................................................................70 Hydrogenases .........................................................................................................70 Structural Basis for Catalytic Bias in [FeFe]-hydrogenases ..................................78 Conclusions ..................................................................................................................81 Materials and methods .................................................................................................81 Growth Conditions .................................................................................................81 Genome Sequencing ..............................................................................................82 Quantitative RT-PCR (qRT-PCR) .........................................................................84 Bioinformatics .......................................................................................................85 References ....................................................................................................................90 4. DEVELOPMENT OF HYDROGENASE EXPRESSION AND EPR SPECTROSCOPIC DECONVOLUTION .................................................94 Introduction ..................................................................................................................94 Expression and Purification of CpI ..............................................................................96 Development of Plasmid System ...........................................................................96 Expression of CpI*EFG .........................................................................................97 Hydrogenase Activity Assays ................................................................................98 CpI Purification .....................................................................................................99 CpII Expression and Purification .........................................................................100 Spectral Deconvolution of CpI ..................................................................................102 Spectral Deconvolution Using EasySpin .............................................................104 Spectral Deconvolution of CpII .................................................................................108 Conclusions ................................................................................................................109 References ..................................................................................................................111
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