From Unnatural Amino Acid Incorporation to Artificial Metalloenzymes

Handle URI:
http://hdl.handle.net/10754/621994
Title:
From Unnatural Amino Acid Incorporation to Artificial Metalloenzymes
Authors:
Makki, Arwa A. ( 0000-0002-5540-0162 )
Abstract:
Studies and development of artificial metalloenzymes have developed into vibrant areas of research. It is expected that artificial metalloenzymes will be able to combine the best of enzymatic and homogenous catalysis, that is, a broad catalytic scope, high selectivity and activity under mild, aqueous conditions. Artificial metalloenzyme consist of a host protein and a newly introduced artificial metal center. The host protein merely functions as ligand controlling selectivity and augmenting reactivity, while the metal center determines the reactivity. Potential applications range from catalytic production of fine chemicals and feedstock to electron transfer utilization (e.g. fuel cells, water splitting) and medical research (e.g. metabolic screening). Particularly modern asymmetric synthesis is expected to benefit from a successful combination of the power of biocatalysis (substrate conversion via multi-step or cascade reactions, potentially immortal catalyst, unparalleled selectivity and optimization by evolutionary methods) with the versatility and mechanism based optimization methods of homogeneous catalysis. However, so far systems are either limited in structural diversity (biotin-avidin technology) or fail to deliver the selectivities expected (covalent approaches). This thesis explores a novel strategy based on the site-selective incorporation of unnatural, metal binding amino acids into a host protein. The unnatural amino acids can either serve directly as metal binding centers can be used as anchoring points for artificial metallo-cofactors. The identification expression, purification and modification of a suitable protein scaffolds is fundamental to successfully develop this field. Chapter 2 and 3 detail a rational approach leading to a highly engineered host protein. Starting with fluorescent proteins, which combine high thermal and pH stability, high expression yields, and fluorescence for ease of quantification and monitoring an efficient and fast purification protocol was developed first. The purification protocol uses a combination of heat precipitation and three-phase-partitioning (TPP). It provides high yield and purity without requiring any tag. Building on the favourable properties of fluorescent proteins, the non-metal binding, highly stable host-scaffold mTFP* was generated through rational design. The incorporation of artificial metal binding sites, the allowed the selective formation of artificial metalloenzymes, which show catalytic activity and moderat to good chiral induction in the Diels-Alder Cyclization and Friedl-Crafts Acylation Chapter 4 of the thesis describes the use of UAA incorporation to generate artificial metal binding sites. Computational studies and homology modelling successfully highlighted several positions in mTFP*, which are particularly suitable for UAA incorporation without any disruption of the protein structure. Application of a functional orthogonal aaRS/tRNA pair developed by P.G. Schultz and co-workers allowed the site-specific incorporation of UAAs in the host protein framework. Changes in fluorescence intensity revealed preferences of varieous UAAs for specific incorporations sites. The three UAAs, pIF, pAzF, and pEynF were incorporated into mTFP* in good yields, while pBF does only deliver low protein yields. A successfully established on-protein MIYAURA borylation reaction allows convert well-incorporated pIF into pBF circumventing the problem of low expression yields. Chapter 5 details the use of the azide-functionality of pAzF for the bioconjugation of artificial metal-binding cofactors through CuAAC. The triazole ring formed during this reaction serves as an additional moderate σ -donor/π –acceptor ligand of the metal binding site. We demonstrated the potential of site-specific modifications within the protein host with a versatile subset of artificial cofactors. Following transition metal binding, the newly created metal sites show catalytic activities that nature does not provide. The proof of concept study highlights the potential of the present mTFP* based catalysts in asymmetric Tsuji Trost allylation reactions and Diels-Alder cycloadditions. Dual anchoring of the cofactor lead to increased enantioselectivities, which is a direct result of a better-defined orientation of the catalytic center on the protein surface. Following the utilization of the CuAAC click reaction for the generation of artificial metalloenzymes, the last chapter of this thesis reports the development of a heterogeneous catalyst system for this reaction, which overcomes limitations of homogenous protocols. The recyclable core-shell structured Cu2O/Cu-nanowire catalyst is highly active, does not lead to protein precipitation, can be filtered off after the reaction and provides copper free bioconjugation products.
Advisors:
Eppinger, Jorg ( 0000-0001-7886-7059 )
Committee Member:
Peinemann, Klaus-Viktor ( 0000-0003-0309-9598 ) ; Arold, Stefan T. ( 0000-0001-5278-0668 ) ; Elmoslimany, Wael
KAUST Department:
Physical Sciences and Engineering (PSE) Division
Program:
Chemical and Biological Engineering
Issue Date:
4-Dec-2016
Type:
Dissertation
Appears in Collections:
Dissertations

Full metadata record

DC FieldValue Language
dc.contributor.advisorEppinger, Jorgen
dc.contributor.authorMakki, Arwa A.en
dc.date.accessioned2016-12-11T10:46:38Z-
dc.date.available2016-12-11T10:46:38Z-
dc.date.issued2016-12-04-
dc.identifier.urihttp://hdl.handle.net/10754/621994-
dc.description.abstractStudies and development of artificial metalloenzymes have developed into vibrant areas of research. It is expected that artificial metalloenzymes will be able to combine the best of enzymatic and homogenous catalysis, that is, a broad catalytic scope, high selectivity and activity under mild, aqueous conditions. Artificial metalloenzyme consist of a host protein and a newly introduced artificial metal center. The host protein merely functions as ligand controlling selectivity and augmenting reactivity, while the metal center determines the reactivity. Potential applications range from catalytic production of fine chemicals and feedstock to electron transfer utilization (e.g. fuel cells, water splitting) and medical research (e.g. metabolic screening). Particularly modern asymmetric synthesis is expected to benefit from a successful combination of the power of biocatalysis (substrate conversion via multi-step or cascade reactions, potentially immortal catalyst, unparalleled selectivity and optimization by evolutionary methods) with the versatility and mechanism based optimization methods of homogeneous catalysis. However, so far systems are either limited in structural diversity (biotin-avidin technology) or fail to deliver the selectivities expected (covalent approaches). This thesis explores a novel strategy based on the site-selective incorporation of unnatural, metal binding amino acids into a host protein. The unnatural amino acids can either serve directly as metal binding centers can be used as anchoring points for artificial metallo-cofactors. The identification expression, purification and modification of a suitable protein scaffolds is fundamental to successfully develop this field. Chapter 2 and 3 detail a rational approach leading to a highly engineered host protein. Starting with fluorescent proteins, which combine high thermal and pH stability, high expression yields, and fluorescence for ease of quantification and monitoring an efficient and fast purification protocol was developed first. The purification protocol uses a combination of heat precipitation and three-phase-partitioning (TPP). It provides high yield and purity without requiring any tag. Building on the favourable properties of fluorescent proteins, the non-metal binding, highly stable host-scaffold mTFP* was generated through rational design. The incorporation of artificial metal binding sites, the allowed the selective formation of artificial metalloenzymes, which show catalytic activity and moderat to good chiral induction in the Diels-Alder Cyclization and Friedl-Crafts Acylation Chapter 4 of the thesis describes the use of UAA incorporation to generate artificial metal binding sites. Computational studies and homology modelling successfully highlighted several positions in mTFP*, which are particularly suitable for UAA incorporation without any disruption of the protein structure. Application of a functional orthogonal aaRS/tRNA pair developed by P.G. Schultz and co-workers allowed the site-specific incorporation of UAAs in the host protein framework. Changes in fluorescence intensity revealed preferences of varieous UAAs for specific incorporations sites. The three UAAs, pIF, pAzF, and pEynF were incorporated into mTFP* in good yields, while pBF does only deliver low protein yields. A successfully established on-protein MIYAURA borylation reaction allows convert well-incorporated pIF into pBF circumventing the problem of low expression yields. Chapter 5 details the use of the azide-functionality of pAzF for the bioconjugation of artificial metal-binding cofactors through CuAAC. The triazole ring formed during this reaction serves as an additional moderate σ -donor/π –acceptor ligand of the metal binding site. We demonstrated the potential of site-specific modifications within the protein host with a versatile subset of artificial cofactors. Following transition metal binding, the newly created metal sites show catalytic activities that nature does not provide. The proof of concept study highlights the potential of the present mTFP* based catalysts in asymmetric Tsuji Trost allylation reactions and Diels-Alder cycloadditions. Dual anchoring of the cofactor lead to increased enantioselectivities, which is a direct result of a better-defined orientation of the catalytic center on the protein surface. Following the utilization of the CuAAC click reaction for the generation of artificial metalloenzymes, the last chapter of this thesis reports the development of a heterogeneous catalyst system for this reaction, which overcomes limitations of homogenous protocols. The recyclable core-shell structured Cu2O/Cu-nanowire catalyst is highly active, does not lead to protein precipitation, can be filtered off after the reaction and provides copper free bioconjugation products.en
dc.language.isoenen
dc.subjectArtificial metalloenzymeen
dc.subjectCatalysisen
dc.subjectfluorescent proteinen
dc.subjectClick Chemistryen
dc.subjectUnnationalen
dc.subjectUnnatural Amino Acidsen
dc.titleFrom Unnatural Amino Acid Incorporation to Artificial Metalloenzymesen
dc.typeDissertationen
dc.contributor.departmentPhysical Sciences and Engineering (PSE) Divisionen
thesis.degree.grantorKing Abdullah University of Science and Technologyen_GB
dc.contributor.committeememberPeinemann, Klaus-Viktoren
dc.contributor.committeememberArold, Stefan T.en
dc.contributor.committeememberElmoslimany, Waelen
thesis.degree.disciplineChemical and Biological Engineeringen
thesis.degree.nameDoctor of Philosophyen
dc.person.id113082en
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