Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers

Next-generation metabolic models informed by biomolecular simulations

Metabolic modeling is essential for understanding the mechanistic bases of cellular metabolism in various organisms, from microbes to humans, and the design of fitter microbial strains. Metabolic networks focus on the overall fluxes through biochemical reactions that implicitly rely on several biochemical processes, such as active or diffusive uptake (or export) of nutrients (or metabolites), enzymatic turnover of metabolites, and metal-cofactor enzyme interactions. Despite independent progress in biomolecular simulations, they have yet to be integrated to inform metabolic models. We explore the evolution of computational metabolic modeling approaches, starting with flux balance analysis, dynamic, kinetic delineations of metabolic shifts in single organisms within cells and across tissues, and mutually informing, community-level modeling frameworks and provide a narrative to tie in biomolecular simulations and machine learning predictions to usher the new phase of structure-guided synthetic biology applications. These additions and prospective novel ones are likely to open hitherto untapped paradigms for optimizing/understanding metabolic pathways toward improving bioproduction of protein and small molecule products with downstream applications in health, environment, energy, and sustainability.

Electroactive biofilm communities in microbial fuel cells for the synergistic treatment of wastewater and bioelectricity generation

Increasing industrialization and urbanization have contributed to a significant rise in wastewater discharge and exerted extensive pressure on the existing natural energy resources. Microbial fuel cell (MFC) is a sustainable technology that utilizes wastewater for electricity generation. MFC comprises a bioelectrochemical system employing electroactive biofilms of several aerobic and anaerobic bacteria, such as Geobacter sulfurreducens, Shewanella oneidensis, Pseudomonas aeruginosa, and Ochrobacterum pseudiintermedium. Since the electroactive biofilms constitute a vital part of the MFC, it is crucial to understand the biofilm-mediated pollutant metabolism and electron transfer mechanisms. Engineering electroactive biofilm communities for improved biofilm formation and extracellular polymeric substances (EPS) secretion can positively impact the bioelectrochemical system and improve fuel cell performance. This review article summarizes the role of electroactive bacterial communities in MFC for wastewater treatment and bioelectricity generation. A significant focus has been laid on understanding the composition, structure, and function of electroactive biofilms in MFC. Various electron transport mechanisms, including direct electron transfer (DET), indirect electron transfer (IET), and long-distance electron transfer (LDET), have been discussed. A detailed summary of the optimization of process parameters and genetic engineering strategies for improving the performance of MFC has been provided. Lastly, the applications of MFC for wastewater treatment, bioelectricity generation, and biosensor development have been reviewed.

Enhancing anammox granular sludge for mainstream anammox process by adding iron-loaded diatomite: Performance and intrinsic mechanism

Iron-loaded diatomite (Fe-DE) was developed as the innovative material to enhance anammox granular sludge (AnGS) and mainstream anammox performance. By adding Fe-DE with the Fe:DE ratio of 1:20 and the dosage of 3 g/L, the start-up period of mainstream anammox process was shortened from 29 d to 17 d and its nitrogen removal rate was increased from 0.234 kg N/(m3·d) to 0.437 kg N/(m3·d). AnGS generated more hydrophobic functional groups and redox substances, forming the robust particle structure and improving the electron transfer of anammox reaction. In addition, the key genes PleC, PleD and TrpE/G, related to quorum sensing, increased from 502.69, 91.18 and 18.25 CPM to 532.84, 103.66 and 19.96 CPM. The key genes hzs and hdh related to anammox process also increased by 30.76% and 24.26%. As a result, formation of AnGS was promoted and the enrichment level of Candidatus Brocadia was improved. This study provides a novel insight into the development of innovative material for enhancing mainstream anammox process.

Determination of Thiol Protonation States by Sulfur X-ray Spectroscopy in Biological Systems

Cysteine is one of the most functionally diverse of the proteinogenic amino acids, owing to its reactive thiol side chain that can undergo deprotonation to form a strongly nucleophilic thiolate. However, few techniques can directly interrogate sulfur charge and covalency in cysteine, particularly in proteins. X-ray spectroscopies provide an element specific probe of sulfur. We demonstrate the sensitivity of S Kβ and Kα X-ray emission spectroscopy (XES) to cysteine ionization and compare it to S K-edge X-ray absorption spectroscopy (XAS) in the physiologically relevant biomolecules l-cysteine and N-acetyl-l-cysteine at room temperature in solution phase. Kβ XES and K-edge XAS are most sensitive to chemical changes at the cysteine thiol and can be used to evaluate the composition of thiol/thiolate mixtures. These results provide a foundation for assessing the pKa of functionally significant cysteine residues in proteins and open the door to time-resolved studies of cysteine-dependent enzymes.

The golden goal of entatic state model design: lowering the internal reorganization energy leads to exponential increase in electron transfer rate

We report a novel guanidine quinolinyl entatic state model system with an electron transfer rate on the order of 105 M-1 s-1 and remarkably little internal reorganization. Comparison between this system and previously reported TMGqu systems reveals an exponential correlation between the internal reorganization energy and the electron transfer rate.

Redox-Guided DNA Scanning by the Dynamic Repair Enzyme Endonuclease III

Endonuclease III (EndoIII), a key enzyme in the base excision repair (BER) pathway, contains a [4Fe4S] cluster that facilitates DNA repair through DNA-mediated charge transfer. Recent findings indicate that the redox state of this cluster influences EndoIII's binding affinity for DNA, modulating the enzyme's activity. In this study, we investigated the structural and electronic changes of the [4Fe4S] cluster upon binding to double-stranded DNA (dsDNA) using Fourier transform infrared spectroscopy, density functional theory calculations, and machine learning models. Our results reveal shifts in Fe-S bond vibrational modes, suggesting stabilization of the oxidized [4Fe4S] cluster in proximity to negatively charged DNA. A machine learning model, trained on the spectral features of the EndoIII/DNA complex, predicted the enzyme-DNA binding distance, providing further insights into the structural changes upon binding. We correlated the electrochemical stabilization potential of 150 mV in the [4Fe4S] cluster with the enzyme's DNA-binding properties, demonstrating how the cluster's redox state plays a crucial role in both structural stability and DNA repair.

Crystal Structure of a Thioredoxin-like Ferredoxin Encoded Within a Cobalamin Biosynthetic Operon of Rhodobacter capsulatus

Thioredoxin-like ferredoxin is a small homodimeric protein containing a [2Fe-2S] cluster in each monomer. It is only found in bacteria but its physiological function remains largely unknown. The cobalamin biosynthetic operon in the genome of the purple phototroph Rhodobacter capsulatus encodes a putative ferredoxin dubbed as CfrX. To characterize this protein, we cloned, expressed, purified, and crystalized the recombinant CfrX in the iron-sulfur cluster-bound state, and solved the structure at 2.1-Å resolution. Adopting a typical thioredoxin-like ferredoxin fold, a CfrX monomer binds one [2Fe-2S] cluster through four Cys residues located on two protruding loops. Unexpectedly, CfrX dimerizes in a previously unreported manner. With the structural information, we ascertained CfrX as a thioredoxin-like ferredoxin. While the precise function of CfrX in cobalamin biosynthesis is elusive, a link between CfrX and aerobic cobaltochelatase should exist due to the gene clustering pattern. We also discussed the possible relationship among CfrX, CobW, and CobNST with respect to the [2Fe-2S] cluster.

Design of a light and Ca2+ switchable organic-peptide hybrid

The design of organic-peptide hybrids has the potential to combine our vast knowledge of protein design with small molecule engineering to create hybrid structures with complex functions. Here, we describe the computational design of a photoswitchable Ca2+-binding organic-peptide hybrid. The designed molecule, designated Ca2+-binding switch (CaBS), combines an EF-hand motif from classical Ca2+-binding proteins such as calmodulin with a photoswitchable group that can be reversibly isomerized between a spiropyran (SP) and merocyanine (MC) state in response to different wavelengths of light. The MC/SP group acts both as a photoswitch as well as an optical sensor of Ca2+ binding. Photoconversion of the SP to the corresponding MC unmasks an acidic phenol, which CaBS uses as an integral part of both its Ca2+-binding site as well as its tertiary and quaternary structure. By design, the SP state of CaBS is monomeric, while the Ca2+-bound form of the MC state is an obligate dimer, with two Ca2+-binding sites formed at the interface of a domain-swapped dimer. Thus, light and Ca2+ were expected to serve as an "AND gate" that powers a change in backbone structure/dynamics, oligomerization state, and fluorescence properties of the designed molecule. CaBS was designed using Rosetta and molecular dynamics simulations, and experimentally characterized by nuclear magnetic resonance, isothermal titration calorimetry, and optical titrations. These data illustrate the potential of combining small molecule engineering with de novo protein design to develop sensors whose conformation, association state, and optical properties respond to multiple environmental cues.

Redox potential tuning by calcium ions in a novel c-type cytochrome from an anammox organism

The electrochemical potentials of redox-active proteins need to be tuned accurately to the correct values for proper biological function. Here, we describe a diheme cytochrome c with high heme redox potentials of about +350 mV, despite having a large overall negative charge, which typically reduces redox potentials. High-resolution crystal structures, spectroelectrochemical measurements, and high-end computational methods show how this is achieved: each heme iron has a calcium cation positioned next to it at a distance of only 6.9 Å, raising their redox potentials by several hundred millivolts through electrostatic interaction. We suggest that this has evolved to provide the protein with a high redox potential despite its large negative surface charge, which it likely requires for interactions with redox partners.

Selective Adsorption of Thiol-Containing Molecules on Copper Sulfide Surfaces via Molecule-Surface Disulfide Bridges

Recent results in the fields of nanoenhanced agriculture and expanding interest in prebiotic chemistry have placed increased emphasis on understanding the chemically selective interaction of small molecules with the surfaces of metal sulfides. We present an integrated experimental and computational study of the interaction of thiol-containing molecules with copper sulfide (covellite) surfaces in aqueous media. In situ Fourier-transform infrared (FTIR) measurements and ex situ X-ray photoelectron spectroscopy (XPS) measurements show that molecules bearing free thiol groups, including glutathione and cysteine, bind strongly to CuS (covellite) nanoparticles and to CuS (001) single crystals, while control studies show that similar molecules lacking the free thiol group exhibit much less binding. Additional experiments show that these thiol-containing molecules interact transiently with CuO nanoparticle surfaces but are readily removed by rinsing. The FTIR and XPS experiments demonstrate that adsorption of molecular thiols to CuS surfaces occurs in a chemically selective manner. Further experimental studies and density functional calculations show that the preferred mode of binding is through the surface S atoms, forming a Solid-S-S-Molecule disulfide linkage. While the role of disulfide linkages in controlling structure and function of proteins and other biomolecules is widely known, the formation of surface disulfide linkages as a motif for covalent molecular binding at surfaces has not been established previously.

Azurin a potent anticancer and antimicrobial agent isolated from a novel Pseudomonas aeruginosa strain

Azurin, a bacterial blue-copper protein, has garnered significant attention as a potential anticancer drug in recent years. Among twenty Pseudomonas aeruginosa isolates, we identified one isolate that demonstrated potent and remarkable azurin synthesis using the VITEK 2 system and 16S rRNA sequencing. The presence of the azurin gene was confirmed in the genomic DNA using specific oligonucleotide primers, and azurin expression was also detected in the synthesized cDNA, which revealed that the azurin expression is active. Furthermore, crude azurin protein was extracted, precipitated using 70% ammonium sulfate, dialyzed, and subjected to purification using carboxymethyl-Sephadex in affinity chromatography as a cheap method for purification. The partially purified azurin protein was characterized using polyacrylamide gel electrophoresis, energy-dispersive X-ray spectroscopy, Fourier-transform infrared spectroscopy, and nuclear magnetic resonance spectroscopy. Notably, qualitative elemental analysis by EDX showed the presence of copper and sulfur, corresponding to the copper-core and disulfide-bridge, respectively, in the purified azurin fraction. Moreover, FTIR spectroscopy revealed characteristic amide I and II absorption peaks (1500-1700 cm- 1), revealing the possible secondary structure of azurin. The results of NMR revealed the presence of characteristic amino acids such as methionine and cysteine, which confirmed the EDX results for sulfur-containing amino acids. Purified azurin exhibited antimicrobial activity against Staphylococcus aureus, Bacillus subtilis, Escherichia coli, and Klebsiella pneumoniae. Additionally, its anticancer properties were determined using the MTT assay and cell cycle analysis, revealing a preference for inhibiting the MCF7 breast cancer cell line where breast cancer is most common in Egypt. Overall, the research findings suggest that the local isolate, P. aeruginosa strain 105, could be a potential source of azurin protein for incorporation into cancer treatment strategies.

Imidazolate-Stabilized Cu(III): Dioxygen to Oxides at Type 3 Copper Sites

Imidazole ligation of metals through histidine is extensive among metalloproteins, yet the role of the imidazolate conjugate base is often neglected, despite its potential accessibility when bonded to an oxidized metal center. Using synthetic models of oxygenated tyrosinase enzymes ligated exclusively by monodentate imidazoles, we find that deprotonation of the μ2-η2:η2-peroxidodicopper(II) species triggers redox isomerization to an imidazolate-ligated bis(μ2-oxido)dicopper(III) species. Formal two-electron oxidation to Cu(III) remains biologically unprecedented, yet is effected readily by addition of base. Spectrophotometric titrations by UV/Visible/near-IR and copper K-edge X-ray absorption spectroscopies are interpreted most simply as two cooperative, 2H+ transformations in which the peroxide O-O is cleaved in the first step. Elaboration from simple imidazoles to a protected histidine extends this isomerization into an amino acid environment. The role of phenolate as a base suggests this four-electron reduction of O2 is energetically viable in a biological context and requires only two copper centers, which act as two-electron shuttles when imidazole deprotonation assists. This existential precedent of viable imidazolate intermediates invites speculation into an alternative mechanism for phenol hydroxylation not previously considered at Type 3 copper sites such as tyrosinases. Structural biological evidence suggests imidazolate ligation of copper may be more widespread than generally understood.

Strain-Induced Photochemical Opening of Ferrocene[6]cycloparaphenylene: Uncaging of Fe2+ with Green Light

We present the synthesis, structural analysis, and remarkable reactivity of the first carbon nanohoop that fully incorporates ferrocene in the macrocyclic backbone. The high strain imposed on the ferrocene by the curved nanohoop structure enables unprecedented photochemical reactivity of this otherwise photochemically inert metallocene complex. Visible light activation triggers a ring-opening of the nanohoop structure, fully dissociating the Fe-cyclopentadienyl bonds in the presence of 1,10-phenanthroline. This process uncages Fe2+ ions captured in the form of [Fe(phen)3]2+ complex in high chemical yield and can operate efficiently in a water-rich solvent with green light excitation. The measured quantum yields of [Fe(phen)3]2+ formation show that embedding ferrocene into a strained nanohoop boosts its photoreactivity by 3 orders of magnitude compared to an unstrained ferrocene macrocycle or ferrocene itself. Our data suggest that the dissociation occurs by intercepting the photoexcited triplet state of the nanohoop by a nucleophilic solvent or external ligand. The strategy portrayed in this work proposes that new, tunable reactivity of analogous metallamacrocycles can be achieved with spatial and temporal control, which will aid and abet the development of responsive materials for metal ion delivery and supramolecular, organometallic, or polymer chemistry.

"Cofactors" for Natural Products

Cofactors are non-protein entities necessary for proteins to operate. They provide "functional groups" beyond those of the 20 canonical amino acids and enable proteins to carry out more diverse functions. Such a viewpoint is rarely mentioned, if at all, when it comes to natural products and is the theme of this Concept. Even though the mechanisms of action (MOA) of only a few natural products are known to require cofactors, we believe that cofactor mediated MOA in natural products are far more prevalent than what we currently know. Bleomycin is a case in point. It binds iron cation to form a pseudoenzyme that generates reactive oxygen species. As another example, calcium cations induce laspartomycin to "fold" into the active conformation. Iron and calcium are bona fide cofactors for bleomycin and laspartomycin, respectively, as these natural products do not display their characteristic anticancer and antibacterial activities without Fe(II) and Ca(II). These types of cofactor mediated MOA in natural products were discovered mostly serendipitously, and being conscious of such a possibility is the first step toward identifying more novel chemistry that nature performs.

Electron transfer kinetics of a series of copper complexes with tripodal tetradentate guanidine quinolinyl ligands

Copper complexes of tripodal ligands have been used as model systems for electron transfer proteins for decades, displaying a broad range of electron self-exchange rates. We herein report a group of six tripodal tetradentate triarylamine ligands which display a varying number of guanidine and 2-methylquinolinyl moieties. Their corresponding Cu(I) complexes have been (re)synthesized and studied with regard to their electron transfer properties. While their molecular structures in the solid state are four-coordinate and display an uncommon umbrella distortion, DFT studies of the Cu(II) systems reveal that they gain an additional ligand in the form of a solvent molecule and exhibit a range of possible conformers that likely co-exist in thermal equilibrium. The redox-couples' electron self-exchange rates were analyzed using Marcus theory and vary over four orders of magnitude which cyclic voltammetry studies suggest to be due to a gated addition-oxidation electron transfer mechanism. This mechanism deviates from previously studied systems, likely due to the structural anomalies of the Cu(I) systems. This demonstrates that the chosen path of tripodal model systems can be influenced by molecular design.

Comparative analysis of Polyethylene-Degrading Laccases: Redox Properties and Enzyme-Polyethylene Interaction Mechanism

Laccases that oxidize low-density polyethylene (LDPE) represent a promising strategy for bioremediation purposes. To rationalize or optimize their PE-oxidative activity, two fundamental factors must be considered: the enzyme's redox potential and its binding affinity/mode towards LDPE. Indeed, a stable laccase-PE complex may facilitate a thermodynamically unfavorable electron transfer, even without redox mediators. In this study, we compared the redox potential and the LDPE-binding properties of three different PE-oxidizing laccases: a fungal high-redox potential laccase from Trametes versicolor, a bacterial low-redox potential laccase from Bacillus subtilis, and the recently characterized LMCO2 from Rhodococcus opacus R7. First we found that LMCO2 is a low-potential laccase (E°=413 mV), as reported in other bacterial variants. Using computational tools, we simulated the interactions of these laccases with a large LDPE model and highlighted the key role of hydrophobic residues surrounding the T1 site. Notably, a methionine-rich loop in LMCO2 appears to enhance the formation of a stable complex with LDPE, potentially facilitating electron transfer. This study underscores the necessity for comprehensive computational strategies to analyze enzyme-polymer interactions beyond simplistic models, uncovering critical binding determinants and informing future mutagenesis experiments, in order to enhance laccase performance and rationalize variations in enzymatic activity.

A Closer Look at the FeS Heme Bonds in Azotobacter vinelandii Bacterioferritin: QM/MM and Local Mode Analysis

Using the QM/MM methodology and a local mode analysis, we investigated a character and a strength of FeS bonds of heme groups in oxidized and reduced forms of Bacterioferritin from Azotobacter vinelandii. The strength of the FeS bonds was correlated with a bond length, an energy density at a bond critical point, and a charge difference of the F and S atoms. Changing the oxidation state from ferrous to ferric generally makes the FeS bonds weaker, longer, more covalent, and more polar. We also investigated the SFeS bond bending and found that the stronger FeS bond, generally makes the SFeS bond bending stiffer, which could play a key role in the balance between ferric and ferrous oxidation states and related biological activities.

Towards Bacterial Resistance via the Membrane Strategy: Enzymatic, Biophysical and Biomimetic Studies of the Lipid cis-trans Isomerase of Pseudomonas aeruginosa

The lipid cis-trans isomerase (Cti) is a periplasmic heme-c enzyme found in several bacteria including Pseudomonas aeruginosa, a pathogen known for causing nosocomial infections. This metalloenzyme catalyzes the cis-trans isomerization of unsaturated fatty acids in order to rapidly modulate membrane fluidity in response to stresses that impede bacterial growth. As a consequence, breakthrough in the elucidation of the mechanism of this metalloenzyme might lead to new strategies to combat bacterial antibiotic resistance. We report the first comprehensive biochemical, electrochemical and spectroscopic characterization of a Cti enzyme. This has been possible by the successful purification of Cti from P. aeruginosa (Pa-Cti) in favorable yields with enzyme activity of 0.41 μmol/min/mg when tested with palmitoleic acid. Through a synergistic approach involving enzymology, site-directed mutagenesis, Raman spectroscopy, Mössbauer spectroscopy and electrochemistry, we identified the heme coordination and redox state, pinpointing Met163 as the sixth ligand of the FeII of heme-c in Pa-Cti. Significantly, the development of an innovative assay based on liposomes demonstrated for the first time that Cti catalyzes cis-trans isomerization directly using phospholipids as substrates without the need of protein partners, answering the important question about the substrate of Cti within the bacterial membrane.

Steering acidic oxygen reduction selectivity of single-atom catalysts through the second sphere effect

Natural enzymes feature distinctive second spheres near their active sites, leading to exquisite catalytic reactivity. However, incumbent synthetic strategies offer limited versatility in functionalizing the second spheres of heterogeneous catalysts. Here, we prepare an enzyme-mimetic single Co-N4 atom catalyst with an elaborately configured pendant amine group in the second sphere via 1,3-dipolar cycloaddition, which switches the oxygen reduction reaction selectivity from the 4e- to the 2e- pathway under acidic conditions. Proton inventory studies and theoretical calculations reveal that the introduced pendant amine acts as a proton relay and promotes the protonation of *O2 to *OOH on the Co-N4 active site, facilitating H2O2 production. The second sphere-tailored Co-N4 sites reach optima H2O2 selectivity of 97% ± 1.13%, showing a 3.46-fold enhancement to bare Co-N4 catalyst (28% ± 1.75%). This work provides an appealed approach for enzyme-like catalyst design, bridging the gap between enzymatic and heterogeneous catalysis.

Machine Learning Guided Rational Design of a Non-Heme Iron-Based Lysine Dioxygenase Improves its Total Turnover Number

Highly selective C-H functionalization remains an ongoing challenge in organic synthetic methodologies. Biocatalysts are robust tools for achieving these difficult chemical transformations. Biocatalyst engineering has often required directed evolution or structure-based rational design campaigns to improve their activities. In recent years, machine learning has been integrated into these workflows to improve the discovery of beneficial enzyme variants. In this work, we combine a structure-based self-supervised machine learning framework, MutComputeX, with classical molecular dynamics simulations to down select mutations for rational design of a non-heme iron-dependent lysine dioxygenase, LDO. This approach consistently resulted in functional LDO mutants and circumvents the need for extensive study of mutational activity before-hand. Our rationally designed single mutants purified with up to 2-fold higher expression yields than WT and displayed higher total turnover numbers (TTN). Combining five such single mutations into a pentamutant variant, LPNYI LDO, leads to a 40 % improvement in the TTN (218±3) as compared to WT LDO (TTN=160±2). Overall, this work offers a low-barrier approach for those seeking to synergize machine learning algorithms with pre-existing protein engineering strategies.

A select thiosemicarbazone copper(II) complex induces apoptosis in gastric cancer and targets cancer stem cells reducing pluripotency markers

Copper(II)-based complexes are promising candidates as anti-cancer agents due to their ability to target cancer cells. Here we describe the synthesis and characterization of two copper(II) thiosemicarbazone complexes with the ligands 4-(dimethylamino)benzaldehyde N4-methylthiosemicarbazone (HL1) and 4-(dimethylamino)benzaldehyde N4-(4-(dimethylamino)phenylthiosemicarbazone (HL2) and general formula [Cu(L)2]. The complexes show stability in aqueous solution with 1 % of DMSO that allows to stablish its solution profile in biological buffers. Compound [Cu(L1)₂] lipophilicity was lower than [Cu(L2)₂], however, its solubility in biological buffer was not only better but also its DLS and ζ-potential data. In vitro studies demonstrate a higher cytotoxic effect of [Cu(L1)₂] on gastric cancer cells. The proposed mechanism of action consists in the generation of free radicals that induce DNA lesions, oxidative stress and ultimately autophagy deregulation and apoptosis. Additionally, [Cu(L1)₂] is equally active on gastric cancer stem cells and tumor cells resistant to cisplatin. More importantly, stem cells treated with [Cu(L1)₂] show a downregulation of pluripotency markers such as TWIST, NANOG and OCT4. Overall, our results with [Cu(L1)₂] prompt a significant advancement in the development of rational-designed pharmaceuticals for combating cancer.

Advanced strategies for enzyme-electrode interfacing in bioelectrocatalytic systems

Advances in protein engineering-enabled enzyme immobilization technologies have significantly improved enzyme-electrode wiring in enzymatic electrochemical systems, which harness natural biological machinery to either generate electricity or synthesize biochemicals. In this review, we provide guidelines for designing enzyme-electrodes, focusing on how performance variables change depending on electron transfer (ET) mechanisms. Recent advancements in enzyme immobilization technologies are summarized, highlighting their contributions to extending enzyme-electrode sustainability (up to months), enhancing biosensor sensitivity, improving biofuel cell performance, and setting a new benchmark for turnover frequency in bioelectrocatalysis. We also highlight state-of-the-art protein-engineering approaches that enhance enzyme-electrode interfacing through three key principles: protein-protein, protein-ligand, and protein-inorganic interactions. Finally, we discuss prospective avenues in strategic protein design for real-world applications.

Importance of Electron Correlation on the Geometry and Electronic Structure of [2Fe-2S] Systems: A Benchmark Study of the [Fe2S2(SCH3)4]2-,3-,4-, [Fe2S2(SCys)4]2-, [Fe2S2(S-p-tol)4]2-, and [Fe2S2(S-o-xyl)4]2- Complexes

Iron-sulfur clusters are crucial for biological electron transport and catalysis. Obtaining accurate geometries, energetics, manifolds of their excited electronic states, and reduction energies is important to understand their role in these processes. Using a [2Fe-2S] model complex with FeII and FeIII oxidation states, which leads to different charges, i.e., [Fe2S2(SMe)4]2-,3-,4-, we benchmarked a variety of computational methodologies ranging from density functional theory (DFT) to post-Hartree-Fock methods, including complete active space self-consistent field (CASSCF), multireference configuration interaction, the second-order N-electron valence state perturbation theory (NEVPT2), and the linearized integrand approximation of adiabatic connection (AC0) approaches. Additionally, we studied three experimentally well-characterized complexes, [Fe2S2(SCys)4]2-, [Fe2S2(S-o-tol)4]2-, and [Fe2S2(S-o-xyl)4]2-, via DFT methods. We conclude that the dynamic electron correlation is important for accurately predicting the geometry of these complexes. Broken symmetry (BS) DFT correctly predicts experimental geometries of low-spin multiplicity, while CASSCF does not. However, BS-DFT significantly overestimates the difference between the low- and high-spin electronic states for a given oxidation state. At the same time, CASSCF underestimates it but provides relative energies closer to the reference NEVPT2 results. Finally, AC0 provides energetics of NEVPT2 quality with the additional advantage of being able to use large CASSCF sizes. NEVPT2 gives the best estimates of the FeIII/FeIII → FeII/FeIII (4.27 eV) and FeII/FIII → FeII/FII (7.72 eV) reduction energies. The results provide insight into the electronic structure of these complexes and assist in the understanding of their physical properties.

Recycled lithium battery nanomaterials as a sustainable nanofertilizer: Reduced peanut allergenicity and improved seed quality

The rapidly increasing amount of end-of-life lithium iron phosphate (LiFePO4) batteries has raised significant environmental concerns. This study offers a strategy for a paradigm shift by transforming this growing waste into a valuable resource by recycling discarded LiFePO4 batteries and safely integrating the materials into sustainable agriculture. We used five types of LiFePO4 (10, 50 mg kg-1) applied to soil planted with peanuts in a full-culture experiment. Our results show that addition of <50 mg kg-1 of recycled nano-LiFePO4 (rn-LiFePO4) has a multifaceted positive impact on peanut because of sustainable release of nutrients and nano-specific effects, not only enhancing photosynthesis and root growth but also increasing yield by 22 %-34 % while simultaneously elevating seed nutritional quality. Moreover, a remarkable reduction (up to 99.78 % at 10 mg kg-1 rn-LiFePO4) in the expression of allergen genes was evident following exposure to LiFePO4, which showed a significant negative correlation with Fe content in the seeds. The decreased peanut allergen gene expression was mediated by a downregulation of metabolites associated with protein digestion and absorption. Furthermore, rhizosphere soil immune system enhancement may indirectly enhance immune responses to peanut allergy. This study suggests the significant potential of nanoscale LiFePO4 recycled from Li battery, including enhancing crop yield quality and mitigating peanut allergy concerns while simultaneously addressing a growing waste stream of concern.

Electron transfer in biological systems

Examples of how metalloproteins feature in electron transfer processes in biological systems are reviewed. Attention is focused on the electron transport chains of cellular respiration and photosynthesis, and on metalloproteins that directly couple electron transfer to a chemical reaction. Brief mention is also made of extracellular electron transport. While covering highlights of the recent and the current literature, this review is aimed primarily at introducing the senior undergraduate and the novice postgraduate student to this important aspect of bioinorganic chemistry.

The role of cystathionine β-synthase in cancer

Cystathionine β-synthase (CBS) occupies a key position as the initiating and rate-limiting enzyme in the sulfur transfer pathway and plays a vital role in health and disease. CBS is responsible for regulating the metabolism of cysteine, the precursor of glutathione (GSH), an important antioxidant in the body. Additionally, CBS is one of the three enzymes that produce hydrogen sulfide (H2S) in mammals through a variety of mechanisms. The dysregulation of CBS expression in cancer cells affects H2S production through direct or indirect pathways, thereby influencing cancer growth and metastasis by inducing angiogenesis, facilitating proliferation, migration, and invasion, modulating cellular energy metabolism, promoting cell cycle progression, and inhibiting apoptosis. It is noteworthy that CBS expression exhibits complex changes in different cancer models. In this paper, we focus on the CBS synthesis and metabolism, tissue distribution, potential mechanisms influencing tumor growth, and relevant signaling pathways. We also discuss the impact of pharmacological CBS inhibitors and silencing CBS in preclinical cancer models, supporting their potential as targeted cancer therapies.

Modification of MM force fields around heme-Fe in the CYP-ligand complex and ab initio FMO calculations for the complex

Cytochrome P450 (CYP) enzymes play essential roles in the synthesis and metabolic activation of physiologically active substances. CYP has a prosthetic heme (iron protoporphyrin IX) in its active center, where Fe ion (heme-Fe) is deeply involved in enzymatic reactions of CYP. To precisely describe the structure and electronic states around heme-Fe, we modified the force fields (FFs) around heme-Fe in molecular mechanics (MM) simulations and conducted ab initio fragment molecular orbital (FMO) calculations for the CYP-ligand complex. To describe the coordination bond between heme-Fe and its coordinated ligand (ketoconazole), we added FF between heme-Fe and the N atom of ketoconazole, and then the structure of the complex was optimized using the modified FF. Its adequacy was confirmed by comparing the MM-optimized structure with the X-ray crystal one of the CYP-ketoconazole complex. We also performed 100 ns molecular dynamics simulations and revealed that the coordination bonds around heme-Fe were maintained even at 310 K and that the CYP-ketoconazole structure was kept similar to the X-ray structure. Furthermore, we investigated the electronic states of the complex using the ab initio FMO method to identify the CYP residues and parts of ketoconazole that contribute to strong binding between CYP and ketoconazole. The present procedure of constructing FF between heme-Fe and ketoconazole can be applicable to other CYP-ligand complexes, and the modified FF can provide their accurate structures useful for predicting the specific interactions between CYP and its ligands.

Temperature-Dependent Characterization of Long-Range Conduction in Conductive Protein Fibers of Cable Bacteria

Multicellular cable bacteria display an exceptional form of biological conduction, channeling electric currents across centimeter distances through a regular network of protein fibers embedded in the cell envelope. The fiber conductivity is among the highest recorded for biomaterials, but the underlying mechanism of electron transport remains elusive. Here, we performed detailed characterization of the conductance from room temperature down to liquid helium temperature to attain insight into the mechanism of long-range conduction. A consistent behavior is seen within and across individual filaments. The conductance near room temperature reveals thermally activated behavior, yet with a low activation energy. At cryogenic temperatures, the conductance at moderate electric fields becomes virtually independent of temperature, suggesting that quantum vibrations couple to the charge transport through nuclear tunneling. Our data support an incoherent multistep hopping model within parallel conduction channels with a low activation energy and high transfer efficiency between hopping sites. This model explains the capacity of cable bacteria to transport electrons across centimeter-scale distances, thus illustrating how electric currents can be guided through extremely long supramolecular protein structures.

Single-cell transcriptional analysis of murine norovirus infection in a human intestinal cell line

Noroviruses are a major agent of acute gastroenteritis in humans, but host cell requirements for efficient replication in vitro have not been established. We engineered a human intestinal cell line (designated mCD300lf-hCaco2) expressing the murine norovirus (MNV) receptor, mouse CD300lf to become fully permissive for MNV replication. To explore the replicative machinery and host response of these cells, we performed a single-cell RNA sequencing (scRNA-seq) transcriptomics analysis of an MNV infection over time. Marked similarities were observed between certain global features of MNV infection in human cells compared to those previously reported in mouse cells by whole population transcriptomics such as downregulation of ribosome biogenesis, mitochondrial dysfunction, and cell cycle preference for G1. Our scRNA-seq analysis allowed further resolution of an infected cell population into distinct clusters with varying levels of viral RNA and interferon-stimulated gene ISG15 transcripts. Cells with high viral replication displayed downregulated ribosomal protein small (RPS) and large (RPL) genes and mitochondrial complexes I, III, IV, and V genes during exponential viral propagation. Ferritin subunit genes FTL and FTH1 were also downregulated during active MNV replication, suggesting that inhibition of iron metabolism may increase replication efficiency. Consistent with this, transcriptional activation of these genes with ferric ammonium citrate and overexpression of FTL lowered virus yields. Comparative studies of cells that support varying levels of norovirus replication efficiency, as determined by scRNA-seq may lead to improved human cell-based culture systems and effective viral interventions.IMPORTANCEHuman noroviruses cause acute gastroenteritis in all age groups. Vaccines and antiviral drugs are not yet available, in part, because it is difficult to propagate the viruses causing human disease in standard laboratory cell culture systems. In contrast, a norovirus found in mice [murine norovirus (MNV)] replicates efficiently in murine-based cell culture and has served as a model system. In this study, we established a new human intestinal cell line that was genetically modified to express the murine norovirus receptor so that the human cells became permissive to murine norovirus infection. We then defined the host response to MNV infection in the engineered human cell line at a single-cell resolution and identified cellular genes associated with the highest levels of MNV replication. This study may lead to the improvement of the current human norovirus cell culture systems and help to identify norovirus-host interactions that could be targeted for antiviral drugs.

Iron-sulfur cluster-dependent enzymes and molybdenum-dependent reductases in the anaerobic metabolism of human gut microbes

Metalloenzymes play central roles in the anaerobic metabolism of human gut microbes. They facilitate redox and radical-based chemistry that enables microbial degradation and modification of various endogenous, dietary, and xenobiotic nutrients in the anoxic gut environment. In this review, we highlight major families of iron-sulfur (Fe-S) cluster-dependent enzymes and molybdenum cofactor-containing enzymes used by human gut microbes. We describe the metabolic functions of 2-hydroxyacyl-CoA dehydratases, glycyl radical enzyme activating enzymes, Fe-S cluster-dependent flavoenzymes, U32 oxidases, and molybdenum-dependent reductases and catechol dehydroxylases in the human gut microbiota. We demonstrate the widespread distribution and prevalence of these metalloenzyme families across 5000 human gut microbial genomes. Lastly, we discuss opportunities for metalloenzyme discovery in the human gut microbiota to reveal new chemistry and biology in this important community.

Methanobactins: Structures, Biosynthesis, and Microbial Diversity

Methanobactins (Mbns) are ribosomally synthesized and posttranslationally modified peptide natural products released by methanotrophic bacteria under conditions of copper scarcity. Mbns bind Cu(I) with high affinity via nitrogen-containing heterocycles and thioamide groups installed on a precursor peptide, MbnA, by a core biosynthetic enzyme complex, MbnBC. Additional stabilizing modifications are enacted by other, less universal biosynthetic enzymes. Copper-loaded Mbn is imported into the cell by TonB-dependent transporters called MbnTs, and copper is mobilized by an unknown mechanism. The machinery to biosynthesize and transport Mbn is encoded in operons that are also found in the genomes of nonmethanotrophic bacteria. In this review, we provide an update on the state of the Mbn field, highlighting recent discoveries regarding Mbn structure, biosynthesis, and handling as well as the emerging roles of Mbns in the environment and their potential use as therapeutics.

Operando spectroscopy investigations of the redox reactions in heme and heme-proteins

Operando spectroscopic investigations during molecular redox processes provide unique insights into complex molecular structures and their transformations. Herein, a combination of a potentiodynamic method with spectroscopy has been employed to holistically investigate the structural transformations during Fe-redox (Fe3+ ↔ Fe2+) of hemin vis á vis heme-proteins, e.g. myoglobin (Mb), hemoglobin (Hb) and cytochrome-C (Cyt-C). The UV-vis findings reveal the formation of hemozoin (≈heme-dimer), which can be selectively prevented via a high concentration of strongly interacting ligands, e.g. histidine (the fifth coordinating ligand in the heme-based protein). On the other hand, methionine does not prevent the formation of hemozoin. In Mb, Hb, and Cyt-C, as the fifth coordination site is occupied by histidine, hemozoin formation is inhibited. During Fe3+→ Fe2+, operando circular dichroism exhibits a decrease in the initial helical component in Hb from nearly 40% to 28%, which is close to the initial helix component of Mb (≈25%), strongly indicating denaturation of the protein in the redox pathway. The rate of change of the helices versus potential is almost identical for Mb and Hb, but comparatively faster than Cyt-C. In addition, from the Raman bands of M-N dynamics and protein agglomeration, it is concluded that Cyt-C prefers to agglomerate in the 2+ state, whereas Mb/Hb in the 3+ state. In this report, the power of operando spectroscopy is utilized to unearth the dynamics of hemin and heme-based proteins for comprehending the underlying complexities associated with the molecular redox, which have deep implications in electrocatalysis, energy storage, and sensing.

Atomic-level design of biomimetic iron-sulfur clusters for biocatalysis

Designing biomimetic materials with high activity and customized biological functions by mimicking the central structure of biomolecules has become an important avenue for the development of medical materials. As an essential electron carrier, the iron-sulfur (Fe-S) clusters have the advantages of simple structure and high electron transport capacity. To rationally design and accurately construct functional materials, it is crucial to clarify the electronic structure and conformational relationships of Fe-S clusters. However, due to the complex catalytic mechanism and synthetic process in vitro, it is hard to reveal the structure-activity relationship of Fe-S clusters accurately. This review introduces the main structural types of Fe-S clusters and their catalytic mechanisms first. Then, several typical structural design strategies of biomimetic Fe-S clusters are systematically introduced. Furthermore, the development of Fe-S clusters in the biocatalytic field is enumerated, including tumor treatment, antibacterial, virus inhibition and plant photoprotection. Finally, the problems and development directions of Fe-S clusters are summarized. This review aims to guide people to accurately understand and regulate the electronic structure of Fe-S at the atomic level, which is of great significance for designing biomimetic materials with specific functions and expanding their applications in biocatalysis.

Iron-Sulfur Peptides Mimicking Ferredoxin for an Efficient Electron Transfer to Hydrogenase

In the green alga Chlamydomonas reinhardtii, hydrogenase HydA1 converts protons and electrons to H2 at the H-cluster, which includes a [4Fe-4S] cluster linked to a [2Fe] cluster. The yield of H2 is limited by the electron transfer to HydA1, mediated by the iron-sulfur unit of a photosynthetic electron transfer ferredoxin (PetF). In this study, I have investigated by molecular dynamics and the hybrid quantum mechanics/molecular mechanics method two canonical iron-sulfur peptides (PM1 and FBM) that hold potential as PetF replacements. Using a docking approach, I predict that the distance between the two iron-sulfur clusters in FBM/HydA1 is shorter than in PM1/HydA1, ensuring a greater electron transfer rate. This finding is in line with the reported higher H2 production rates for FBM/HydA1. I also show that the redox potential of these peptides, and therefore their electron transfer properties, can be changed by single-residue mutations in the secondary coordination sphere of their cluster. In particular, I have designed a PM1 variant that disrupts the hydrogen-bonding network between water and the cluster, shifting the redox potential negatively compared to PM1. These results will guide experiments aimed at replacing PetF with peptides that can unlock the biotechnological potential of the alga.

Additive Effects in Metal/Lewis Acid Cooperativity Assessed in a Tetrahedral Copper Hydrazine Complex Featuring an Appended Borane

Within metal/ligand cooperative systems employing acidic groups, studies that empirically assess distance relationships are needed to maximize cooperative interactions with substrates. We report the formation of two Cu(I)-N2H4 complexes using 1,4,7-triazacyclononane ligand frameworks bearing two tert-butyl groups and either a Lewis acidic trialkylborane or an inert alkyl group. Metal/Lewis acid cooperativity imparts heightened acidification of the hydrazine substrate and plays a key role in the release of substrate to a competitive Lewis acidic group.

Cryo-EM structure of HQNO-bound alternative complex III from the anoxygenic phototrophic bacterium Chloroflexus aurantiacus

Alternative complex III (ACIII) couples quinol oxidation and electron acceptor reduction with potential transmembrane proton translocation. It is compositionally and structurally different from the cytochrome bc1/b6f complexes but functionally replaces these enzymes in the photosynthetic and/or respiratory electron transport chains (ETCs) of many bacteria. However, the true compositions and architectures of ACIIIs remain unclear, as do their structural and functional relevance in mediating the ETCs. We here determined cryogenic electron microscopy structures of photosynthetic ACIII isolated from Chloroflexus aurantiacus (CaACIIIp), in apo-form and in complexed form bound to a menadiol analog 2-heptyl-4-hydroxyquinoline-N-oxide. Besides 6 canonical subunits (ActABCDEF), the structures revealed conformations of 2 previously unresolved subunits, ActG and I, which contributed to the complex stability. We also elucidated the structural basis of menaquinol oxidation and subsequent electron transfer along the [3Fe-4S]-6 hemes wire to its periplasmic electron acceptors, using electron paramagnetic resonance, spectroelectrochemistry, enzymatic analyses, and molecular dynamics simulations. A unique insertion loop in ActE was shown to function in determining the binding specificity of CaACIIIp for downstream electron acceptors. This study broadens our understanding of the structural diversity and molecular evolution of ACIIIs, enabling further investigation of the (mena)quinol oxidoreductases-evolved coupling mechanism in bacterial energy conservation.

Reversible Photochromic Phenomenon of Plasmonic Metal/Semiconductor Heterostructures via Photoinduced Electron Storage

The transfer and migration process of the photogenerated charge carriers in plasmonic metal/semiconductor heterostructures not only affects their photocatalytic performance but also triggers some captivating phenomena. Here, a reversible photochromic behavior is observed on the Au/CdS heterostructures when they are investigated as photocatalysts for hydrogen production. The photochromism takes place upon excitation of the CdS component, in which the photogenerated holes are rapidly consumed by ethanol, while the electrons are transferred and stored on the Au cores, resulting in the blue shift of their localized surface plasmon resonance. The colloidal solution can restore its initial color after pumping with air, and the photochromic behavior can be cycled five times without obvious degradation. The finding represents great progress toward the photochromic mechanism of metal/semiconductor heterostructures and also reveals the importance of understanding the dynamic process of the photogenerated charge carriers in these heterostructures.

Proteomic strategies to interrogate the Fe-S proteome

Iron‑sulfur (Fe-S) clusters, inorganic cofactors composed of iron and sulfide, participate in numerous essential redox, non-redox, structural, and regulatory biological processes within the cell. Though structurally and functionally diverse, the list of all proteins in an organism capable of binding one or more Fe-S clusters is referred to as its Fe-S proteome. Importantly, the Fe-S proteome is highly dynamic, with continuous cluster synthesis and delivery by complex Fe-S cluster biogenesis pathways. This cluster delivery is balanced out by processes that can result in loss of Fe-S cluster binding, such as redox state changes, iron availability, and oxygen sensitivity. Despite continued expansion of the Fe-S protein catalogue, it remains a challenge to reliably identify novel Fe-S proteins. As such, high-throughput techniques that can report on native Fe-S cluster binding are required to both identify new Fe-S proteins, as well as characterize the in vivo dynamics of Fe-S cluster binding. Due to the recent rapid growth in mass spectrometry, proteomics, and chemical biology, there has been a host of techniques developed that are applicable to the study of native Fe-S proteins. This review will detail both the current understanding of the Fe-S proteome and Fe-S cluster biology as well as describing state-of-the-art proteomic strategies for the study of Fe-S clusters within the context of a native proteome.

Theoretical insights into the reduction of Azurin metal site with unnatural amino acid substitutions

Copper-containing proteins play crucial roles in biological systems. Azurin is a copper-containing protein which has a Type 1 copper site that facilitates electron transfer in the cytochrome chain. Previous research has highlighted the significant impact of mutations in the axial Met121 of the copper site on the reduction potential. However, the mechanism of this regulation has not been fully established. In this study, we employed theoretical modeling to investigate the reduction of the Type 1 copper site, focusing on how unnatural amino acid substitutions at Met121 influence its behavior. Our findings demonstrated a strong linear correlation between electrostatic interactions and the reduction potential of the copper site, which indicates that the perturbation of the reduction potential is primarily influenced by electrostatic interactions between the metal ion and the ligating atom. Furthermore, we found that CF/π and CF…H interactions could induce subtle changes in geometry and hence impact the electronic properties of the systems under study. In addition, our calculations suggest the coordination mode and ion-ligand distance could significantly impact the reduction potential of a copper site. Overall, this study offers valuable insights into the structural and electronic properties of the Type 1 copper site, which could potentially guide the design of future artificial catalysts.

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.

Cellular Site-Specific Incorporation of Noncanonical Amino Acids in Synthetic Biology

Over the past two decades, genetic code expansion (GCE)-enabled methods for incorporating noncanonical amino acids (ncAAs) into proteins have significantly advanced the field of synthetic biology while also reaping substantial benefits from it. On one hand, they provide synthetic biologists with a powerful toolkit to enhance and diversify biological designs beyond natural constraints. Conversely, synthetic biology has not only propelled the development of ncAA incorporation through sophisticated tools and innovative strategies but also broadened its potential applications across various fields. This Review delves into the methodological advancements and primary applications of site-specific cellular incorporation of ncAAs in synthetic biology. The topics encompass expanding the genetic code through noncanonical codon addition, creating semiautonomous and autonomous organisms, designing regulatory elements, and manipulating and extending peptide natural product biosynthetic pathways. The Review concludes by examining the ongoing challenges and future prospects of GCE-enabled ncAA incorporation in synthetic biology and highlighting opportunities for further advancements in this rapidly evolving field.

Undulating Free Energy Landscapes Buffer Redox Chains from Environmental Fluctuations

Roller-coaster or undulating free energy landscapes, with alternating high and low potential cofactors, occur frequently in biological redox chains. Yet, there is little understanding of the possible advantages created by these landscapes. We examined the tetraheme subunit associated with Blastochloris viridis reaction centers, comparing the dynamics of the native protein and of hypothetical (in silico) mutants. We computed the variation in the total number of electrons in wild type (WT) and mutant tetrahemes connected to an electron reservoir in the presence of a time-varying potential, as a model for a fluctuating redox environment. We found that roller-coaster free energy landscapes buffer the redox cofactor populations from these fluctuations. The WT roller-coaster landscape slows forward and backward electron transfer in the face of fluctuations, and may offer the advantage of sustaining the reduction of essential cofactors, such as the chlorophyll special pair in photosynthesis, even though an undulating landscape introduces thermodynamically uphill steps in multistep redox chains.

Spectroscopically Validated pH-dependent MSOX Movies Provide Detailed Mechanism of Copper Nitrite Reductases

Copper nitrite reductases (CuNiRs) exhibit a strong pH dependence of their catalytic activity. Structural movies can be obtained by serially recording multiple structures (frames) from the same spot of a crystal using the MSOX serial crystallography approach. This method has been combined with on-line single crystal optical spectroscopy to capture the pH-dependent structural changes that accompany during turnover of CuNiRs from two Rhizobia species. The structural movies, initiated by the redox activation of a type-1 copper site (T1Cu) via X-ray generated photoelectrons, have been obtained for the substrate-free and substrate-bound states at low (high enzymatic activity) and high (low enzymatic activity) pH. At low pH, formation of the product nitric oxide (NO) is complete at the catalytic type-2 copper site (T2Cu) after a dose of 3 MGy (frame 5) with full bleaching of the T1Cu ligand-to-metal charge transfer (LMCT) 455 nm band (S(σ)Cys → T1Cu2+) which in itself indicates the electronic route of proton-coupled electron transfer (PCET) from T1Cu to T2Cu. In contrast at high pH, the changes in optical spectra are relatively small and the formation of NO is only observed in later frames (frame 15 in Br2DNiR, 10 MGy), consistent with the loss of PCET required for catalysis. This is accompanied by decarboxylation of the catalytic AspCAT residue, with CO2 trapped in the catalytic pocket.

57Fe nuclear resonance vibrational spectroscopic studies of tetranuclear iron clusters bearing terminal iron(iii)-oxido/hydroxido moieties

57Fe nuclear resonance vibrational spectroscopy (NRVS) has been applied to study a series of tetranuclear iron ([Fe4]) clusters based on a multidentate ligand platform (L3-) anchored by a 1,3,5-triarylbenzene linker and pyrazolate or (tertbutylamino)pyrazolate ligand (PzNH t Bu-). These clusters bear a terminal Fe(iii)-O/OH moiety at the apical position and three additional iron centers forming the basal positions. The three basal irons are connected with the apical iron center via a μ4-oxido ligand. Detailed vibrational analysis via density functional theory calculations revealed that strong NRVS spectral features below 400 cm-1 can be used as an oxidation state marker for the overall [Fe4] cluster core. The terminal Fe(iii)-O/OH stretching frequencies, which were observed in the range of 500-700 cm-1, can be strongly modulated (energy shifts of 20-40 cm-1 were observed) upon redox events at the three remote basal iron centers of the [Fe4] cluster without the change of the terminal Fe(iii) oxidation state and its coordination environment. Therefore, the current study provides a quantitative vibrational analysis of how the remote iron centers within the same iron cluster exert exquisite control of the chemical reactivities and thermodynamic properties of the specific iron site that is responsible for small molecule activation.

Filamentous morphology engineering of bacteria by iron metabolism modulation through MagR expression

The morphology is the consequence of evolution and adaptation. Escherichia coli is rod-shaped bacillus with regular dimension of about 1.5 μm long and 0.5 μm wide. Many shape-related genes have been identified and used in morphology engineering of this bacteria. However, little is known about if specific metabolism and metal irons could modulate bacteria morphology. Here in this study, we discovered filamentous shape change of E. coli cells overexpressing pigeon MagR, a putative magnetoreceptor and extremely conserved iron-sulfur protein. Comparative transcriptomic analysis strongly suggested that the iron metabolism change and iron accumulation due to the overproduction of MagR was the key to the morphological change. This model was further validated, and filamentous morphological change was also achieved by supplement E. coli cells with iron in culture medium or by increase the iron uptake genes such as entB and fepA. Our study extended our understanding of morphology regulation of bacteria, and may also serves as a prototype of morphology engineering by modulating the iron metabolism.

Influence of Copper on Oleidesulfovibrio alaskensis G20 Biofilm Formation

Copper is known to have toxic effects on bacterial growth. This study aimed to determine the influence of copper ions on Oleidesulfovibrio alaskensis G20 biofilm formation in a lactate-C medium supplemented with variable copper ion concentrations. OA G20, when grown in media supplemented with high copper ion concentrations of 5, 15, and 30 µM, exhibited inhibited growth in its planktonic state. Conversely, under similar copper concentrations, OA G20 demonstrated enhanced biofilm formation on glass coupons. Microscopic studies revealed that biofilms exposed to copper stress demonstrated a change in cellular morphology and more accumulation of carbohydrates and proteins than controls. Consistent with these findings, sulfur (dsrA, dsrB, sat, aprA) and electron transport (NiFeSe, NiFe, ldh, cyt3) genes, polysaccharide synthesis (poI), and genes involved in stress response (sodB) were significantly upregulated in copper-induced biofilms, while genes (ftsZ, ftsA, ftsQ) related to cellular division were negatively regulated compared to controls. These results indicate that the presence of copper ions triggers alterations in cellular morphology and gene expression levels in OA G20, impacting cell attachment and EPS production. This adaptation, characterized by increased biofilm formation, represents a crucial strategy employed by OA G20 to resist metal ion stress.

Glycopolypeptide Coordinated Nanovaccine: Fabrication, Characterization, and Antitumor Immune Response

Cancer nanovaccine is a frontier immunotherapy strategy, in which the delivery carrier can protect antigen and adjuvant from degradation, increase blood circulation half-life, and improve antigen permeability and presentation, thus enhancing the security and potency of nanovaccine. To address the barriers of antigen delivery, we design and fabricate a kind of intracellular pH-sensitive glycopolypeptide coordinated nanovaccine (OVA-HPGM-Mn) with ∼30% loading capacity of ovalbumin (OVA). The nanovaccine OVA-HPGM-Mn could specifically deliver antigen to dendritic cells (DCs) and effectively escape from endolysosomes to cytoplasm after 6 h of incubation, while the blank counterpart HPGM-Mn acted as an adjuvant to promote DCs maturation and increase the percentage of maturated cells to 26.5% from 11.8% in vitro. Furthermore, the mannosylated polypeptide nanovaccine prolonged the retention time of OVA for 72 h to facilitate 29.5% DCs maturation in lymph nodes, activated 48.8% CD8+T cells in spleen, increased the CD8+/CD4+T cell ratio twice to 1.06, and upregulated the levels of pro-inflammatory cytokines including TNF-α, IFN-γ, and IL-6, thus inhibiting the tumor growth of ∼80%. Consequently, this work provides a versatile strategy for the fabrication of glycosylated polypeptide coordinated nanomaterials for antigen delivery and cancer immunotherapy.

Biocompatible Co-organic Composite Thin Film Deposited by VHF Plasma-Enhanced Atomic Layer Deposition at a Low Temperature

Although metal-organic thin films are required for many biorelated applications, traditional deposition methods have proven challenging in preparing these composite materials. Here, a Co-organic composite thin film was prepared by plasma-enhanced atomic layer deposition (PEALD) with cobaltocene (Co(Cp)2) on polydimethylsiloxane (PDMS), using two very high frequency (VHF) NH3 plasmas (60 and 100 MHz), for use as a tissue culture scaffold. VHF PEALD was employed to reduce the temperature and control the thickness and composition. In the result of the VHF PEALD process, the Young's modulus of the Co-organic composite thin film ranged from 82.0 ± 28.6 to 166.0 ± 15.2 MPa, which is similar to the Young's modulus of soft tissues. In addition, the deposited Co ion on the Co-organic composite thin film was released into the cell culture media under a nontoxic level for the biological environment. The proliferation of both L929, the mouse fibroblast cell line, and C2C12, the mouse myoblast cell line, increased to 164.9 ± 23.4% during 7 days of incubation. Here, this novel bioactive Co-organic composite thin film on an elastic PDMS substrate enhanced the proliferation of L929 and C2C12 cell lines, thereby expanding the application range of VHF PEALD in biological fields.

Functional metalloenzymes based on myoglobin and neuroglobin that exploit covalent interactions

Globins, such as myoglobin (Mb) and neuroglobin (Ngb), are ideal protein scaffolds for the design of functional metalloenzymes. To date, numerous approaches have been developed for enzyme design. This review presents a summary of the progress made in the design of functional metalloenzymes based on Mb and Ngb, with a focus on the exploitation of covalent interactions, including coordination bonds and covalent modifications. These include the construction of a metal-binding site, the incorporation of a non-native metal cofactor, the formation of Cys/Tyr-heme covalent links, and the design of disulfide bonds, as well as other Cys-covalent modifications. As exemplified by recent studies from our group and others, the designed metalloenzymes have potential applications in biocatalysis and bioconversions. Furthermore, we discuss the current trends in the design of functional metalloenzymes and highlight the importance of covalent interactions in the design of functional metalloenzymes.

Position of substituents directs the electron transfer properties of entatic state complexes: new insights from guanidine-quinoline copper complexes

In a previous study, we showed that the properties and the ability as an entatic state model of copper guanidine quinoline complexes are significantly influenced by a methyl or methyl ester substituent in the 2-position. To prove the importance of the 2-position of the substituent, two novel guanidine quinoline ligands with a methyl or methyl ester substituent in the 4-position and the corresponding copper complexes were synthesized and characterized in this study. The influence of the substituent position on the copper complexes was investigated with various experimental and theoretical methods. The molecular structures of the copper complexes were examined in the solid state by single-crystal X-ray diffraction (SCXRD) and by density functional theory (DFT) calculations indicating a strong dependency on the substituent position compared to the systems substituted in the 2-position from the previous study. Further, the significantly different influence on the donor properties in dependency on the substituent position was analyzed with natural bond orbital (NBO) calculations. By the determination of the redox potentials, the impact on the electrochemical stabilization was examined. With regard to further previously analyzed guanidine quinoline copper complexes, the electrochemical stabilization was correlated with the charge-transfer energies calculated by NBO analysis and ground state energies, revealing the substituent influence and enabling a comparatively easy and accurate possibility for the theoretical calculation of the relative redox potential. Finally, the electron transfer properties were quantified by determining the electron self-exchange rates via the Marcus theory and by theoretical calculation of the reorganization energies via Nelsen's four-point method. The results gave important insights into the dependency between the ability of the copper complexes as entatic state model and the type and position of the substituent.