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Title: Integration of peroxidase functionality into a de novo, hyperthermophilic, cytochrome c maquette
Author: Watkins, Daniel William
ISNI:       0000 0004 6059 0372
Awarding Body: University of Bristol
Current Institution: University of Bristol
Date of Award: 2016
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The superfamily of enzymes known as oxidoreductases catalyse many cellular electron transfer reactions. These proteins range from simple globular structures to multi-cofactor binding, mega dalton complexes such as those involved in oxidative phosphorylation. Many of the challenging processes they catalyse, such as site-specific hydrocarbon oxidation and photosynthetic water oxidation, are of great interest for biotechnology and synthetic biology. As we seek to harness these valuable functions, it is essential that we endeavour to understand the functional mechanisms that underpin them. The ultimate test of our understanding of oxidoreductases is reproducing their functions in de novo proteins. A field of de novo protein design known as the maquette approach involves the construction of simple artificial oxidoreductases by attaching redox active cofactors to four-helix bundles. The primary sequences of these protein maquettes contain only essential information for protein function, such as folding into a stable tertiary structure, cofactor binding and protein solubility. Maquettes are therefore purpose-built, mutable and tolerant to extensive protein engineering. These de novo proteins reproduce key features of oxidoreductases and provide significant insights into functional mechanisms such as cofactor binding, inter- and intraprotein electron transfer reactions, redox-gated conformational switching and oxygen binding. This work focusses on the iterative modification of an oxygen binding, heme B/C binding maquette. This four-helix bundle is expressed in Escherichia coli and heme C is subsequently appended to the protein backbone by hijacking E. coli's native cytochrome c maturation system. Chapter two describes the design of a suite of heme B/C and di-heme C binding maquettes, constructed by modifying the location and type of heme attached to each heme binding site within the four helix bundle scaffold. These proteins retain the essential features of the parent design and exhibit varying thermostabilities due to the orientation of the heme C propionate groups, thus, rules have been gleaned for an optimised maquette heme binding site. Chapter three describes the design of a mono-histidine ligated heme C maquette, with the overarching aim of designing a peroxidase maquette. Starting with a relatively thermostable heme B/C maquette described in chapter one, the bis-histidine heme B binding site was replaced with two phenylalanine residues that gave rise to a thermophilic maquette with an unfolding midpoint temperature of 84°C. An accessible distal coordination site is essential for hydrogen peroxide binding to heme to initiate peroxidase catalysis. Therefore, the heme C iron distal histidine ligand was removed, allowing small ligands such as cyanide, azide, and carbon monoxide to readily bind to the distal coordination site. Chapter four describes the kinetic characterisation of the peroxidase maquette. Despite containing the minimum requirements for peroxidase catalysis, this maquette catalyses the oxidation of a host of substrates and exhibits diffusion limited catalysis for ABTS oxidation. Tested substrates include hydrogen peroxide, a host of aromatic molecules, halophenols and cytochrome c. The catalytic properties are significantly influenced by pH, suggesting the immediate heme environment plays a key role in catalysis. Morover, catalytic activity is retained in high concentrations of organic solvent, which may facilitate reactions with substrates that exhibit low solubility in aqueous solutions. An intermediate state was isolated by rapid mixing of the maquette with hydrogen peroxide and characterised by EPR and UV-visible spectroscopy. This work exemplifies the effectiveness of maquettes as proof of principle models for natural oxidoreductases and demonstrates that maquettes are viable scaffolds for the construction of artificial biocatalysts. Despite a minimalist design procedure, the peroxidase maquette rivals natural peroxidases in terms of catalytic efficiency and exhibits significant promiscuity, most likely a feature of primitive enzymes that do not contain specific substrate binding sites. The heme C maquettes described within lay groundwork for the construction of artificial oxidoreductases that complement, hijack or supplement cellular electron transfer pathways.
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available