UC Irvine

The evolution of oxidative metabolism has shaped life on Earth, from ancient anaerobic microorganisms to the complex aerobic metabolism in modern organisms. Chapter 1 explores the emergence of oxygenic photosynthesis, the rise of aerobic respiration, and the pivotal roles of metalloenzymes in oxygen evolution, activation and utilization. Advances in bioinorganic chemistry have provided insight into metalloprotein mechanisms through the development of artificial metalloproteins (ArMs) and bioinspired catalysts. Exploring the interplay between metalloproteins, metabolism, and oxidative stress provides valuable insights into human health and disease. Maintaining systemic metal ion balance is essential for metabolic stability, and the involvement of metal ions in host-microbe interactions further influences physiological and pathological processes. By bridging perspectives from bioinorganic chemistry, enzymology, synthetic biology, microbiome research and biomedicine, this chapter establishes a foundation for understanding metal ion-driven biological transformations and their broader applications. Chapter 2 describes work towards understanding Cu-containing oxygenase enzymes through the design and interrogation of Cu-ArMs. The influence of secondary coordination sphere interactions—specifically, aromatic residues—on Cu reactivity in engineered ArMs is explored. By introducing aromatic residues in defined spatial orientations, this study reveals their critical role in oxidant activation and oxidation selectivity. The findings may reveal potential inactivation pathways in Cu-containing enzymes such as lytic polysaccharide monooxygenases (LPMOs) that break down complex polysaccharides, or suggest key primary coordination sphere features in particulate methane monooxygenases (pMMOs). Furthermore, these findings may provide insight into the molecular-level tuning of Cu-based oxidation processes in both natural and synthetic systems. At the core of oxidative chemistry performed by metalloenzymes are highly reactive metal-oxygen intermediates that drive catalytic transformations essential for biological and synthetic oxidation processes. In comparison to Mn-, Fe- or Cu- containing oxygenase enzymes, Co-containing oxygenase enzymes are rare. Chapter 3 discusses efforts to generate, stabilize, and characterize Co-oxygen species within a protein scaffold, leveraging the protein environment to modulate reactivity through secondary coordination sphere interactions, steric effects, and protonation dynamics. Understanding the nature of these reactive species and the structure-function relationships that govern their behavior provides valuable insights into metal-mediated oxidation reactions, ultimately informing the rational design of novel (bio)catalysts. Building on some of the design concepts, Chapter 4 explores the preparation and characterization of Co-, Ni-, Cu- and Zn- containing ArMs that mimic naturally occurring dioxygenase enzymes such as quercetin dioxygenases. By systematically comparing metal-substituted ArM variants, this work examines the role of metal ion identity and the local environment surrounding the metal center in modulating substrate binding and reactivity. These studies may provide mechanistic insights into metalloenzyme function and metal-based functional switching. Beyond the individual metalloproteins, Chapter 5 investigates how transition metal ions and metalloenzymes are more broadly involved in bacterial metabolism and pathological oxidation reactions linked to neurodegenerative diseases. This chapter examines how gut microbiome dysbiosis alters redox conditions to promote dopamine oxidation and α-synuclein aggregation, suggesting a potential pathway for Parkinson’s disease progression. These findings highlight how microbial metabolism may be involved in host-disease mechanisms and further suggests potential strategies to mitigate oxidative stress in the gut-brain axis. Overall, metal ions play critical roles in biological oxidation processes, serving as essential cofactors in enzymatic catalysis while also contributing to oxidative stress in pathological conditions. This dissertation explores the interplay between metal ion coordination, oxidation chemistry, and structure-function relationships in both enzymatic and disease-relevant systems. Using ArMs as biomimetic models, the studies presented herein elucidate key factors governing metal-based reactivity and oxidative transformations. Additionally, the pathological implications of metal-catalyzed oxidation are examined in the context of the gut microbiome and Parkinson’s disease. By bridging fundamental enzymatic studies with disease-related oxidative stress, this work provides insight into metal-driven oxidation chemistry with broader implications for catalysis, biomimetic design, and disease mechanisms.