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Resonance Raman Spectroscopy of Redox-Active Metal Clusters in Proteins and Model Compounds

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Resonance Raman Spectroscopy of Redox-Active Metal Clusters in Proteins and Model Compounds Resonance Raman Spectroscopy of Redox-Active Metal Clusters in Proteins and Model Compounds Jonathan D. Cohen B.A., University of California at Santa Barbara, 1989 A dissertation submitted to the faculty of the Oregon Graduate Institute of Science and Technology in partial fblfillment of the requirements for the degree Doctor of Philosophy in Chemistry February, 1997 The dissertation "Resonance Raman Spectroscopy of Redox-Active Metal Clusters as Models for Metalloproteins" by Jonathan D. Cohen has been examined and approved by the following Examination Committee: Thomas M. Loehr Professor and Dissertation Advisor Joann Sanders-Loehr V \ Professor and Dissertation Advisor binian J. Blackbum Pkfedsor-1 and Department Head James K. Hurst fessor and External Examiner n State University, Pullman, WA Acknowledgments First and foremost, I want to express my deepest thanks to Profs. Thomas Loehr and Joann-Sanders Loehr for taking a chance on an unknown chemist and giving me the opportunity to study under their expert tutelage. I also wish to thank my other Ph.D. committee members, Profs. Ninian Blackburn and Jim Hurst, who have served as expert teachers both in the classroom and in research seminars, and for taking the time to carefblly review my dissertation. I am also gratefbl to Prof. V. Renganathan, Dr. Wenjun Bao, and Sai Subramaniam for their purification of the cellobiose dehydrogenase samples; Prof. Mike Fryzuk and Dr. Murugesapillai Mylvaganam for providing the zirconium dinitrogen compounds; Prof Karl Hagen and Sonha Payne for providing the mixed- valence diiron compounds; and Prof. Liz Theil, Dana Danger, and Dr. John Fetter for providing the femtin samples. I also want to express my thanks to Dr. Jie Sun for the countless discussions and insights he provided. I also wish to thank, in no particular order, Prof. Mike Khalow, Prof. Shankar Rananavare, Mary Vatne, Dr. Kevin Maloney, Ciro DiMeglio, Dr. Pierre Mbeme-Loccoz, Dr. Nobumasa Nakamura, Julie Wilson, and Steve Dodge for helping me in ways they may not even know. Finally I wish to dedicate this thesis to Laura Cohen, my wife and best fiiend for tolerating my thoughtless, irrational and sometimes juvenile delinquent behavior during my Ph.D. studies; my parents for providing me with love, a home, and an education; and to the Flat Earth Society in the hopes that they may one day learn that two half-truths do not make a whole truth. Table of Contents Page ... Acknowledgments .......................................... m List of Tables ............................................. vii List of Figures ............................................ vii Abstract ................................................ xi Chapter 1: Metal Clusters in Proteins and Model Compounds Multinuclear Metal Clusters in Enzymes. ...................... 1 Characterization of Metal Clusters by Spectroscopy ............... 3 Model Compounds as Learning Tools ........................ 4 Instructive Examples Nitrogenase .................................... 4 Ribonucleotide Reductase ........................... 8 Flavocytochrome bz ............................... 12 Ferritin ....................................... 15 Focus of Present Research ............................... 16 References .......................................... 17 Chapter 2: N2 bound to Zr2 Clusters as Models of Nitrogenase. Distinguishing the p-ql:qland p-q2 .q 2 states by Resonance Raman Spectroscopy Abstract ........................................... 24 Introduction ......................................... 25 Experimental ........................................ 30 Results and Discussion .................................. 32 Conclusion .......................................... 44 Addendum .......................................... 46 Acknowledgments ..................................... 48 References and Notes ................................... 49 Chapter 3 : A Mixed-Valence Dinuclear Iron Compound with Unusual Asymmetry . RR Evidence for a Trapped-Valence State Abstract ........................................... 54 Introduction ......................................... 55 Experimental ........................................ 60 Results and Discussion .................................. 61 Conclusions ......................................... 75 References and Notes ................................... 83 Chapter 4: Resonance Raman Studies of Cellobiose Dehydrogenase from Phanaerochaete Chrysosporium Abstract ........................................... 88 Introduction ......................................... 89 Materials and Methods .................................. 91 Results and Discussion .................................. 92 Acknowledgments ..................................... 104 References .......................................... 105 Chapter 5: Rapid Fe Uptake by Wild-Type and Mutant Frog Ferritin . Resonance Raman Detection of [Fe-Tyr] Intermediates . Abstract ........................................... 110 Introduction ......................................... 111 Experimental ........................................ 118 Results ........................................ 121 Discussion .......................................... 130 References and Notes ................................... 139 Biographical Note .......................................... 143 List of Tables Page Resonance Raman Frequencies and Proposed Assignments for the Dinuclear Zr2N2Complexes 1and 2 in the Solid and in Solution ....... 3 5 Electronic Absorption Maxima of Selected Diiron Proteins and Model Compounds ......................................... Frequencies and Intensities of Fe-0-Fe Vibrational Modes for Selected Diiron Proteins and Model Compounds ....................... Intervalence Transfer Properties of Selected Mixed-Valence Diiron Compounds .......*................................. Resonance Raman Frequencies and Assignments of of Flavin Modes of CDEX,Flavin Domain of CDH, Flavocyt b2 and Observed Frequency Ranges of Flavins and Flavoproteins ......................... Resonance Raman Frequencies And Assignments of the Heme Modes of CDH, Heme Domain of CDH, Flavocyt b2, and F~'PP(I~)~.......... Amino Acid Sequences of Several Vertebrate Ferritins ............. Frequencies of Specific Fe-Tyrosinate Vibrations in the RR Spectra of Femtins and Other Iron-Tyrosinate Proteins .................... Decay of the [~e~'-~yr]Intermediate for WT and Mutant Femtins ..... Correlation of Tyrosine Composition in Frog Fenitin with Formation of the [Fe-Tyr] Intermediate ................................ List of Figures Page Schematic of the P-cluster of the Nitrogenase MoFe-Protein ......... 6 Schematic of the FeMo-Cofactor of the Nitrogenase MoFe-Protein ..... 7 Schematic of the Iron Binding Site of Ribonucleotide Reductase ....... 10 Proposed Reaction Scheme of Ribonucleotide Reductase and Methane Monooxygenase ...................................... 11 X-ray crystal structure of flavocytochrome b2 showing the two domains and the heme and flavin cofactors. adapted from reference 62 ......... 13 Schematic ofthe b-Type Heme and FAD Cofactors of CDH ......... 14 Molecular Structure of Complex 1 .......................... 27 Molecular Structure of Complex 2 .......................... 28 Resonance Raman Spectra of Complex 1 in the Solid State .......... 34 N-N Stretching Frequencies of Selected Dinitrogen Compounds of Different Bond Orders as a Power Function of their N-N Bond Lengths . 36 Resonance Raman Spectra of Complex 1 in Toluene Solution ........ 37 Resonance Raman Spectra of Complex 2 in the Solid State .......... 39 Resonance Raman Spectra of Complex 2 in THF Solution ........... 41 Resonance Raman Spectra of Derivatives of Complex 2 ............ 43 Crystal Structures of Compounds 1 and 2 ..................... 56 Formation of Compounds 2 and 3 by Sequential Addition of Oxidants ... 57 Vector Diagram of Fe-0-Fe Vibrational Modes .................. 59 Resonance Rarnan Spectra of Compound 1 (CF3SOd salt. crystals) ..... 62 Electronic Spectra of Compounds 2 and 3 @Phi salts) in CHzClz and the Resonance Enhancement Profile of Compound 2 ................. Resonance Raman Spectra of Compound 2 (CF3S0i salt. powder) ..... Resonance Raman Spectra of Compound 2 (BPh; salt. powder) ....... Resonance Raman Spectra of Compound 2 (BPk' salt. crystals) ....... Resonance Raman Spectra of Compound 2 (CFsSO< salt) in CH3CN Solution ........................................... Resonance Raman Spectra of Compound 3 (CF3SO; salt) in CH3CN Solution ........................................... Potential Energy Diagram of Asymmetric Class I and I1 Mixed- Valence Complexes .......................................... Proposed mechanism for the oxidation of 1 to 2 by Oz via an outer-sphere mechanism .......................................... Electronic Absorption Spectra of isolated CDH Domains ........... Resonance Raman Spectra of CDH Using 442-nm Excitation ......... Resonance Raman Spectra of CDH Using 4 13-nm Excitation ......... Resonance Raman Spectra of CDH Heme Domain ................ Resonance Raman Spectra of CDH Flavin Domain ................ Schematic of 24-Subunit Structure of FTN ..................... Ribbon Diagram of Human FTN-H .......................... Plot of W-Vis Absorbance Changes at 550 and 420 nm During Fmoidation ........................................ Resonance Raman Spectra of Pre-Mixed Samples of Wild-Type and MutantFTN-H ....................................... Kinetic Plots of [Fe-Tyr] and A550 Decay for Wild-Type and Mutant FTN.H ...........................................
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