A Specific Guide for Metalloenzyme Designers: Introduction and Evolution of Metal-Coordination Spheres Embedded in Protein Environments

Exploiting SpyTag/SpyCatcher Technology to Design New Artificial Catalytic Copper Proteins

Designing artificial metal binding sites within a protein is challenging since amino acid residues need to be placed in desired positions in the final construct and the use of non-natural amino acids is difficult. The alternative approach of directing the insertion of artificial metal coordination systems presents the difficulty of grafting such site in a single desired position. Spy protein is composed of a protein component (SpyCatcher) which binds spontaneously an oligopeptide (SpyTag) with formation of an isopeptide bond. A SpyTag peptide equipped with an ATCUN (amino terminal copper and nickel) binding site is designed to bind copper(II) with high femtomolar affinity both in the absence of SpyCatcher and in the reconstituted Spy construct. The Cu2+ ATCUN site in the reconstituted Spy protein presents a catalytic activity in reactive oxygen species production, higher than that of the SpyTag peptide alone. This method offers a novel approach for constructing artificial metalloproteins by incorporating functional metal binding sites into a peptide, which can then be clicked onto its protein counterpart. The small size and modularity of this construct make it versatile for integration into other protein systems, eventually moving the complexity from a protein to a peptide and highlighting its potential for protein design.

A semisynthetic, multicofactor artificial metalloenzyme retains independent site activity

Native metalloenzymes are unparalleled in their ability to perform efficient small molecule activation reactions, converting simple substrates into complex products. Most of these natural systems possess multiple metallocofactors to facilitate electron transfer or cascade catalysis. While the field of artificial metalloenzymes is growing at a rapid rate, examples of artificial enzymes that leverage two distinct cofactors remain scarce. In this work, we describe a new class of artificial enzymes containing two different metallocofactors, incorporated through bioorthogonal strategies. Nickel-substituted rubredoxin (NiRd), which is a structural and functional mimic of [NiFe] hydrogenases, is used as a scaffold. Incorporation of a synthetic bimetallic inorganic complex based on a macrocyclic biquinazoline ligand (MMBQ) was accomplished using a novel chelating thioether linker. Neither the structure of the NiRd active site nor the MMBQ were altered upon attachment, and each site retained independent redox activity. Electrocatalysis was observed from each site, with the switchability of the system demonstrated through the use of catalytically inert metal centers. This MMBQ-NiRd platform offers a new avenue to create multicofactor artificial metalloenzymes in a robust system that can be easily tuned both through modifications to the protein scaffold and the synthetic moiety, with applications for redox catalysis and tandem reactivity.

Hybrid Metal Catalysts as Valuable Tools in Organic Synthesis: An Overview of the Recent Advances in Asymmetric C─C Bond Formation Reactions

Carbon-carbon bond formation represents a key reaction in organic synthesis, resulting in paramount importance for constructing the carbon backbone of organic molecules. However, traditional metal-based catalysis, despite its advantages, often struggles with issues related to efficiency, selectivity, and sustainability. On the other hand, while biocatalysis offers superior selectivity due to an extraordinary recognition process of the substrate, the scope of its applicable reactions remains somewhat limited. In this context, Artificial Metalloenzymes (ArMs) and Metallo Peptides (MPs) offer a promising and not fully explored solution, merging the two fields of transition metal catalysis and biotransformations, by inserting a catalytically active metal cofactor into a customizable protein scaffold or coordinating the metal ion directly to a short and tunable amino acid (Aa) sequence, respectively. As a result, these hybrid catalysts have gained attention as valuable tools for challenging catalytic transformations, providing systems with new-to-nature properties in organic synthesis. This review offers an overview of recent advances in the development of ArMs and MPs, focusing on their application in the asymmetric carbon-carbon bond-forming reactions, such as carbene insertion, Michael additions, Friedel-Crafts and cross-coupling reactions, and cyclopropanation, underscoring the versatility of these systems in synthesizing biologically relevant compounds.

Peptides and metal ions: A successful marriage for developing artificial metalloproteins

The mutual relationship between peptides and metal ions enables metalloproteins to have crucial roles in biological systems, including structural, sensing, electron transport, and catalytic functions. The effort to reproduce or/and enhance these roles, or even to create unprecedented functions, is the focus of protein design, the first step toward the comprehension of the complex machinery of nature. Nowadays, protein design allows the building of sophisticated scaffolds, with novel functions and exceptional stability. Recent progress in metalloprotein design has led to the building of peptides/proteins capable of orchestrating the desired functions of different metal cofactors. The structural diversity of peptides allows proper selection of first- and second-shell ligands, as well as long-range electrostatic and hydrophobic interactions, which represent precious tools for tuning metal properties. The scope of this review is to discuss the construction of metal sites in de novo designed and miniaturized scaffolds. Selected examples of mono-, di-, and multi-nuclear binding sites, from the last 20 years will be described in an effort to highlight key artificial models of catalytic or electron-transfer metalloproteins. The authors' goal is to make readers feel like guests at the marriage between peptides and metal ions while offering sources of inspiration for future architects of innovative, artificial metalloproteins.

Understanding the role of negative charge in the scaffold of an artificial enzyme for CO2 hydrogenation on catalysis

We have approached the construction of an artificial enzyme by employing a robust protein scaffold, lactococcal multidrug resistance regulator, LmrR, providing a structured secondary and outer coordination spheres around a molecular rhodium complex, [RhI(PEt2NglyPEt2)2]-. Previously, we demonstrated a 2-3 fold increase in activity for one Rh-LmrR construct by introducing positive charge in the secondary coordination sphere. In this study, a series of variants was made through site-directed mutagenesis where the negative charge is located in the secondary sphere or outer coordination sphere, with additional variants made with increasingly negative charge in the outer coordination sphere while keeping a positive charge in the secondary sphere. Placing a negative charge in the secondary or outer coordination sphere demonstrates decreased activity by a factor of two compared to the wild-type Rh-LmrR. Interestingly, addition of positive charge in the secondary sphere, with the negatively charged outer coordination sphere restores activity. Vibrational and NMR spectroscopy suggest minimal changes to the electronic density at the rhodium center, regardless of inclusion of a negative or positive charge in the secondary sphere, suggesting another mechanism is impacting catalytic activity, explored in the discussion.

Artificial Photosynthases: Single-Chain Nanoparticles with Manifold Visible-Light Photocatalytic Activity for Challenging "in Water" Organic Reactions

Photocatalyzed reactions of organic substances in aqueous media are challenging transformations, often because of scarce solubility of substrates and catalyst deactivation. Herein, we report single-chain nanoparticles, SCNPs, capable of efficiently catalyzing four different "in water" organic reactions by employing visible light as the only external energy source. Specifically, we decorated a high-molecular-weight copolymer, poly(OEGMA300-r-AEMA), with iridium(III) cyclometalated complex pendants at varying content amounts. The isolated functionalized copolymers demonstrated self-assembly into noncovalent, amphiphilic SCNPs in water, which enabled efficient visible-light photocatalysis of two reactions unprecedentedly reported in water, namely, [2 + 2] photocycloaddition of vinyl arenes and α-arylation of N-arylamines. Additionally, aerobic oxidation of 9-substituted anthracenes and β-sulfonylation of α-methylstyrene were successfully carried out in aqueous media. Hence, by merging metal-mediated photocatalysis and SCNPs for the fabrication of artificial photoenzyme-like nano-objects─i.e., artificial photosynthases (APS)─our work broadens the possibilities for performing challenging "in water" organic transformations via visible-light photocatalysis.

In Silico Analysis of Protein-Protein Interactions of Putative Endoplasmic Reticulum Metallopeptidase 1 in Schizosaccharomyces pombe

Ermp1 is a putative metalloprotease from Schizosaccharomyces pombe and a member of the Fxna peptidases. Although their function is unknown, orthologous proteins from rats and humans have been associated with the maturation of ovarian follicles and increased ER stress. This study focuses on proposing the first prediction of PPI by comparison of the interologues between humans and yeasts, as well as the molecular docking and dynamics of the M28 domain of Ermp1 with possible target proteins. As results, 45 proteins are proposed that could interact with the metalloprotease. Most of these proteins are related to the transport of Ca2+ and the metabolism of amino acids and proteins. Docking and molecular dynamics suggest that the M28 domain of Ermp1 could hydrolyze leucine and methionine residues of Amk2, Ypt5 and Pex12. These results could support future experimental investigations of other Fxna peptidases, such as human ERMP1.