Nitrite reductase activity within an antiparallel de novo scaffold

Nitrite Reductases in Biomedicine: From Natural Enzymes to Artificial Mimics

Nitrite reductases (NiRs) are natural enzymes that facilitate the reduction of nitrite. They are essential for the microbial nitrogen cycle and play a vital role in regulating numerous physiological and pathological processes associated with nitric oxide (NO) in living organisms. By the merits of protein engineering, a variety of artificial NiR mimics have been developed. These include traditional artificial proteins, metal-azacycle complexes, and nanozymes such as metal, metal oxide/sulfide nanoparticles, metal-organic frameworks, bioinorganic nanohybrids, and advanced single-atom nanozymes. This development marks an important milestone in broadening the application of enzyme-like catalytic nitrite reduction across various fields, such as biomedicine, biosensing, food science, and environmental science. In this review, we first outline the different types of NiRs, along with their active center structures and catalytic mechanisms, drawing from recent research and discoveries. We then classify the reported NiR mimic materials, discussing their active center structures and enzyme-like catalytic mechanisms. Additionally, we explore the potential future applications and challenges facing NiR mimics in the field of biomedicine.

Recent advances in de novo designed metallopeptides as tailored enzyme mimics

Advances in de novo design of metallopeptides have paved the way for customized metalloenzyme mimics with impressive catalytic capabilities. Over the last few years, incorporation of transition metals into simplified peptide scaffolds has allowed for catalytic efficiencies similar to or greater than those found in natural metalloenzymes. Artificial de novo peptide scaffolds highlight how precise modifications to metal coordination environments can improve scaffold stability and catalytic efficiency for a wide range of applications towards redox, non redox, synthetic, and energy conversion chemistry. These insights deepen our understanding of enzyme evolution and set a solid foundation for new directions in biocatalysis.

Molecular Origami: Designing Functional Molecules of the Future

In the field of chemical biology, DNA origami has been actively researched. This technique, which involves folding DNA strands like origami to assemble them into desired shapes, has made it possible to create complex nanometer-sized structures, marking a major breakthrough in nanotechnology. On the other hand, controlling the folding mechanisms and folded structures of proteins or shorter peptides has been challenging. However, recent advances in techniques such as protein origami, peptide origami, and de novo design peptides have made it possible to construct various nanoscale structures and create functional molecules. These approaches suggest the emergence of new molecular design principles, which can be termed "molecular origami". In this review, we provide an overview of recent research trends in protein/peptide origami and DNA/RNA origami and explore potential future applications of molecular origami technologies in electrochemical biosensors.

Discussing the Terms Biomimetic and Bioinspired within Bioinorganic Chemistry

The terms biomimetic and bioinspired are very relevant in the field of bioinorganic chemistry and have been widely applied. Although they were defined by the International Organization for Standardization in 2015, these terms have at times been used rather ambiguously in the literature. This may be due to the inherent complexity of bioinorganic systems where, for example, a structural model of an enzyme active site may not replicate its function. Conversely, the function of an enzyme may be reproduced in a system where the structure does not resemble the enzyme's active site. To address this, we suggest definitions for the terms biomimetic and bioinspired wherein structure and function have been decoupled. With the help of some representative case studies we have outlined the challenges that may arise and make suggestions on how to apply terminology with careful intention.

A De Novo-Designed Type 3 Copper Protein Tunes Catechol Substrate Recognition and Reactivity

De novo metalloprotein design is a remarkable approach to shape protein scaffolds toward specific functions. Here, we report the design and characterization of Due Rame 1 (DR1), a de novo designed protein housing a di-copper site and mimicking the Type 3 (T3) copper-containing polyphenol oxidases (PPOs). To achieve this goal, we hierarchically designed the first and the second di-metal coordination spheres to engineer the di-copper site into a simple four-helix bundle scaffold. Spectroscopic, thermodynamic, and functional characterization revealed that DR1 recapitulates the T3 copper site, supporting different copper redox states, and being active in the O₂ -dependent oxidation of catechols to o-quinones. Careful design of the residues lining the substrate access site endows DR1 with substrate recognition, as revealed by Hammet analysis and computational studies on substituted catechols. This study represents a premier example in the construction of a functional T3 copper site into a designed four-helix bundle protein.

Catalysis and Electron Transfer in De Novo Designed Metalloproteins

One of the hallmark advances in our understanding of metalloprotein function is showcased in our ability to design new, non-native, catalytically active protein scaffolds. This review highlights progress and milestone achievements in the field of de novo metalloprotein design focused on reports from the past decade with special emphasis on de novo designs couched within common subfields of bioinorganic study: heme binding proteins, monometal- and dimetal-containing catalytic sites, and metal-containing electron transfer sites. Within each subfield, we highlight several of what we have identified as significant and important contributions to either our understanding of that subfield or de novo metalloprotein design as a discipline. These reports are placed in context both historically and scientifically. General suggestions for future directions that we feel will be important to advance our understanding or accelerate discovery are discussed.