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Structural and Functional Analysis of the Reaction Center Complexes from the Photosynthetic Green Sulfur Bacteria Guannan He Washington University in St

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Structural and Functional Analysis of the Reaction Center Complexes from the Photosynthetic Green Sulfur Bacteria Guannan He Washington University in St Washington University in St. Louis Washington University Open Scholarship Arts & Sciences Electronic Theses and Dissertations Arts & Sciences Summer 8-15-2015 Structural and Functional Analysis of the Reaction Center Complexes from the Photosynthetic Green Sulfur Bacteria Guannan He Washington University in St. Louis Follow this and additional works at: https://openscholarship.wustl.edu/art_sci_etds Part of the Chemistry Commons Recommended Citation He, Guannan, "Structural and Functional Analysis of the Reaction Center Complexes from the Photosynthetic Green Sulfur Bacteria" (2015). Arts & Sciences Electronic Theses and Dissertations. 554. https://openscholarship.wustl.edu/art_sci_etds/554 This Dissertation is brought to you for free and open access by the Arts & Sciences at Washington University Open Scholarship. It has been accepted for inclusion in Arts & Sciences Electronic Theses and Dissertations by an authorized administrator of Washington University Open Scholarship. For more information, please contact [email protected]. WASHINGTON UNIVERSITY IN ST. LOUIS Department of Chemistry Dissertation Examination Committee: Robert E. Blankenship, Chair Michael L. Gross Dewey Holten Joseph Jez Liviu Mirica Timothy Wencewicz Structural and Functional Analysis of the Reaction Center Complexes from the Photosynthetic Green Sulfur Bacteria by Guannan He A dissertation presented to the Graduate School of Arts & Sciences of Washington University in partial fulfillment of the requirements for the degree of Doctor of Philosophy August 2015 St. Louis, Missouri © 2015, Guannan He Table of Contents List of Figures ................................................................................................................................ iv List of Tables ................................................................................................................................ vii Acknowledgments........................................................................................................................ viii Abstract of the dissertation ............................................................................................................. x Chapter 1: Introduction to the Structure and Energy Transfer Mechanism of the Reaction Center Complexes from the Green Sulfur Bacteria .................................................................................... 1 1.1 Antenna complexes in the green sulfur bacteria .............................................................. 1 1.2 The reaction center complexes from green sulfur bacteria .............................................. 6 1.3 Energy and electron transfer mechanisms ...................................................................... 10 1.4 Thesis statement ............................................................................................................. 14 References ..................................................................................................................................... 15 Chapter 2: Structural Analysis of the Homodimeric Reaction Center Complex from the Photosynthetic Green Sulfur Bacterium Chlorobaculum tepidum ............................................... 20 2.1 Introduction .................................................................................................................... 21 2.2 Materials and methods ................................................................................................... 23 2.2.1 FMO-RCC complex purification ........................................................................................ 23 2.2.2 Chemically cross-linked FMO-RCC complex .................................................................... 24 2.2.3 LC-MS/MS and Data Analysis ........................................................................................... 25 2.3 Results and discussion .................................................................................................... 25 2.3.1 Purification and identification of FMO-RCC complex ....................................................... 25 2.3.2 Cross-linking by BS3, DSS and DTSSP .............................................................................. 26 2.3.3 Structural analysis by chemical cross-linking and LC-MS/MS .......................................... 29 2.4 Conclusions .................................................................................................................... 44 References ..................................................................................................................................... 46 Chapter 3: Dynamics of Energy and Electron Transfer in the FMO-Reaction Center Core Complex from the Phototrophic Green Sulfur Bacterium Chlorobaculum tepidum .................... 49 3.1 Introduction .................................................................................................................... 50 3.2 Materials and methods ................................................................................................... 53 3.2.1 Protein purification and basic spectroscopic characterization ............................................ 53 3.2.2 Time-resolved absorption and fluorescence spectroscopies ............................................... 54 ii 3.2.2 Spectroscopic datasets correction and analysis ................................................................... 55 3.2.3 LC-MS/MS and Data Analysis ........................................................................................... 55 3.3 Results and discussion .................................................................................................... 56 3.3.1 Purification and identification of the FMO-RCC and RCC complexes .............................. 56 3.3.2 Steady-state and time-resolved fluorescence of FMO-RCC ............................................... 60 3.3.3 Transient Absorption Spectroscopy of the RCC complex .................................................. 66 3.3.4 Transient Absorption Spectroscopy of the FMO-RCC complex ........................................ 72 3.4 Conclusions .................................................................................................................... 81 References ..................................................................................................................................... 83 Chapter 4: Dynamics of Energy and Electron Transfer in the Reaction Center Core Complex from the Green Sulfur Bacterium Prosthecochloris aestuarii ...................................................... 87 4.1 Introduction .................................................................................................................... 87 4.2 Materials and methods ................................................................................................... 90 4.2.1 Protein purification and basic spectroscopic characterization ............................................ 90 4.2.2 LC-MS/MS and Data Analysis ........................................................................................... 91 4.2.3 Time-resolved absorption spectroscopy .............................................................................. 91 4.2.4 Spectroscopic dataset correction and analysis .................................................................... 92 4.3 Results and discussion .................................................................................................... 92 4.3.1 Purification and identification of the PscA-PscB complexes .............................................. 92 4.3.2 Transient absorption spectroscopy ...................................................................................... 95 4.4 Conclusion .................................................................................................................... 100 References ................................................................................................................................... 101 Chapter 5: Conclusions and Future Directions ........................................................................... 104 iii List of Figures Figure 1.1: Structures of chlorophyll a and bacteriachlorophyll a …………………………….…2 Figure 1.2: Structure of phycocyanobilin……………………………….. ………………….……3 Figure 1.3: Structure of β–carotene …………………………………………………………....…3 Figure 1.4: Schematic models of chlorosomes…………………………….. …………………….5 Figure 1.5: Orientation of the trimetric FMO protein with RCC……………………………....…6 Figure 1.6: STEM dark field image of C. tepidum RC complexes…………………...…………. .8 Figure 1.7: The 3D reconstruction of the RC complex……………………………………………9 Figure 1.8: Electron microscopy of PscA-PscC complexes…………………...………………….9 Figure 1.9: Crystal structure of PscC soluble domain………………………………………...…10 Figure 1.10: Electron transfer in the P840-reaction center…………………….. ……………….12 Figure 1.11: Two models for energy transfer in the P840-reaction center………………………13 Figure 2.1: A structural model of the FMO-RCC complex………….. ………………………....22 Figure 2.2: Absorption spectrum and SDS-PAGE of the FMO-RCC complex…………...….…26 Figure 2.3: SDS-PAGE and BN gel of cross-linked FMO-RCC complex………………………27 Figure 2.4: Chemically cross-linked FMO-RCC identified by SDS-PAGE and LC-MS/MS…...28 Figure 2.5: Mono-linked lysines of soluble domain of PscC……………………………..……...30 Figure 2.6: Intra-linked lysines of FMO…………………………….. …………………...……..31 Figure 2.7: Crosslinks of FMO-RCC and membrane topological model of PscA ……………...33 Figure 2.8: MS/MS spectra of the
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