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Preparation and Characterization of Lignin The Pennsylvania State University The Graduate School College of Agricultural Sciences PREPARATION AND CHARACTERIZATION OF LIGNIN- PROTEIN COVALENT LINKAGES A Dissertation in Biorenewable Systems by Brett Galen Diehl ©2014 Brett Galen Diehl Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy May 2014 The dissertation of Brett Galen Diehl was reviewed and approved* by the following: Nicole R. Brown Associate Professor of Wood Chemistry Dissertation Adviser Chair of Committee John E. Carlson Professor of Molecular Genetics Jeffrey M. Catchmark Associate Professor of Agricultural and Biological Engineering Emmanuel Hatzakis Director of NMR facility John Ralph Special Member Professor of Biochemistry University of Wisconsin at Madison Paul Smith Head of Biorenewable Systems department *Signatures are on file in the Graduate School. ii Abstract Lignin is a natural aromatic polymer that is bio-synthesized in the cell walls of almost all land plants. Great strides have been made in understanding lignin’s biological origins and chemical and physical properties. However, many unanswered questions remain. For example, the extent to which lignin interacts with other cell wall components, such as proteins, is largely unknown. In order to help address this question, the preparation and characterization of lignin- protein covalent linkages is reported here for the first time. Chapter 1 provides a more detailed introduction, justification, and literature review. Chapter 2 focuses on the preparation of low molecular weight lignin-protein model compounds. The compounds were not prepared under biomimetic conditions. Instead, the primary focus of this study was on the characterization of the model compounds, leading to the identification of diagnostic lignin-protein NMR chemical shifts. Chapter 3 describes the characterization of lignin-protein linkages prepared under biomimetic conditions of lignin DHP formation. NMR showed that cysteine and tyrosine containing peptides covalently crosslink with lignin, while other amino acids do not. IR and EDS were useful for showing the general incorporation of protein into the lignin, but were incapable of distinguishing covalent and non-covalent interactions. Chapter 4 describes the interaction between lignin and gelatin protein. It was found, using EDS and IR, that gelatin was incorporated into lignin DHP. However, a lack of diagnostic NMR signatures revealed that the crosslinking was likely dominated by non-covalent interactions such as physical entanglement. This seems likely, as gelatin is lacking in both cysteine and tyrosine residues, which were shown to be the only reactive amino acids towards lignin. Chapter 5 details attempts at identifying lignin-protein linkages in wild type Arabidopsis. Arabidopsis was grown to maturity, then lignin was extracted from cell wall material using acidified dioxane. Elemental analysis was used to show that the lignin was contaminated with about 3.75% protein; however, NMR was not able to identify lignin-protein covalent linkages. Chapter 6 details some future experiments that could be used to explore lignin-protein linkages, and it is hoped that this work will pave the way for such studies. iii TABLE OF CONTENTS List of Figures…………………………………………………………………………………....vii List of Tables……………………………………………………………………………………viii Abbreviations……………………………………………………………………………………..ix Acknowledgements…………………………………………………………………………..........x Chapter 1. Introduction ...………………………………………………………………………... 1 1.1. Problem statement ...………………………………………………………………… 1 1.2. Literature review ……………………………………………………………………. 1 1.2.1. Lignin biosynthesis ……………………………………………………….. 1 1.2.2. Plant cell wall structural proteins …………………………………………. 6 1.2.3. Evidence for lignin-protein linkages …………………………………….. 10 1.3. Methods for investigating lignin-protein linkages ………………………………… 12 1.3.1. Preparation of lignin-protein compounds ……………………………….. 12 1.3.1. Characterization of lignin-protein compounds ………………………….. 16 1.4. References …………………………………………………………………………. 21 Chapter 2. Towards lignin-protein crosslinking: Amino acid adducts of a lignin model quinone methide …………………………………………………………………………………………. 25 2.1. Abstract ……………………………………………………………………………. 25 2.2. Introduction ………………………………………………………………………... 25 2.3. Experimental ………………………………………………………………………. 28 2.3.1. Materials ………………………………………………………………… 28 2.3.2. Model compound preparations ………………………………………….. 28 2.3.3. Model compound properties …………………………………………….. 29 2.3.4. Nuclear magnetic resonance spectroscopy ……………………………… 42 2.3.5. Mass spectrometry ………………………………………………………. 42 2.3.6. Computational methods …………………………………………………. 43 2.4. Results and discussion …………………………………………………………….. 44 2.4.1. Preparation of quinone methide-amino acid adducts ……………………. 44 2.4.2. Solution-state NMR of compounds 3-9 and density functional theory calculations for compounds 10 and 11 …………………………………. 46 2.4.3. Adduct isomer determination ……………………………………………. 50 2.5. Conclusions ………………………………………………………………………... 50 2.6. Acknowledgements ………………………………………………………………... 51 2.7. References …………………………………………………………………………. 51 Chapter 3. Lignin crosslinks with peptides under biomimetic conditions ……………………... 55 3.1. Abstract ……………………………………………………………………………. 55 3.2. Introduction ………………………………………………………………………... 55 3.3. Experimental ………………………………………………………………………. 57 iv 3.3.1. Materials ………………………………………………………………… 57 3.3.2. Synthesis of lignin DHP and lignin-peptide adducts ……………………. 57 3.3.3. Scanning electron microscopy and energy dispersive X-ray spectroscopy 57 3.3.4. Nuclear magnetic resonance spectroscopy ……………………………… 58 3.3.5. Fourier-transform infrared spectroscopy ………………………………... 58 3.4. Results and discussion …………………………………………………………….. 58 3.4.1. Preparation and yields of the lignin-peptide adducts ……………………. 58 3.4.2. Lignin-peptide morphology ……………………………………………... 59 3.4.3. Lignin-peptide linkage identification ……………………………………. 60 3.4.4. Supporting techniques for lignin-peptide characterization ……………… 64 3.5. Conclusions ………………………………………………………………………... 66 3.6. Acknowledgments …………………………………………………………………. 67 3.7. References …………………………………………………………………………. 67 Chapter 4. Preparation and characterization of lignin-gelatin complexes ……………………... 71 4.1. Abstract ……………………………………………………………………………. 71 4.2. Introduction ………………………………………………………………………... 71 4.3. Experimental ………………………………………………………………………. 73 4.3.1. Materials ………………………………………………………………… 73 4.3.2. DHP and DHP-Gel syntheses …………………………………………… 74 4.3.3. Fourier-transform infrared spectroscopy ………………………………... 74 4.3.4. X-ray photoelectron spectroscopy ………………………………………. 74 4.3.5. Scanning electron microscopy and energy dispersive X-ray spectroscopy 75 4.3.6. Nuclear magnetic resonance spectroscopy ……………………………… 75 4.4. Results and discussion …………………………………………………………….. 75 4.4.1. Preparation of DHP-Gel adducts ………………………………………... 75 4.4.2. Fourier-transform infrared spectroscopy of DHP-Gel adducts ………….. 76 4.4.3. Morphology and nitrogen content of DHP-Gel adducts ………………… 77 4.4.4. Nuclear magnetic resonance spectroscopy of DHP-Gel adducts ………... 80 4.5. Conclusions ………………………………………………………………………... 82 4.6. Acknowledgments …………………………………………………………………. 82 4.7. References …………………………………………………………………………. 83 Chapter 5. Searching for lignin-protein linkages in Arabidopsis ……………………………… 86 5.1. Abstract ……………………………………………………………………………. 86 5.2. Introduction ………………………………………………………………………... 86 5.3. Experimental ………………………………………………………………………. 87 5.3.1. Growth and lignin extraction from Arabidopsis ………………………… 87 5.3.2. Elemental analysis of Arabidopsis lignin ……………………………….. 88 5.3.3. Nuclear magnetic resonance spectroscopy of Arabidopsis lignin ………. 88 5.4. Results and discussion …………………………………………………………….. 88 v 5.4.1. Lignin extractions from Arabidopsis ……………………………………. 88 5.4.2. Protein content of Arabidopsis extracts …………………………………. 89 5.4.3. Nuclear magnetic resonance spectroscopy of Arabidopsis lignin ………. 90 5.5. Conclusions ………………………………………………………………………... 91 5.6. Acknowledgments …………………………………………………………………. 92 5.7. References …………………………………………………………………………. 92 Chapter 6. Conclusions ………………………………………………………………………… 93 6.1. Research summary ………………………………………………………………… 93 6.2. Future endeavors …………………………………………………………………... 94 6.3. References …………………………………………………………………………. 97 vi List of Figures 1.1. Three ‘common’ and three ‘uncommon’ monolignols …………………………………...….3 1.2. Resonance forms of monolignol radicals ………………………………………………….....3 1.3. Typical lignin inter-unit linkages …………………………………………………….……....4 1.4. Formation via radical coupling of β-ether QMs during lignin polymerization ……………...5 1.5. Nucleophilic amino acids that could potentially react with lignin QMs …………………….5 1.6. Tyrosine radicals and cross-coupled products ……………………………………………….7 1.7. Lignin-protein complex formed via lignin-carbohydrate linkage ....…………………………9 1.8. Preparation of a lignin β-ether model compound and its corresponding QM analog ...…….13 1.9. Preparation of lignin DHP ...………………………………………………………………..14 1.10. General structure of peptides added to lignin DHP preparations ...……………………….14 1.11. 1H NMR spectrum of lignin DHP ...……………………………………………………….17 1.12. HSQC spectrum of lignin DHP ...………………………………………………………….18 1.13. FT-IR ATR spectrum of lignin DHP ...……………………………………………………19 1.14. SEM image of lignin DHP ...………………………………………………………………20 2.1. Formation of β-ether QMs via radical coupling, and their rearomatization ...……………...26 2.2. Guaiacylglycerol-β-guaiacyl ether 1 and its derived quinone methide (QM) 2 ...………….27
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