Small-Molecule Tunnels in Metalloenzymes Viewed as Extensions of the Active Site

Characterization of the Bottlenecks and Pathways for Inhibitor Dissociation from [NiFe] Hydrogenase

[NiFe] hydrogenases can act as efficient catalysts for hydrogen oxidation and biofuel production. However, some [NiFe] hydrogenases are inhibited by gas molecules present in the environment, such as O2 and CO. One strategy to engineer [NiFe] hydrogenases and achieve O2- and CO-tolerant enzymes is by introducing point mutations to block the access of inhibitors to the catalytic site. In this work, we characterized the unbinding pathways of CO in the complex with the wild-type and 10 different mutants of [NiFe] hydrogenase from Desulfovibrio fructosovorans using τ-random accelerated molecular dynamics (τRAMD) to enhance the sampling of unbinding events. The ranking provided by the relative residence times computed with τRAMD is in agreement with experiments. Extensive data analysis of the simulations revealed that from the two bottlenecks proposed in previous studies for the transit of gas molecules (residues 74 and 122 and residues 74 and 476), only one of them (residues 74 and 122) effectively modulates diffusion and residence times for CO. We also computed pathway probabilities for the unbinding of CO, O2, and H2 from the wild-type [NiFe] hydrogenase, and we observed that while the most probable pathways are the same, the secondary pathways are different. We propose that introducing mutations to block the most probable paths, in combination with mutations to open the main secondary path used by H2, can be a feasible strategy to achieve CO and O2 resistance in the [NiFe] hydrogenase from Desulfovibrio fructosovorans.

Coupling CO2 Reduction and Acetyl-CoA Formation: The Role of a CO Capturing Tunnel in Enzymatic Catalysis

The bifunctional CO-dehydrogenase/acetyl-CoA synthase (CODH/ACS) complex couples the reduction of CO2 to the condensation of CO with a methyl moiety and CoA to acetyl-CoA. Catalysis occurs at two sites connected by a tunnel transporting the CO. In this study, we investigated how the bifunctional complex and its tunnel support catalysis using the CODH/ACS from Carboxydothermus hydrogenoformans as a model. Although CODH/ACS adapted to form a stable bifunctional complex with a secluded substrate tunnel, catalysis and CO transport is even more efficient when two monofunctional enzymes are coupled. Efficient CO channeling appears to be ensured by hydrophobic binding sites for CO, which act in a bucket-brigade fashion rather than as a simple tube. Tunnel remodeling showed that opening the tunnel increased activity but impaired directed transport of CO. Constricting the tunnel impaired activity and CO transport, suggesting that the tunnel evolved to sequester CO rather than to maximize turnover.

Contact-Electro-Catalysis for Direct Oxidation of Methane under Ambient Conditions

The conversion of methane under ambient conditions has attracted significant attention. Although advancements have been made using active oxygen species from photo- and electro- chemical processes, challenges such as complex catalyst design, costly oxidants, and unwanted byproducts remain. This study exploits the concept of contact-electro-catalysis, initiating chemical reactions through charge exchange at a solid-liquid interface, to report a novel process for directly converting methane under ambient conditions. Utilizing the electrification of commercially available Fluorinated Ethylene Propylene (FEP) with water under ultrasound, we demonstrate how this interaction promote the activation of methane and oxygen molecules. Our results show that the yield of HCHO and CH3OH can reach 467.5 and 151.2 μmol ⋅ gcat -1, respectively. We utilized electron paramagnetic resonance (EPR) to confirm the evolution of hydroxyl radicals (⋅OH) and superoxide radicals (⋅OOH). Isotope mass spectrometry (MS) was employed to analyze the elemental origin of CH3OH, which can be further oxidized to HCHO. Additionally, we conducted density functional theory (DFT) simulations to assess the reaction energies of FEP with H2O, O2, and CH4 under these conditions. The implications of this methodology, with its potential applicability to a wider array of gas-phase catalytic reactions, underscore a significant advance in catalysis.

The thin line between monooxygenases and peroxygenases. P450s, UPOs, MMOs, and LPMOs: A brick to bridge fields of expertise

Many scientific fields, although driven by similar purposes and dealing with similar technologies, often appear so isolated and far from each other that even the vocabularies to describe the very same phenomenon might differ. Concerning the vast field of biocatalysis, a special role is played by those redox enzymes that employ oxygen-based chemistry to unlock transformations otherwise possible only with metal-based catalysts. As such, greener chemical synthesis methods and environmentally-driven biotechnological approaches were enabled over the last decades by the use of several enzymes and ultimately resulted in the first industrial applications. Among what can be called today the environmental biorefinery sector, biomass transformation, greenhouse gas reduction, bio-gas/fuels production, bioremediation, as well as bulk or fine chemicals and even pharmaceuticals manufacturing are all examples of fields in which successful prototypes have been demonstrated employing redox enzymes. In this review we decided to focus on the most prominent enzymes (MMOs, LPMO, P450 and UPO) capable of overcoming the ∼100 kcal mol-1 barrier of inactivated CH bonds for the oxyfunctionalization of organic compounds. Harnessing the enormous potential that lies within these enzymes is of extreme value to develop sustainable industrial schemes and it is still deeply coveted by many within the aforementioned fields of application. Hence, the ambitious scope of this account is to bridge the current cutting-edge knowledge gathered upon each enzyme. By creating a broad comparison, scientists belonging to the different fields may find inspiration and might overcome obstacles already solved by the others. This work is organised in three major parts: a first section will be serving as an introduction to each one of the enzymes regarding their structural and activity diversity, whereas a second one will be encompassing the mechanistic aspects of their catalysis. In this regard, the machineries that lead to analogous catalytic outcomes are depicted, highlighting the major differences and similarities. Finally, a third section will be focusing on the elements that allow the oxyfunctionalization chemistry to occur by delivering redox equivalents to the enzyme by the action of diverse redox partners. Redox partners are often overlooked in comparison to the catalytic counterparts, yet they represent fundamental elements to better understand and further develop practical applications based on mono- and peroxygenases.

Direct Methane Oxidation by Copper- and Iron-Dependent Methane Monooxygenases

Methane is a potent greenhouse gas that contributes significantly to climate change and is primarily regulated in Nature by methanotrophic bacteria, which consume methane gas as their source of energy and carbon, first by oxidizing it to methanol. The direct oxidation of methane to methanol is a chemically difficult transformation, accomplished in methanotrophs by complex methane monooxygenase (MMO) enzyme systems. These enzymes use iron or copper metallocofactors and have been the subject of detailed investigation. While the structure, function, and active site architecture of the copper-dependent particulate methane monooxygenase (pMMO) have been investigated extensively, its putative quaternary interactions, regulation, requisite cofactors, and mechanism remain enigmatic. The iron-dependent soluble methane monooxygenase (sMMO) has been characterized biochemically, structurally, spectroscopically, and, for the most part, mechanistically. Here, we review the history of MMO research, focusing on recent developments and providing an outlook for future directions of the field. Engineered biological catalysis systems and bioinspired synthetic catalysts may continue to emerge along with a deeper understanding of the molecular mechanisms of biological methane oxidation. Harnessing the power of these enzymes will necessitate combined efforts in biochemistry, structural biology, inorganic chemistry, microbiology, computational biology, and engineering.

Tunnel engineering of gas-converting enzymes for inhibitor retardation and substrate acceleration

Carbon monoxide dehydrogenase (CODH), formate dehydrogenase (FDH), hydrogenase (H2ase), and nitrogenase (N2ase) are crucial enzymatic catalysts that facilitate the conversion of industrially significant gases such as CO, CO2, H2, and N2. The tunnels in the gas-converting enzymes serve as conduits for these low molecular weight gases to access deeply buried catalytic sites. The identification of the substrate tunnels is imperative for comprehending the substrate selectivity mechanism underlying these gas-converting enzymes. This knowledge also holds substantial value for industrial applications, particularly in addressing the challenges associated with separation and utilization of byproduct gases. In this comprehensive review, we delve into the emerging field of tunnel engineering, presenting a range of approaches and analyses. Additionally, we propose methodologies for the systematic design of enzymes, with the ultimate goal of advancing protein engineering strategies.

Selective methane oxidation by molecular iron catalysts in aqueous medium

Using natural gas as chemical feedstock requires efficient oxidation of the constituent alkanes-and primarily methane1,2. The current industrial process uses steam reforming at high temperatures and pressures3,4 to generate a gas mixture that is then further converted into products such as methanol. Molecular Pt catalysts5-7 have also been used to convert methane to methanol8, but their selectivity is generally low owing to overoxidation-the initial oxidation products tend to be easier to oxidize than methane itself. Here we show that N-heterocyclic carbene-ligated FeII complexes with a hydrophobic cavity capture hydrophobic methane substrate from an aqueous solution and, after oxidation by the Fe centre, release a hydrophilic methanol product back into the solution. We find that increasing the size of the hydrophobic cavities enhances this effect, giving a turnover number of 5.0 × 102 and a methanol selectivity of 83% during a 3-h methane oxidation reaction. If the transport limitations arising from the processing of methane in an aqueous medium can be overcome, this catch-and-release strategy provides an efficient and selective approach to using naturally abundant alkane resources.

Bio-Inspired Iron Pentadentate Complexes as Dioxygen Activators in the Oxidation of Cyclohexene and Limonene

The use of dioxygen as an oxidant in fine chemicals production is an emerging problem in chemistry for environmental and economical reasons. In acetonitrile, the [(N4Py)Fe^II]²⁺ complex, [N4Py-N,N-bis(2-pyridylmethyl)-N-(bis-2-pyridylmethyl)amine] in the presence of the substrate activates dioxygen for the oxygenation of cyclohexene and limonene. Cyclohexane is oxidized mainly to 2-cyclohexen-1-one, and 2-cyclohexen-1-ol, cyclohexene oxide is formed in much smaller amounts. Limonene gives as the main products limonene oxide, carvone, and carveol. Perillaldehyde and perillyl alcohol are also present in the products but to a lesser extent. The investigated system is twice as efficient as the [(bpy)₂Fe^II]²⁺/O₂/cyclohexene system and comparable to the [(bpy)₂Mn^II]²⁺/O₂/limonene system. Using cyclic voltammetry, it has been shown that, when the catalyst, dioxgen, and substrate are present simultaneously in the reaction mixture, the iron(IV) oxo adduct [(N4Py)Fe^IV=O]²⁺ is formed, which is the oxidative species. This observation is supported by DFT calculations.

Metallocavitins as Advanced Enzyme Mimics and Promising Chemical Catalysts

The supramolecular approach is becoming increasingly dominant in biomimetics and chemical catalysis due to the expansion of the enzyme active center idea, which now includes binding cavities (hydrophobic pockets), channels and canals for transporting substrates and products. For a long time, the mimetic strategy was mainly focused on the first coordination sphere of the metal ion. Understanding that a highly organized cavity-like enzymatic pocket plays a key role in the sophisticated functionality of enzymes and that the activity and selectivity of natural metalloenzymes are due to the effects of the second coordination sphere, created by the protein framework, opens up new perspectives in biomimetic chemistry and catalysis. There are two main goals of mimicking enzymatic catalysis: (1) scientific curiosity to gain insight into the mysterious nature of enzymes, and (2) practical tasks of mankind: to learn from nature and adopt from its many years of evolutionary experience. Understanding the chemistry within the enzyme nanocavity (confinement effect) requires the use of relatively simple model systems. The performance of the transition metal catalyst increases due to its retention in molecular nanocontainers (cavitins). Given the greater potential of chemical synthesis, it is hoped that these promising bioinspired catalysts will achieve catalytic efficiency and selectivity comparable to and even superior to the creations of nature. Now it is obvious that the cavity structure of molecular nanocontainers and the real possibility of modifying their cavities provide unlimited possibilities for simulating the active centers of metalloenzymes. This review will focus on how chemical reactivity is controlled in a well-defined cavitin nanospace. The author also intends to discuss advanced metal–cavitin catalysts related to the study of the main stages of artificial photosynthesis, including energy transfer and storage, water oxidation and proton reduction, as well as highlight the current challenges of activating small molecules, such as H2O, CO2, N2, O2, H2, and CH4.

Engineering Rieske oxygenase activity one piece at a time

Enzyme engineering plays a central role in the development of biocatalysts for biotechnology, chemical and pharmaceutical manufacturing, and environmental remediation. Rational design of proteins has historically relied on targeting active site residues to confer a protein with desirable catalytic properties. However, additional "hotspots" are also known to exist beyond the active site. Structural elements such as subunit-subunit interactions, entrance tunnels, and flexible loops influence enzyme catalysis and serve as potential "hotspots" for engineering. For the Rieske oxygenases, which use a Rieske cluster and mononuclear iron center to catalyze a challenging set of reactions, these outside of the active site regions are increasingly being shown to drive catalytic outcomes. Therefore, here, we highlight recent work on structurally characterized Rieske oxygenases that implicates architectural pieces inside and outside of the active site as key dictators of catalysis, and we suggest that these features may warrant attention in efforts aimed at Rieske oxygenase engineering.

The Mechanism of Biochemical NO‐Sensing: Insights from Computational Chemistry

The binding of small gas molecules such as NO and CO plays a major role in the signaling routes of the human body. The sole NO‐receptor in humans is soluble guanylyl cyclase (sGC) – a histidine‐ligated heme protein, which, upon NO binding, activates a downstream signaling cascade. Impairment of NO‐signaling is linked, among others, to cardiovascular and inflammatory diseases. In the present work, we use a combination of theoretical tools such as MD simulations, high‐level quantum chemical calculations and hybrid QM/MM methods to address various aspects of NO binding and to elucidate the most likely reaction paths and the potential intermediates of the reaction. As a model system, the H‐NOX protein from Shewanella oneidensis (So H‐NOX) homologous to the NO‐binding domain of sGC is used. The signaling route is predicted to involve NO binding to form a six‐coordinate intermediate heme‐NO complex, followed by relatively facile His decoordination yielding a five‐coordinate adduct with NO on the distal side with possible isomerization to the proximal side through binding of a second NO and release of the first one. MD simulations show that the His sidechain can quite easily rotate outward into solvent, with this motion being accompanied in our simulations by shifts in helix positions that are consistent with this decoordination leading to significant conformational change in the protein.

Second and Outer Coordination Sphere Effects in Nitrogenase, Hydrogenase, Formate Dehydrogenase, and CO Dehydrogenase

Gases like H₂, N₂, CO₂, and CO are increasingly recognized as critical feedstock in "green" energy conversion and as sources of nitrogen and carbon for the agricultural and chemical sectors. However, the industrial transformation of N₂, CO₂, and CO and the production of H₂ require significant energy input, which renders processes like steam reforming and the Haber-Bosch reaction economically and environmentally unviable. Nature, on the other hand, performs similar tasks efficiently at ambient temperature and pressure, exploiting gas-processing metalloenzymes (GPMs) that bind low-valent metal cofactors based on iron, nickel, molybdenum, tungsten, and sulfur. Such systems are studied to understand the biocatalytic principles of gas conversion including N₂ fixation by nitrogenase and H₂ production by hydrogenase as well as CO₂ and CO conversion by formate dehydrogenase, carbon monoxide dehydrogenase, and nitrogenase. In this review, we emphasize the importance of the cofactor/protein interface, discussing how second and outer coordination sphere effects determine, modulate, and optimize the catalytic activity of GPMs. These may comprise ionic interactions in the second coordination sphere that shape the electron density distribution across the cofactor, hydrogen bonding changes, and allosteric effects. In the outer coordination sphere, proton transfer and electron transfer are discussed, alongside the role of hydrophobic substrate channels and protein structural changes. Combining the information gained from structural biology, enzyme kinetics, and various spectroscopic techniques, we aim toward a comprehensive understanding of catalysis beyond the first coordination sphere.

Metallocavitins as Promising Industrial Catalysts: Recent Advances

The energy, material, and environmental problems of society require clean materials and impose an urgent need to develop effective chemical processes for obtaining and converting energy to ensure further sustainable development. To solve these challenges, it is necessary, first of all, to learn solar energy harvesting through the development of artificial photosynthesis. In our planet, water, carbon dioxide, and methane are such affordable and inexhaustible clean materials. Electro/photocatalytic water splitting, and also CO₂ and CH₄ transforming into valuable products, requires the search for relevant efficient and selective processes and catalysts. Of great interest is the emerging new generation of bioinspired catalysts—metallocavitins (MCs). MCs are attracting increasing attention of researchers as advanced models of metalloenzymes, whose efficiency and selectivity are well known. The primary field of MC application is fine organic synthesis and enantioselective catalysis. On the other hand, MCs demonstrate high activity for energy challenging reactions involving small gas molecules and high selectivity for converting them into valuable products. This mini-review will highlight some recent advances in the synthesis of organic substances using MCs, but its main focus will be on the rapid development of advanced catalysts for the activation of small molecules, such as H₂O, CO₂, and CH₄, and the prospects for creating related technological processes in the future.

Design principles for site-selective hydroxylation by a Rieske oxygenase

Rieske oxygenases exploit the reactivity of iron to perform chemically challenging C–H bond functionalization reactions. Thus far, only a handful of Rieske oxygenases have been structurally characterized and remarkably little information exists regarding how these enzymes use a common architecture and set of metallocenters to facilitate a diverse range of reactions. Herein, we detail how two Rieske oxygenases SxtT and GxtA use different protein regions to influence the site-selectivity of their catalyzed monohydroxylation reactions. We present high resolution crystal structures of SxtT and GxtA with the native β-saxitoxinol and saxitoxin substrates bound in addition to a Xenon-pressurized structure of GxtA that reveals the location of a substrate access tunnel to the active site. Ultimately, this structural information allowed for the identification of six residues distributed between three regions of SxtT that together control the selectivity of the C–H hydroxylation event. Substitution of these residues produces a SxtT variant that is fully adapted to exhibit the non-native site-selectivity and substrate scope of GxtA. Importantly, we also found that these selectivity regions are conserved in other structurally characterized Rieske oxygenases, providing a framework for predictively repurposing and manipulating Rieske oxygenases as biocatalysts.

SxtT and GxtA are Rieske oxygenases that are involved in paralytic shellfish toxin biosynthesis and catalyze monohydroxylation reactions at different positions on the toxin scaffold. Here, the authors present crystal structures of SxtT and GxtA with the native substrates β-saxitoxinol and saxitoxin as well as a Xenon-pressurized structure of GxtA, which reveal a substrate access tunnel to the active site. Through structure-based mutagenesis studies the authors identify six residues in three different protein regions that determine the substrate specificity and site selectivity of SxtT and GxtA. These findings will aid the rational engineering of other Rieske oxygenases.

X-ray Crystal Structures of Methane Monooxygenase Hydroxylase Complexes with Variants of Its Regulatory Component: Correlations with Altered Reaction Cycle Dynamics

Full activity of soluble methane monooxygenase (sMMO) depends upon the formation of a 1:1 complex of the regulatory protein MMOB with each alpha subunit of the (αβγ)₂ hydroxylase, sMMOH. Previous studies have shown that mutations in the core region of MMOB and in the N- and C-termini cause dramatic changes in the rate constants for steps in the sMMOH reaction cycle. Here, X-ray crystal structures are reported for the sMMOH complex with two double variants within the core region of MMOB, DBL1 (N107G/S110A), and DBL2 (S109A/T111A), as well as two variants in the MMOB N-terminal region, H33A and H5A. DBL1 causes a 150-fold decrease in the formation rate constant of the reaction cycle intermediate P, whereas DBL2 accelerates the reaction of the dinuclear Fe(IV) intermediate Q with substrates larger than methane by three- to fourfold. H33A also greatly slows P formation, while H5A modestly slows both formation of Q and its reactions with substrates. Complexation with DBL1 or H33A alters the position of sMMOH residue R245, which is part of a conserved hydrogen-bonding network encompassing the active site diiron cluster where P is formed. Accordingly, electron paramagnetic resonance spectra of sMMOH:DBL1 and sMMOH:H33A complexes differ markedly from that of sMMOH:MMOB, showing an altered electronic environment. In the sMMOH:DBL2 complex, the position of M247 in sMMOH is altered such that it enlarges a molecular tunnel associated with substrate entry into the active site. The H5A variant causes only subtle structural changes despite its kinetic effects, emphasizing the precise alignment of sMMOH and MMOB required for efficient catalysis.

Ferritin-Like Proteins: A Conserved Core for a Myriad of Enzyme Complexes

Ferritin-like proteins share a common fold, a four α-helix bundle core, often coordinating a pair of metal ions. Although conserved, the ferritin fold permits a diverse set of reactions, and is central in a multitude of macromolecular enzyme complexes. Here, we emphasize this diversity through three members of the ferritin-like superfamily: the soluble methane monooxygenase, the class I ribonucleotide reductase and the aldehyde deformylating oxygenase. They all rely on dinuclear metal cofactors to catalyze different challenging oxygen-dependent reactions through the formation of multi-protein complexes. Recent studies using cryo-electron microscopy, serial femtosecond crystallography at an X-ray free electron laser source, or single-crystal X-ray diffraction, have reported the structures of the active protein complexes, and revealed unprecedented insights into the molecular mechanisms of these three enzymes.

Tunnel Architectures in Enzyme Systems that Transport Gaseous Substrates

Molecular tunnels regulate delivery of substrates/intermediates in enzymes which either harbor deep-seated reaction centers or are for transport of reactive/toxic intermediates that need to be specifically delivered. Here, we focus on the importance of structural diversity in tunnel architectures, especially for the gaseous substrate translocation, in rendering differential substrate preferences and directionality. Two major types of tunnels have been discussed, one that transports stable gases from the environment to the active site, namely, external gaseous (EG) tunnels, and the other that transports molecules between active sites, namely, internal gaseous (IG) tunnels. Aspects as to how the gaseous tunnels have shaped during the course of evolution and their potential to modulate the substrate flow and enzymatic function are examined. In conclusion, the review highlights our perspective on the pulsation mechanism that could facilitate unidirectional translocation of the gaseous molecules through buried tunnels.

The Crystal Structure of Cysteamine Dioxygenase Reveals the Origin of the Large Substrate Scope of This Vital Mammalian Enzyme

We report the crystal structure of the mammalian non-heme iron enzyme cysteamine dioxygenase (ADO) at 1.9 Å resolution, which shows an Fe and three-histidine (3-His) active site situated at the end of a wide substrate access channel. The open approach to the active site is consistent with the recent discovery that ADO catalyzes not only the conversion of cysteamine to hypotaurine but also the oxidation of N-terminal cysteine (Nt-Cys) peptides to their corresponding sulfinic acids as part of the eukaryotic N-degron pathway. Whole-protein models of ADO in complex with either cysteamine or an Nt-Cys peptide, generated using molecular dynamics and quantum mechanics/molecular mechanics calculations, suggest occlusion of access to the active site by peptide substrate binding. This finding highlights the importance of a small tunnel that leads from the opposite face of the enzyme into the active site, providing a path through which co-substrate O2 could access the Fe center. Intriguingly, the entrance to this tunnel is guarded by two Cys residues that may form a disulfide bond to regulate O2 delivery in response to changes in the intracellular redox potential. Notably, the Cys and tyrosine residues shown to be capable of forming a cross-link in human ADO reside ∼7 Å from the iron center. As such, cross-link formation may not be structurally or functionally significant in ADO.