Glesner, Tobias (2024)
Development and Screening of
promiscuous aldolases.
Technische Universität Darmstadt
doi: 10.26083/tuprints-00028405
Dissertation, Erstveröffentlichung, Verlagsversion
Kurzbeschreibung (Abstract)
Aldolases are enzymes that play a crucial role in the metabolism of carbohydrates. These enzymes belong to the class of lyases and exhibit catalytic activity, especially in the Aldol reaction, where aldehydes or ketones react with an electrophile to form an aldol bond. Despite impressive achievements in the development of aldolases, their application has been highly specific, such as in the synthesis of building blocks for statin synthesis, as seen in the case of DERA. The significant restriction regarding accepted donors for the aldol reaction in aldolases has limited their widespread use in industrial applications. Geometric analysis of the active center based on existing crystal structures allows for the expansion of aldolase catalytic activity through mutagenesis. The goal is to enlarge the existing space in the active center. In this study, EcDERA enzyme was used as the starting aldolase, which already carries a single-point mutation (F200I) on the surface. Enzyme libraries with up to three additional point mutations in the active center were generated based on the analysis of existing crystal structures. The introduced mutations, all located in the active center, aim to expand the available space by introducing "space-saving" mutations with smaller amino acids. Wild-type EcDERA accepts acetaldehyde, acetone, propanal, and fluoroacetone as donors, demonstrating a relaxed donor spectrum compared to other known aldolases. The introduction of mutations in the active center aims to enable the acceptance of cyclic ketones such as cyclobutanone, cyclopentanone, and cyclohexanone. Additionally, other ketones like chloroacetone, butanone, 1-hydroxybutanone, and many others were tested for activity. The hypothesis that cyclic ketones could be accepted was confirmed. Some enzymes from the mutagenic EcDERA library were able to convert cyclopentanone, but none of the enzyme variants showed activity for cyclobutanone and cyclohexanone. Due to the limited success of the mutagenic EcDERA library and the availability of metagenomic enzyme libraries DERA and FSA from our partner Prozomix®, these were used to find active enzymes for the selection of donors. The use of metagenomic enzyme libraries expanded the known donor spectrum for DERA by three donors. New, previously unknown activities for DERA enzymes included i-valeraldehyde as an acceptor with butanone, methoxyacetone, and chloroacetone. Notably, an aliphatic acceptor was used, unlike the examples presented in the literature, mainly generated with D-glyceraldehyde-3-phosphate, where the natural acceptor compensates for the lower activity with unnatural donors. Thus, the results represent a significant step towards the universal application of aldolases for the production of fine chemicals. The third chapter of this thesis deals with the effects of inorganic salts on enzyme stability. In 1888, Franz Hofmeister published the results of his study "Zur Lehre der Wirkung der Salze" on the salting-out behavior of protein-containing solutions under the influence of inorganic salts. For his experiment, Hofmeister used separated liquid from beaten eggs, which settled overnight. After adding concentrated salt solutions, he observed different time spans until the 246 first signs of precipitated protein appeared in the form of a whitish cloudiness. His results led to the still-relevant "Lyotropic Series" or colloquially known as the Hofmeister series. For this study, the influence of inorganic salts and other compounds on the thermostability of three example enzymes was analyzed. The enzymes used include lysozyme from Gallus gallus, alcohol dehydrogenase from Saccharomyces cerevisiae, and FSA from Escherichia coli. NanoDSF equipment was used to determine the melting point of enzymes in aqueous solution for assessing thermostability. The methodology allows determining the melting point of a total of 48 aqueous protein samples based on intrinsic tryptophane fluorescence within an hour, depending on the temperature gradients used. The literature standard for the temperature gradient is 1°C/minute, and the Prometheus device from NanoTemper can heat the sample up to 115°C, making the methodology suitable for high-throughput screenings of (hyper)thermophilic enzyme libraries. The results of this study confirm the Hofmeister series from 1888. With high salt concentrations, the trend of the Hofmeister series was observed for all tested enzymes. Particularly, the destabilizing portion of the series exhibited consistent behavior with Hofmeister's results
Typ des Eintrags: | Dissertation | ||||
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Erschienen: | 2024 | ||||
Autor(en): | Glesner, Tobias | ||||
Art des Eintrags: | Erstveröffentlichung | ||||
Titel: | Development and Screening of promiscuous aldolases | ||||
Sprache: | Englisch | ||||
Referenten: | Fessner, Prof. Dr. Wolf-Dieter ; Schmitz, Prof. Dr. Katja | ||||
Publikationsjahr: | 16 Dezember 2024 | ||||
Ort: | Darmstadt | ||||
Kollation: | 246 Seiten | ||||
Datum der mündlichen Prüfung: | 6 Mai 2024 | ||||
DOI: | 10.26083/tuprints-00028405 | ||||
URL / URN: | https://tuprints.ulb.tu-darmstadt.de/28405 | ||||
Kurzbeschreibung (Abstract): | Aldolases are enzymes that play a crucial role in the metabolism of carbohydrates. These enzymes belong to the class of lyases and exhibit catalytic activity, especially in the Aldol reaction, where aldehydes or ketones react with an electrophile to form an aldol bond. Despite impressive achievements in the development of aldolases, their application has been highly specific, such as in the synthesis of building blocks for statin synthesis, as seen in the case of DERA. The significant restriction regarding accepted donors for the aldol reaction in aldolases has limited their widespread use in industrial applications. Geometric analysis of the active center based on existing crystal structures allows for the expansion of aldolase catalytic activity through mutagenesis. The goal is to enlarge the existing space in the active center. In this study, EcDERA enzyme was used as the starting aldolase, which already carries a single-point mutation (F200I) on the surface. Enzyme libraries with up to three additional point mutations in the active center were generated based on the analysis of existing crystal structures. The introduced mutations, all located in the active center, aim to expand the available space by introducing "space-saving" mutations with smaller amino acids. Wild-type EcDERA accepts acetaldehyde, acetone, propanal, and fluoroacetone as donors, demonstrating a relaxed donor spectrum compared to other known aldolases. The introduction of mutations in the active center aims to enable the acceptance of cyclic ketones such as cyclobutanone, cyclopentanone, and cyclohexanone. Additionally, other ketones like chloroacetone, butanone, 1-hydroxybutanone, and many others were tested for activity. The hypothesis that cyclic ketones could be accepted was confirmed. Some enzymes from the mutagenic EcDERA library were able to convert cyclopentanone, but none of the enzyme variants showed activity for cyclobutanone and cyclohexanone. Due to the limited success of the mutagenic EcDERA library and the availability of metagenomic enzyme libraries DERA and FSA from our partner Prozomix®, these were used to find active enzymes for the selection of donors. The use of metagenomic enzyme libraries expanded the known donor spectrum for DERA by three donors. New, previously unknown activities for DERA enzymes included i-valeraldehyde as an acceptor with butanone, methoxyacetone, and chloroacetone. Notably, an aliphatic acceptor was used, unlike the examples presented in the literature, mainly generated with D-glyceraldehyde-3-phosphate, where the natural acceptor compensates for the lower activity with unnatural donors. Thus, the results represent a significant step towards the universal application of aldolases for the production of fine chemicals. The third chapter of this thesis deals with the effects of inorganic salts on enzyme stability. In 1888, Franz Hofmeister published the results of his study "Zur Lehre der Wirkung der Salze" on the salting-out behavior of protein-containing solutions under the influence of inorganic salts. For his experiment, Hofmeister used separated liquid from beaten eggs, which settled overnight. After adding concentrated salt solutions, he observed different time spans until the 246 first signs of precipitated protein appeared in the form of a whitish cloudiness. His results led to the still-relevant "Lyotropic Series" or colloquially known as the Hofmeister series. For this study, the influence of inorganic salts and other compounds on the thermostability of three example enzymes was analyzed. The enzymes used include lysozyme from Gallus gallus, alcohol dehydrogenase from Saccharomyces cerevisiae, and FSA from Escherichia coli. NanoDSF equipment was used to determine the melting point of enzymes in aqueous solution for assessing thermostability. The methodology allows determining the melting point of a total of 48 aqueous protein samples based on intrinsic tryptophane fluorescence within an hour, depending on the temperature gradients used. The literature standard for the temperature gradient is 1°C/minute, and the Prometheus device from NanoTemper can heat the sample up to 115°C, making the methodology suitable for high-throughput screenings of (hyper)thermophilic enzyme libraries. The results of this study confirm the Hofmeister series from 1888. With high salt concentrations, the trend of the Hofmeister series was observed for all tested enzymes. Particularly, the destabilizing portion of the series exhibited consistent behavior with Hofmeister's results |
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Alternatives oder übersetztes Abstract: |
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Status: | Verlagsversion | ||||
URN: | urn:nbn:de:tuda-tuprints-284053 | ||||
Sachgruppe der Dewey Dezimalklassifikatin (DDC): | 500 Naturwissenschaften und Mathematik > 540 Chemie | ||||
Fachbereich(e)/-gebiet(e): | 07 Fachbereich Chemie 07 Fachbereich Chemie > Clemens-Schöpf-Institut 07 Fachbereich Chemie > Clemens-Schöpf-Institut > Fachgebiet Organische Chemie |
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Hinterlegungsdatum: | 16 Dez 2024 12:59 | ||||
Letzte Änderung: | 17 Dez 2024 08:16 | ||||
PPN: | |||||
Referenten: | Fessner, Prof. Dr. Wolf-Dieter ; Schmitz, Prof. Dr. Katja | ||||
Datum der mündlichen Prüfung / Verteidigung / mdl. Prüfung: | 6 Mai 2024 | ||||
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