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Bacterial Β-Aminopeptidases: Function, Structure and Applications

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Bacterial Β-Aminopeptidases: Function, Structure and Applications Eawag_06815 Diss. ETH No. 18869 Bacterial β-Aminopeptidases: Function, Structure and Applications A dissertation submitted to ETH ZÜRICH for the degree of Doctor of Sciences presented by TOBIAS HECK Dipl. Biol. Eberhard Karls Universität Tübingen, Germany born on April 5, 1980 citizen of Germany accepted on the recommendation of Prof. Dr. Donald Hilvert, examiner Dr. Hans-Peter E. Kohler, co-examiner Prof. Dr. Sven Panke, co-examiner Zürich, 2010 Dank Nach beinahe fünf ereignisreichen Jahren Eawag bietet sich mir an dieser Stelle die passende Gelgenheit, die Zeit seit meiner Diplomarbeit 2005 bis zum Ende der Doktorarbeit 2010 Revue passieren zu lassen. Ich möchte hier die wichtigsten Personen herausheben, die meinen Aufenthalt in der Schweiz in wissenschaftlicher und persönlicher Hinsicht in so unvergesslicher Weise geprägt haben. Ganz besonders glücklich schätzen konnte ich mich über die grandiose Betreuung und Unterstützung durch Birgit Geueke und Hans-Peter Kohler. Ihr habt es verstanden die richtige Richtung vorzugeben und mir trotzdem genügend Freiraum gelassen, meinen eigenen Weg zu finden und meine Ideen und Interessen in die Tat umzusetzen – für mich DIE PERFEKTE MISCHUNG. Mehr gibt es dazu eigentlich nicht zu sagen, vielen vielen Dank! Im weiteren möchte ich mich ganz herzlich bedanken bei: Donald Hilvert für die Übernahme des Referats, seine Hilfsbereitschaft und seine Ideen im Rahmen der Subgroup Meetings. Sven Panke für das Übernehmen des Koreferats. Dieter Seebach und der ganzen Gruppe an der ETH, speziell Albert Beck, Michael Limbach, Oliver Flögel, James Gardiner, Stefania Capone, Aneta Lukaszuk und Gildas Deniau für die überaus fruchtbare und enge Zusammenarbeit über die vergangenen fünf Jahre sowie die “Nachhilfe” in der organischen Chemie. Tobias Merz, Markus Grütter und Beat Blattmann für das Lösen der BapA-Strukturen sowie die Einführung in die Proteinkristallographie und -strukturaufklärung. Steffen Osswald und Matthijs ter Wiel (Evonik Degussa GmbH), Andreas Schmid mit Gruppe (TU Dortmund), Karl-Heinz Wiesmüller und Renate Spohn (EMC Microcollections GmbH) für die Synthese von Substraten und die erfolgreiche Zusammenarbeit. Thomi Fleischmann, Hans-Ueli Weilenmann und Colette Bigosch für ihre unermüdliche Hilfsbereitschaft bei technischen Fragen und ihre Unterstützung im Laboralltag. René Schönenberger und Marc Suter für ihre MS-Kompetenz und das Messen zahlreicher LC-MS Proben. Sudheer Makam und Artur Reimer für ihren Einsatz und ihre akribische Arbeit während ihren Master-/Diplomarbeiten. Den aktuellen und ehemaligen Mitgliedern der Umik-Crew, Birgit G. und W., Hanspi, Thomas, Thomi, Colette, Christoph, Hans-Ueli, Marius, Eva S1. und S2., Liz, Frederik, Frédéric, Fränzi, Stefan, Inés, Margarete, Sudheer, Artur, Vishakha, Samir, Miguel, Ruedi, Johannes, Karin, Toni, Silvana, Teresa, Ivo, Michi, Tiffany und Martin für die angenehme Arbeitsatmosphäre, die vielen schönen Momente auf und neben der Arbeit und die Hilfe im Labor. Den Unihockey-Aktivposten Holger, huwem, chw, Thomas, Anatol, Kim, Jafet, Quang, Judith, Ivo, Régine, Yvonne, etc. für harte aber faire Hockey-Schlachten und so manchen schläfrigen Mittwochnachmittag. Allen aktiven, zurückgetretenen und langzeitverletzten Filigrantechnikern der Eawag Fussball-Truppe, i.e. Martin F. und S., Stephan, Simon, Sebi, Lukas, Christian A. und S., Aurea, Merle, Jürgen Nr. 1, Matteo, Lars, Fabian, Michael, Miguel, Holger, Tobi, Johannes, Peter, Enriquinho, Robert, Jörg, Thomas, Matheus, Simone, Bouziane und dem Rest der Truppe fürs Draussen und Drinnen Tschute. Scrätschi, Corine, Nathalie, das Party-Office (Dani, Flavio, Mirjam F. und Régine), Etienne, Christian, Mirjam K., Anne, Daya, Tati, Jannis, Lukas, Nadine, Ilona, Bettina, Etienne, Beat, Anita, Christina, Manu, Damian, Philipp, Susanne, Luba, Simón, Dani P.und R., Maria und dem Empfangsteam und allen weiteren aktuellen und ehemaligen Mitarbeitern, die weder zu den Unihockeyanern noch zu den Fussballern zählen, aber trotzdem dazu beigetragen haben, dass ich mich hier so wohl gefühlt habe. Der Deutschen Bundesstiftung Umwelt und der Eawag für die Finanzierung der Dissertation. Meinen Eltern, meinen Freunden und Ania (cmok!) für ihre stete Unterstützung, unzählige Unternehmungen und unvergessliche Reisen. Table of Contents Summary....................................................................................................................... i Zusammenfassung ........................................................................................................iii 1. General Introduction ............................................................................................... 1 2. Enzyme-Catalyzed Formation of β-Peptides: β-Peptidyl Aminopeptidases BapA and DmpA Acting as β-Peptide-Synthesizing Enzymes ............................................................13 3. Kinetic Analysis of L-Carnosine Formation by β-Aminopeptidases................................33 4. Kinetic Resolution of Aliphatic β-Amino Acid Amides by β-Aminopeptidases.................51 5. β-Aminopeptidase-Catalyzed Biotransformations of β2-Dipeptides: Kinetic Resolution and Enzymatic Coupling ......................................................................................................65 6. Complex Structures of BapA with Penicillin-Derived Inhbitors Reveal New Insights into β-Peptide Conversion by β-Aminopeptidases...................................................................95 7. Protein Maturation and Activity of BapA and Crystal Structure of a Processing-Deficient BapA Precursor ..........................................................................................................121 8. General Conclusions and Outlook ..........................................................................137 References.................................................................................................................143 Curriculum Vitae.........................................................................................................165 List of Publications......................................................................................................167 Summary Summary The incorporation of β-amino acids into peptides induces the formation of unique secondary structures and confers resistance to degradation by most proteolytic enzymes. These properties give rise to interesting new biomedical applications for β-peptides as bioactive α- peptide mimics. The β-aminopeptidases 3-2W4 BapA from Sphingosinicella xenopeptidilytica 3-2W4, Y2 BapA from Sphingosinicella microcystinivorans Y2 and DmpA from Ochrobactrum anthropi LMG7991 possess the unusual catalytic ability to cleave backbone-elongated β3- amino acid residues from the N-termini of synthetic β- and mixed β,α-peptides that are otherwise resistant to proteolytic breakdown. The growing demand for β-amino acid-derived compounds to be used in the pharmaceutical industry and as fine chemicals suggested interesting applications for β-aminopeptidases, such as biocatalytic production of enantiopure β-amino acids by kinetic resolution and synthesis of β-amino acid-containing peptides. The hydrolysis of four racemic β3-amino acid amides with aliphatic side chains was catalyzed by the enzymes 3-2W4 BapA, Y2 BapA and 3 DmpA in a highly L-enantioselective reaction and gave access to L-β -amino acids of high enantiopurity. In addition to their hydrolytic properties, the enzymes were capable of coupling various β3-amino acids to the unprotected N-termini of α-amino acids, β-amino acids, and short peptides. β-Aminopeptidase-catalyzed peptide formation was under kinetic control and required the use of C-terminally activated β3-amino acids in an aqueous reaction system at alkaline pH. The enzymatic synthesis of the naturally occurring β,α-dipeptide L- carnosine was of special interest due to the commercial potential and biological relevance of this compound. A detailed kinetic study indicated the usefulness of the β-aminopeptidases 3- 2W4 BapA and DmpA for the biocatalytic production of L-carnosine, but also pointed out drawbacks of these enzyme-catalyzed reactions, such as competing substrate and product hydrolysis and formation of various peptidic byproducts. In addition to β3-amino acid- containing peptides, the enzymes 3-2W4 BapA and DmpA also converted peptides with N- terminal β2-amino acids, which have been less extensively explored due to their limited availability. The BapA-catalyzed transformation of the diastereomeric mixture of a β2- dipeptide was characterized by simultaneously occurring hydrolysis and coupling reactions. i Summary The fact that both peptide hydrolysis and peptide formation were highly (S)-enantioselective indicated that 3-2W4 BapA might be useful as a catalyst for enantioselective preparations of β2-amino acids and β2-peptides. The crystal structure of the β-aminopeptidase 3-2W4 BapA was determined in collaboration with the group of Prof. Grütter at the University of Zürich. The arrangement of the secondary structure elements in 3-2W4 BapA revealed an αββα-core structure, which resembles the consensus fold of the N-terminal nucleophile (Ntn) hydrolase superfamily. Structures of non-covalent BapA-ligand complexes revealed likely interactions of β-peptidic substrates with active site residues, such as Glu133, which is crucial for the stabilization of the ligand’s free N-terminus. The maturation process of 3-2W4 BapA involves the posttranslational cleavage of an inactive precursor polypeptide into a large α- and a small β-
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