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Synthesis of Biomass-Containing Xylan Fragments and Evaluation of Ferulic Acid Esterase Activity Downloaded from orbit.dtu.dk on: Oct 09, 2021 Synthesis of biomass-containing xylan fragments and evaluation of ferulic acid esterase activity Underlin, Emilie Nørmølle Publication date: 2018 Document Version Publisher's PDF, also known as Version of record Link back to DTU Orbit Citation (APA): Underlin, E. N. (2018). Synthesis of biomass-containing xylan fragments and evaluation of ferulic acid esterase activity. Technical University of Denmark. General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. Users may download and print one copy of any publication from the public portal for the purpose of private study or research. You may not further distribute the material or use it for any profit-making activity or commercial gain You may freely distribute the URL identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Synthesis of biomass-containing xylan fragments and evaluation of ferulic acid esterase activity Ph.D. thesis by Emilie Nørmølle Underlin, M.Sc. November 2018 DTU Chemistry ii Preface The work presented in this thesis encompasses the results obtained during my Ph.D. studies from December 2015 to November 2018 at the Department of Chemistry, Technical University of Denmark as part of the Danish program to obtain a Ph.D. degree. The Ph.D. project was conducted under the supervision of Professor Robert Madsen as the main supervisor, and Professor Mads H. Clausen as co-supervisor. The project was financed by the Department of Chemistry, Technical University of Denmark. A three month external stay was carried out at the Food Chemistry Department at Wageningen University and Research, Wageningen, The Netherlands, from April to early July 2018 under the supervision of Associate Professor Mirjam Kabel as part of the Ph.D. studies. This dissertation covers four projects described in six chapters. Chapter one presents an introduction to xylan structures in biomass and the enzymatic breakdown of these as well as a presentation of previously published syntheses of xylan fragments. Chapter two first covers the development of a new glycosylation protocol as developed previously in the group for the synthesis of arabinoxylan fragments, which is followed by a description of the synthesis of three arabinoxylan fragments produced for this thesis. Chapter three first presents the previous efforts expended for the synthesis of glucuronoxylan fragments in the group, then the synthesis of two glucuronoxylans as produced for this thesis is presented. Chapter four covers the investigation into reactivity of ferulic acid esterases done during the external stay. Chapter five presents a short introduction to regioselective glycosylations followed by investigations of regioselective glycosylations catalyzed by molybdenum. Finally, chapter six provides an overall conclusion. Emilie Nørmølle Underlin November 2018, Kgs. Lyngby, Denmark iii iv Acknowledgement First and foremost, I would like to thank my supervisor Professor Robert Madsen for accepting me as a Ph.D. student and guidance during the last three years, which all made it possible for me to be a part of these projects. I would also like to thank Professor Mads H. Clausen for being my co-supervisor and admitting me to the Bioorganic Groups Meetings, where I could discuss carbohydrate chemistry with other carbohydrate chemists. Without the previous work of Ph.D. Maximilian Felix Böhm and Ph.D. Clotilde d’Errico, I would never have been able to get as far with these projects as I have or have been allowed to work with so many different and exciting topics during the last three years. A great thank also goes to Associate Professor Mirjam Kabel for being my supervisor away from home and hosting me for my external stay at Wageningen University and Research. Furthermore I would have been lost without the kind and patient guidance of Ph.D. Matthias Frommhagen, who taught me the way around a biochemistry laboratory. Moreover, the project I worked on would not have been possible without the enzymes provided by Ph.D. Adiphol Dilokpimol and Professor Ronald P. de Vries at Utrecht University. Generally, I would also like to thank all the nice people at Food Chemistry for making my stay there both memorable and very enjoyable. Laboratory work would not have been possible without the help of the technical staff of the chemistry department at DTU, hence thanks to sweet Anne Hector (who promised to stay until I left), Philip Charlie Johansen, Brian Brylle Dideriksen, and Lars Egede Bruhn. Many thanks also goes to the NMR team, Associate Professor Charlotte H. Gotfredsen, Professor Jens Ø. Duus, Kasper Enemark-Rasmussen, and again Anne Hector for maintaining the NMRs at all time. For help with MS measurements I have to thank Anders Holmgaard Hansen at DTU Biosustain. The society does not function without money, so I thank DTU for financing my Ph.D., as well as the Oticon Fond, Tranes Fond, Jørgen Esmers Mindefond, and Knud Højgaards Fond for helping to finance my external stay. The Madsen group, both former and present members, have made the last three years fun and enjoyable. Especially I need to thank Clotilde d’Errico, Carola Santilli, and Simone Samuelsen v for all the long and cosy talks about everything and sometimes absolutely nothing both in the laboratory and in the office. Thanks to the fellow Ph.D. students and Postdocs at the organic department at DTU for providing a pleasant working environment. As special thanks goes to all the member of the “Pasta with Olives”-group, which originally was formed as a lunch group, but now has transformed into the most social group, which does not miss any chance for sharing food and good times. Irene Boss – the first two years at DTU would not have been the same without you. Thanks for endless talks about chemistry and life both at home in Copenhagen and on vacations, and of cause for correcting this thesis. Without your comments and suggestions, this thesis would not have become what it is. Thank you Fabrizio for always being ready with hugs and encouraging words if needed, for just being there and always believing in me. Last but not least, a big thank you goes to my family for their support and love, for always picking up the phone for a talk even during dinnertime or welcoming me with open arms in Nibe or in Copenhagen. vi Abstract Lignocellulosic material from the plant cell wall would be an important and CO2 neutral energy resource, if it could be properly utilised. However, intrinsic recalcitrance hampers the utilisation. Especially enzymatic degradation has received extensive attention as a way to solve this problem. An essential tool for development of new enzymes is well-defined model substrates, which can provide a deeper understanding of the substrate specificity and reactivity. Hence, chemically synthesised model substrates often outcompete isolated substrates from natural sources due to homogeneity, purity, and reproducibility. The research presented in this thesis involved the synthesis of both arabinoxylan and glucuronoxylan fragments designed as model substrates for xylanases, α-arabinofuranosidases, and α-glucuronosidases. The syntheses involved the utilisation of thioxyloside building blocks linked in an iterative glycosylation strategy without pre-activation. The arabinose building block were synthesised through a small linear synthesis. On the other hand, the glucuronate building blocks were derived from the same thioglucopyranoside derivative through a divergent strategy (Figure 1). One known class of the lignocellulosic enzymes are ferulic acid esterases. These enzymes are able to cleave the ester-linkages between monomeric or polymeric ferulic acids and a polysaccharide chain or lignin of the plant cell wall. The ferulic acid ester-linkages of the plant cell wall are known to hamper the degradation by other hemicellulosic enzymes. Hence, ferulic acid esterases are interesting tools for enzymatic degradation. The ferulic esterases can be classified into 13 subfamilies based on a phylogenetic three. In this thesis, 14 enzymes belonging to six different subfamilies were tested for specificity and reactivity towards both synthetic model substrates and natural substrates, thereby, being able to relate the reactivity and specificity to the classification. Furthermore, the catalytic abilities of different molybdenum complexes for regioselective glycosylations have been tested. vii Figure 1: Retrosynthetic overview for the synthesis of arabino- and glucuronoxylan fragments. viii Resume Lignocellulose materiale fra plante celle væggen ville være en vigtig og CO2 neutral energiressource, hvis den kunne blive udnyttet ordentligt. Indbygget recalsistans hindrer dog udnyttelsen. Især enzymatisk nedbrydning har fået meget opmærksomhed som en mulig løsning på problemet. Et essentielt redskab for udviklingen af nye enzymer er veldefinerede model substrater, der kan give en dybere forståelse af substrat specificitet og reaktivitet. Derfor udkonkurrerer kemisk syntetiserede model substrater ofte isolerede substrater fra naturlige kilder i forhold til homogenitet, renhed og reproducerbarhed. Forskningen præsenteret i denne afhandling omhandlede syntese
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