An Artificial Metal-Free Peroxidase Designed Using a Ferritin Cage for Bioinspired Catalysis

Developing artificial enzymes is challenging because it requires precise design of active sites with well-arranged amino acid residues. Histidine-rich oligopeptides have been recently shown to exhibit peroxidase-mimetic activities, but their catalytic function relies on maintaining unique supramolecular structures. This work demonstrates the design of a specific array of histidine residues on the internal surface of the ferritin cage to function as an active center for catalysis. The crystal structures of the ferritin mutants revealed histidine-histidine interactions, forming well-defined histidine clusters (His-clusters). These mutants exhibit peroxidase-mimetic activities by oxidizing 3,3',5,5'-tetramethylbenzidine (TMB) in the presence of hydrogen peroxide. Molecular dynamics simulations further highlight the co-localization of TMB and hydrogen peroxide at the histidine-rich clusters, indicating that the confined environment of the ferritin cage enhances their interactions. This study presents a simple yet effective approach to design metal-free artificial enzymes, paving the way for innovations in bioinspired catalysis.

Region-Directed Enzyme Immobilization through Engineering Protein Surface with Histidine Clusters

Enzyme immobilization is a key enabling technology for a myriad of industrial applications, yet immobilization science is still too empirical to reach highly active and robust heterogeneous biocatalysts through a general approach. Conventional protein immobilization methods lack control over how enzymes are oriented on solid carriers, resulting in negative conformational changes that drive enzyme deactivation. Site-selective enzyme immobilization through peptide tags and protein domains addresses the orientation issue, but this approach limits the possible orientations to the N- and C-termini of the target enzyme. In this work, we engineer the surface of two model dehydrogenases to introduce histidine clusters into flexible regions not involved in catalysis, through which immobilization is driven. By varying the position and the histidine density of the clusters, we create a small library of enzyme variants to be immobilized on different carriers functionalized with different densities of various metal chelates (Co2+, Cu2+, Ni2+, and Fe3+). We first demonstrate that His-clusters can be as efficient as the conventional His-tags in immobilizing enzymes, recovering even more activity and gaining stability against some denaturing agents. Furthermore, we find that the enzyme orientation as well as the type and density of the metal chelates affect the immobilization parameters (immobilization yield and recovered activity) and the stability of the immobilized enzymes. According to proteomic studies, His-clusters enable a different enzyme orientation as compared to His-tag. Finally, these oriented heterogeneous biocatalysts are implemented in batch reactions, demonstrating that the stability achieved by an optimized orientation translates into increased operational stability.

Global Mapping of Metalloproteomes

Metalloproteins play diverse and critical functions in all living systems, and their dysfunctional forms are closely related to many human diseases. The development of methods that enable comprehensive mapping of metalloproteome is of great interest to help elucidate crucial roles of metalloproteins in both physiology and pathology, as well as to discover new metalloproteins. We herein briefly review recent progress in the field of metalloproteomics and provide future outlooks.

Unevolved De Novo Proteins Have Innate Tendencies to Bind Transition Metals

Life as we know it would not exist without the ability of protein sequences to bind metal ions. Transition metals, in particular, play essential roles in a wide range of structural and catalytic functions. The ubiquitous occurrence of metalloproteins in all organisms leads one to ask whether metal binding is an evolved trait that occurred only rarely in ancestral sequences, or alternatively, whether it is an innate property of amino acid sequences, occurring frequently in unevolved sequence space. To address this question, we studied 52 proteins from a combinatorial library of novel sequences designed to fold into 4-helix bundles. Although these sequences were neither designed nor evolved to bind metals, the majority of them have innate tendencies to bind the transition metals copper, cobalt, and zinc with high nanomolar to low-micromolar affinity.

Histidine-based copper tetrapeptides as enantioselective catalysts for aldol reactions

Copper(ii)-peptides are widely used as industrial catalysts such as in the aerobic oxidation of organic molecules, formation of new C–H bonds and in the azide–alkyne cycloaddition reaction. The length of peptides and the effect of adding copper metal into peptides were questioned in their field of applications. Five novel histidine-based tetrapeptides with the sequences HAAD (P1), HAFD (P2), HAVD (P3), AGHD (P4) and PGHD (P5) were synthesized using the solid phase peptide scheme and analysed with high performance liquid chromatography (HPLC) and liquid chromatography-mass spectrometry (LC-MS) with percentage purities as high as 99.5%. All the peptides were positively charged (+1) and the molecular weight calculated from m/z values of MS results coincided with the theoretical molecular weight of the peptides. Copper(ii)-peptides derived from these peptides and copper(ii) acetate monohydrate (CuP1–CuP5) in a 1 : 2 ratio was synthesised, purified and characterised by ultraviolet-visible spectroscopy (UV-Vis), ultraviolet-fluorescence spectroscopy (fluorescence) and fourier transform infrared spectroscopy (FTIR), circular dichroism spectroscopy (CD) and optical rotation polarimetry. It provided the necessary information on the secondary structure and the successful binding of copper(ii) to the specific amino acids, hence leading to the putative geometry of copper(ii)-peptides and the difference in the chirality of amino acids, peptides and copper(ii)-peptides. The catalytic activities of the synthesised complexes were evaluated. CuP1 & CuP3 catalysed both the asymmetric aldol reactions with high enantioselectivity of p-nitrobenzaldehyde with cyclohexanone (% ee = 87.3 & 80.3, respectively) and of p-anisaldehyde with cyclohexanone (% ee = 95.5 & 90.9, respectively).

P5 with the sequence H₂N-PGHD-CONH.

Native electrospray mass spectrometry approaches to probe the interaction between zinc and an anti-angiogenic peptide from histidine-rich glycoprotein

Zinc modulates the biological function of histidine-rich glycoprotein (HRG) through binding to its His-rich region (HRR). The Zn2+-binding properties of a 35 amino-acid biologically-active peptide mimic of the HRR, HRGP330, were investigated using dissociative mass spectrometry approaches in addition to travelling-wave ion mobility mass spectrometry (TWIM-MS). Native mass spectrometry confirmed zinc binding to HRGP330; however, broadening of the 1H NMR resonances upon addition of Zn2+ ions precluded the attainment of structural information. A complementary approach employing TWIM-MS indicated that HRGP330 has a more compact structure in the presence of Zn2+ ions. Top-down MS/MS data supported a metal-binding-induced conformational change, as fewer fragments were observed for Zn2+-bound HRGP330. Zn2+-bound fragments of both N-terminal and C-terminal ends of the peptide were identified from collision-induced dissociation (CID) and electron transfer dissociation/proton transfer reaction (ETD/PTR) experiments, suggesting that multiple binding sites exist within this region of HRG. The combination of mass spectrometry and NMR approaches provides new insight into the highly dynamic interaction between zinc and this His-rich peptide.

Ni²⁺ chemistry in pathogens--a possible target for eradication

The survival of all urease and/or hydrogenase containing pathogens depends on the proper homeostasis of nickel. In the scope of this perspectives paper, details of Ni(2+) metabolism of Helicobacter pylori, a widespread stomach-ulcer causing bacterium, are described. Nickel binding proteins and thermodynamics of such metal complexes are discussed in detail and special focus is given to potential nickel binding sequences in this metal's chaperones and regulators. A list of potential Ni(2+) binding sites in various pathogens is presented, which points out numerous examples of nickel interactions that still need to be understood.

The copper(II) and zinc(II) coordination mode of HExxH and HxxEH motif in small peptides: the role of carboxylate location and hydrogen bonding network

Copper(II) and zinc(II) complexes with two hexapeptides encompassing HExxH and HxxEH motif were characterized by means of a combined experimental and theoretical approach. Parallel tempering and density functional theory (DFT) investigations show the presence of different hydrogen bonding networks between the copper(II) and zinc(II) complexes with the two peptides, suggesting a significant contribution of these non-covalent interactions to the stability constant values. The glutamate carboxylate group has a direct role in metal ion binding. The location of this amino acid along the sequence of the investigated peptides is critical to determine thermodynamic and spectroscopic features of the copper(II) complex species, whereas is less relevant in the zinc(II) complexes formation. Electrospray ionization mass spectrometry (ESI-MS) characterization of the zinc(II) complex species show that in the [ZnH-2L] two deprotonated amide nitrogen atoms are involved in the metal coordination environment, an uncommon behavior in zinc(II) complexes for multi-histidine ligands.

Histidine-rich proteins in prokaryotes: metal homeostasis and environmental habitat-related occurrence

Increasing amounts of histidine-rich proteins (HRPs) have been found in microorganisms. We systematically analyzed the proteomes of 675 prokaryotes including 52 archaea and 623 bacteria for histidine-rich motifs (HRMs). We show that HRPs are widespread in prokaryotic proteomes, with the majority being involved in metal homeostasis. HRPs are frequently found in the proteomes of certain orders of rhizobia and pathogenic Gram-negative bacteria, but are essentially absent in obligate intracellular pathogenic species. The occurrence of HRPs in the proteomes of prokaryotes is related to their habitats. We further revealed a class of globally histidine-rich bacterial proteins. This approach can readily be used to identify other single amino acid rich motifs (and proteins) in microbial proteomes to facilitate the exploration of their functions.