Substrate pathways in the nitrogenase MoFe protein by experimental identification of small molecule binding sites

Understanding non-reducible N2 in the mechanism of Mo-nitrogenase

In my proposed mechanism of Mo-nitrogenase there are two roles for separate N2 molecules. One N2 diffuses into the reaction zone between Fe2 and Fe6 where a strategic gallery of H atoms can capture N2 to form the Fe-bound HNNH intermediate which is then progressively hydrogenated through intermediates containing HNNH2, NH and NH2 entities and then two NH3 in sequence. The second N2 can be parked in an N2-pocket about 3.2 Å from Fe2 or bind end-on at the exo coordination site of Fe2. This second N2 is outside the reaction zone, not exposed to H atom donors, and so is 'non-reducible'. Here density functional calculations using a 485+ atom model describe the thermodynamics for non-reducible N2 moving between the N2-pocket and the exo-Fe2 position, for the resting state and 19 intermediates in the mechanism. The entropy component is estimated and included. The result is that for all intermediates with ligation by H or NHx at the endo-Fe2 position the free energy for association of non-reducible N2 at exo-Fe2 is negative. There remains some uncertainty about the status of exo-Fe2-N2 during the step in which H2 exchanges with the incoming reducible N2, where at least two unbound molecules are present. At Fe2 it is evident that attainment of octahedral coordination stereochemistry dominates the binding thermodynamics for non-reducible N2. Possibilities for experimental support of these computational conclusions are discussed.

The mechanism of Mo-nitrogenase: from N2 capture to first release of NH3

Mo-nitrogenase hydrogenates N2 to NH3. This report continues from the previous paper [I. Dance, Dalton Trans., 2024, 53, 14193-14211] that described how the active site FeMo-co of the enzyme is uniquely able to capture and activate N2, forming a key intermediate with Fe-bound HNNH. Density functional simulations with a 485+ atom model of the active site and its surroundings are used to describe here the further reactions of this HNNH intermediate. The first step is hydrogenation to form HNNH2 bridging Fe2 and Fe6. Then a single-step reaction breaks the N-N bond, generating an Fe2-NH-Fe6 bridge and forming NH3 bound to Fe6. Then NH3 dissociates from Fe6. Reaction potential energies and kinetic barriers for all steps are reported for the most favourable electronic states of the system. The steps that follow the Fe2-NH-Fe6 intermediate, forming and dissociating the second NH3, and regenerating the resting state of the enzyme, are outlined. These results provide an interpretation of the recent steady-state kinetics data and analysis by Harris et al., [Biochemistry, 2022, 61, 2131-2137] who found a slow step after the formation of the HNNH intermediate. The calculated potential energy barriers for the HNNH2 → NH + NH3 reaction (30-36 kcal mol-1) are larger than the potential energy barriers for the N2 → HNNH reaction (19-29 kcal mol-1). I propose that the post-HNNH slow step identified kinetically is the key HNNH2 → NH + NH3 reaction described here. This step and the N2-capture step are the most difficult in the conversion of N2 to 2NH3. The steps in the complete mechanism still to be computationally detailed are relatively straightforward.

Structural evolution of nitrogenase states under alkaline turnover

Biological nitrogen fixation, performed by the enzyme nitrogenase, supplies nearly 50% of the bioavailable nitrogen pool on Earth, yet the structural nature of the enzyme intermediates involved in this cycle remains ambiguous. Here we present four high resolution cryoEM structures of the nitrogenase MoFe-protein, sampled along a time course of alkaline reaction mixtures under an acetylene atmosphere. This series of structures reveals a sequence of salient changes including perturbations to the inorganic framework of the FeMo-cofactor; depletion of the homocitrate moiety; diminished density around the S2B belt sulfur of the FeMo-cofactor; rearrangements of cluster-adjacent side chains; and the asymmetric displacement of the FeMo-cofactor. We further demonstrate that the nitrogenase associated factor T protein can recognize and bind an alkaline inactivated MoFe-protein in vitro. These time-resolved structures provide experimental support for the displacement of S2B and distortions of the FeMo-cofactor at the E0-E3 intermediates of the substrate reduction mechanism, prior to nitrogen binding, highlighting cluster rearrangements potentially relevant to nitrogen fixation by biological and synthetic clusters.

The activating capture of N2 at the active site of Mo-nitrogenase

Dinitrogen is inherently inert. This report describes detailed density functional calculations (with a 485+ atom model) of mechanistic steps by which the enzyme nitrogenase activates unreactive N2 at the intact active site FeMo-co, to form a key intermediate with bound HNNH. This mechanism does not bind N2 first and then add H atoms, but rather captures N2 ('N2-ready') that diffuses in through the substrate channel and enters a strategic gallery of H atom donors in the reaction zone, between Fe2 and Fe6. This occurs at the E4 stage of the complete mechanism. Exploration of possible reactions of N2 in this space leads to the conclusion that the first reaction step is transfer of H on Fe7 to one end of N2-ready, soon followed by Fe-N bond formation, and then a second H transfer from bridging S2BH to the other N. Two H-N bonds and one or two N-Fe bonds are formed, in some cases with a single transition state. The variable positions and orientations of N2-ready lead to various reaction trajectories and products. The favourable products resulting from this capture, judged by the criteria of reaction energies, reaction barriers, and mechanistic competence for further hydrogenation reactions in the nitrogenase cycle, have Fe2-NH-NH bonding. The trajectory of one N2 capture reaction is described in detail, and calculations that separate the H atom component and the 'heavy atom' components of the classical activation energy are described, in the context of possible H atom tunneling in the activation of N2-ready. I present arguments for the activation of N2 by the pathway of concerted hydrogenation and binding of N2-ready, alternative to the commonly assumed pathway of binding N2 first, with subsequent hydrogenation. The active site of nitrogenase is well primed for the thermodynamic and kinetic advantages of N2 capture.

CryoEM-sampling of metastable conformations appearing in cofactor-ligand association and catalysis of glutamate dehydrogenase

Kinetic aspects of enzymatic reactions are described by equations based on the Michaelis-Menten theory for the initial stage. However, the kinetic parameters provide little information on the atomic mechanism of the reaction. In this study, we analyzed structures of glutamate dehydrogenase in the initial and steady stages of the reaction using cryoEM at near-atomic resolution. In the initial stage, four metastable conformations displayed different domain motions and cofactor/ligand association modes. The most striking finding was that the enzyme-cofactor-substrate complex, treated as a single state in the enzyme kinetic theory, comprised at least three different metastable conformations. In the steady stage, seven conformations, including derivatives from the four conformations in the initial stage, made the reaction pathway complicated. Based on the visualized conformations, we discussed stage-dependent pathways to illustrate the dynamics of the enzyme in action.

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.

Mutational Analysis of the Nitrogenase Carbon Monoxide Protective Protein CowN Reveals That a Conserved C-Terminal Glutamic Acid Residue Is Necessary for Its Activity

Nitrogenase is the only enzyme that catalyzes the reduction of nitrogen gas into ammonia. Nitrogenase is tightly inhibited by the environmental gas carbon monoxide (CO). Many nitrogen fixing bacteria protect nitrogenase from CO inhibition using the protective protein CowN. This work demonstrates that a conserved glutamic acid residue near the C-terminus of Gluconacetobacter diazotrophicus CowN is necessary for its function. Mutation of the glutamic acid residue abolishes both CowN's protection against CO inhibition and the ability of CowN to bind to nitrogenase. In contrast, a conserved C-terminal cysteine residue is not important for CO protection by CowN. Overall, this work uncovers structural features in CowN that are required for its function and provides new insights into its nitrogenase binding and CO protection mechanism.

Nitrogenase beyond the Resting State: A Structural Perspective

Nitrogenases have the remarkable ability to catalyze the reduction of dinitrogen to ammonia under physiological conditions. How does this happen? The current view of the nitrogenase mechanism focuses on the role of hydrides, the binding of dinitrogen in a reductive elimination process coupled to loss of dihydrogen, and the binding of substrates to a binuclear site on the active site cofactor. This review focuses on recent experimental characterizations of turnover relevant forms of the enzyme determined by cryo-electron microscopy and other approaches, and comparison of these forms to the resting state enzyme and the broader family of iron sulfur clusters. Emerging themes include the following: (i) The obligatory coupling of protein and electron transfers does not occur in synthetic and small-molecule iron-sulfur clusters. The coupling of these processes in nitrogenase suggests that they may involve unique features of the cofactor, such as hydride formation on the trigonal prismatic arrangement of irons, protonation of belt sulfurs, and/or protonation of the interstitial carbon. (ii) Both the active site cofactor and protein are dynamic under turnover conditions; the changes are such that more highly reduced forms may differ in key ways from the resting-state structure. Homocitrate appears to play a key role in coupling cofactor and protein dynamics. (iii) Structural asymmetries are observed in nitrogenase under turnover-relevant conditions by cryo-electron microscopy, although the mechanistic relevance of these states (such as half-of-sites reactivity) remains to be established.

Coenzyme-binding pathway on glutamate dehydrogenase suggested from multiple-binding sites visualized by cryo-electron microscopy

The structure of hexameric glutamate dehydrogenase (GDH) in the presence of the coenzyme nicotinamide adenine dinucleotide phosphate (NADP) was visualized using cryogenic transmission electron microscopy to investigate the ligand-binding pathways to the active site of the enzyme. Each subunit of GDH comprises one hexamer-forming core domain and one nucleotide-binding domain (NAD domain), which spontaneously opens and closes the active-site cleft situated between the two domains. In the presence of NADP, the potential map of GDH hexamer, assuming D3 symmetry, was determined at a resolution of 2.4 Å, but the NAD domain was blurred due to the conformational variety. After focused classification with respect to the NAD domain, the potential maps interpreted as NADP molecules appeared at five different sites in the active-site cleft. The subunits associated with NADP molecules were close to one of the four metastable conformations in the unliganded state. Three of the five binding sites suggested a pathway of NADP molecules to approach the active-site cleft for initiating the enzymatic reaction. The other two binding modes may rarely appear in the presence of glutamate, as demonstrated by the reaction kinetics. Based on the visualized structures and the results from the enzymatic kinetics, we discussed the binding modes of NADP to GDH in the absence and presence of glutamate.

Structural consequences of turnover-induced homocitrate loss in nitrogenase

Nitrogenase catalyzes the ATP-dependent reduction of dinitrogen to ammonia during the process of biological nitrogen fixation that is essential for sustaining life. The active site FeMo-cofactor contains a [7Fe:1Mo:9S:1C] metallocluster coordinated with an R-homocitrate (HCA) molecule. Here, we establish through single particle cryoEM and chemical analysis of two forms of the Azotobacter vinelandii MoFe-protein - a high pH turnover inactivated species and a ∆NifV variant that cannot synthesize HCA - that loss of HCA is coupled to α-subunit domain and FeMo-cofactor disordering, and formation of a histidine coordination site. We further find a population of the ∆NifV variant complexed to an endogenous protein identified through structural and proteomic approaches as the uncharacterized protein NafT. Recognition by endogenous NafT demonstrates the physiological relevance of the HCA-compromised form, perhaps for cofactor insertion or repair. Our results point towards a dynamic active site in which HCA plays a role in enabling nitrogenase catalysis by facilitating activation of the FeMo-cofactor from a relatively stable form to a state capable of reducing dinitrogen under ambient conditions.

The binding of reducible N2 in the reaction domain of nitrogenase

The binding of N₂ to FeMo-co, the catalytic site of the enzyme nitrogenase, is central to the conversion to NH₃, but also has a separate role in promoting the N₂-dependent HD reaction (D₂ + 2H⁺ + 2e^- → 2HD). The protein surrounding FeMo-co contains a clear channel for ingress of N₂, directly towards the exo-coordination position of Fe2, a position which is outside the catalytic reaction domain. This led to the hypothesis [I. Dance, Dalton Trans., 2022, 51, 12717] of 'promotional' N₂ bound at exo-Fe2, and a second 'reducible' N₂ bound in the reaction domain, specifically the endo-coordination position of Fe2 or Fe6. The range of possibilities for the binding of reducible N₂ in the presence of bound promotional N₂ is described here, using density functional simulations with a 486 atom model of the active site and surrounding protein. The pathway for ingress of the second N₂ through protein, past the first N₂ at exo-Fe2, and tumbling into the binding domain between Fe2 and Fe6, is described. The calculations explore 24 structures involving 6 different forms of hydrogenated FeMo-co, including structures with S2BH unhooked from Fe2 but tethered to Fe6. The calculations use the most probable electronic states. End-on (η¹) binding of N₂ at the endo position of either Fe2 or Fe6 is almost invariably exothermic, with binding potential energies ranging up to -18 kcal mol^-1. Many structures have binding energies in the range -6 to -14 kcal mol^-1. The relevant entropic penalty for N₂ binding from a diffusible position within the protein is estimated to be 4 kcal mol^-1, and so the binding free energies for reducible N₂ are suitably negative. N₂ binding at endo-Fe2 is stronger than at endo-Fe6 in three of the six structure categories. In many cases the reaction domain containing reducible N₂ is expanded. These results inform computational simulation of the subsequent steps in which surrounding H atoms transfer to reducible N₂.

Near ambient N2 fixation on solid electrodes versus enzymes and homogeneous catalysts

The Mo/Fe nitrogenase enzyme is unique in its ability to efficiently reduce dinitrogen to ammonia at atmospheric pressures and room temperature. Should an artificial electrolytic device achieve the same feat, it would revolutionize fertilizer production and even provide an energy-dense, truly carbon-free fuel. This Review provides a coherent comparison of recent progress made in dinitrogen fixation on solid electrodes, homogeneous catalysts and nitrogenases. Specific emphasis is placed on systems for which there is unequivocal evidence that dinitrogen reduction has taken place. By establishing the cross-cutting themes and synergies between these systems, we identify viable avenues for future research.

Biological nitrogen fixation in theory, practice, and reality: a perspective on the molybdenum nitrogenase system

Nitrogenase is the sole enzyme responsible for the ATP-dependent conversion of atmospheric dinitrogen into the bioavailable form of ammonia (NH₃ ), making this protein essential for the maintenance of the nitrogen cycle and thus life itself. Despite the widespread use of the Haber-Bosch process to industrially produce NH₃ , biological nitrogen fixation still accounts for half of the bioavailable nitrogen on Earth. An important feature of nitrogenase is that it operates under physiological conditions, where the equilibrium strongly favours ammonia production. This biological, multielectron reduction is a complex catalytic reaction that has perplexed scientists for decades. In this review, we explore the current understanding of the molybdenum nitrogenase system based on experimental and computational research, as well as the limitations of the crystallographic, spectroscopic, and computational techniques employed. Finally, essential outstanding questions regarding the nitrogenase system will be highlighted alongside suggestions for future experimental and computational work to elucidate this essential yet elusive process.

Structures of the nitrogenase complex prepared under catalytic turnover conditions

The enzyme nitrogenase couples adenosine triphosphate (ATP) hydrolysis to the multielectron reduction of atmospheric dinitrogen into ammonia. Despite extensive research, the mechanistic details of ATP-dependent energy transduction and dinitrogen reduction by nitrogenase are not well understood, requiring new strategies to monitor its structural dynamics during catalytic action. Here, we report cryo-electron microscopy structures of the nitrogenase complex prepared under enzymatic turnover conditions. We observe that asymmetry governs all aspects of the nitrogenase mechanism, including ATP hydrolysis, protein-protein interactions, and catalysis. Conformational changes near the catalytic iron-molybdenum cofactor are correlated with the nucleotide-hydrolysis state of the enzyme.

Statistical analysis of PN clusters in Mo/VFe protein crystals using a bond valence method toward their electronic structures

Nowadays, large numbers of MoFe proteins have been reported and their crystal data obtained by X-ray crystallography and uploaded to the Protein Data Bank (PDB). By big data analysis using a bond valence method, we make conclusions based on 79 selected PN in all 119 P-clusters of 53 MoFe proteins and 10 P-clusters of 5 VFe proteins from all deposited crystallographic data of the PDB. In the condition of MoFe protein crystals, the resting state PN clusters are proposed to have the formal oxidation state of 2Fe(iii)6Fe(ii), hiding two oxidized electron holes with high electron delocalization. The calculations show that Fe1, Fe2, Fe5, Fe6 and Fe7 perform unequivocally as Fe2+, and Fe3 is remarkably prone to Fe(iii), while Fe4 and Fe8 have different degrees of mixed valences. For PN clusters in VFe protein crystals, Fe1, Fe2, Fe4, Fe5 and Fe6 tend to be Fe2+, but the electron distributions rearrange with Fe7 and Fe8 being more oxidized mixed valences, and Fe3 presenting a little more reductive mixed valence than that in MoFe proteins. In terms of spatial location, Fe3 and Fe6 in P-clusters of MoFe proteins are calculated as the most oxidized and reduced irons, which have the shortest distances from homocitrate in the FeMo-cofactor and [Fe4S4] cluster, respectively, and thus could function as potential electron transport sites. This work shows different electron distributions of PN clusters in Mo/VFe protein crystals, from those obtained from previous data from solution with excess reducing agent from which it was concluded that PN clusters are all ferrous according to Mössbauer and electron paramagnetic resonance spectra.

Structures and reaction dynamics of N2 and H2 binding at FeMo-co, the active site of nitrogenase

The chemical reactions occurring at the Fe₇MoS₉C(homocitrate) cluster, FeMo-co, the active site of the enzyme nitrogenase (N₂ → NH₃), are enigmatic. Experimental information collected over a long period reveals aspects of the roles of N₂ and H₂, each with more than one type of reactivity. This paper reports investigations of the binding of H₂ and N₂ at intact FeMo-co, using density functional simulations of a large 486 atom relevant portion of the protein, resulting in 27 new structures containing H₂ and/or N₂ bound at the exo and endo coordination sites of the participating Fe atoms, Fe2 and Fe6. Binding energies and transition states for association/dissociation are determined, and trajectories for the approach, binding and separation of H₂/N₂ are described, including diffusion of these small molecules through proximal protein. Influences of surrounding amino acids are identified. FeMo-co deforms geometrically when binding H₂ or N₂, and a procedure for calculating the energy cost involved, the adaptation energy, is introduced here. Adaptation energies, which range from 7 to 36 kcal mol^-1 for the reported structures, are influenced by the protonation state of the His195 side chain. Seven N₂ structures and three H₂ structures have negative binding free energies, which include the estimated entropy penalties for binding of N₂, H₂ from proximal protein. These favoured structures have N₂ bound end-on at exo-Fe2, exo-Fe6 and endo-Fe2 positions of FeMo-co, and H₂ bound at the endo-Fe2 position. Various postulated structures with N₂ bridging Fe2 and Fe6 revert to end-on-N₂ at endo positions. The structures are also assessed via the calculated potential energy barriers for association and dissociation. Barriers to the binding of H₂ range from 1 to 20 kcal mol^-1 and barriers to dissociation of H₂ range from 3 to 18 kcal mol^-1. Barriers to the binding of N₂, in either side-on or end-on mode, range from 2 to 18 kcal mol^-1, while dissociation of bound N₂ encounters barriers of 3 to 8 kcal mol^-1 for side-on bonding and 7 to 18 kcal mol^-1 for end-on bonding. These results allow formulation of mechanisms for the H₂/N₂ exchange reaction, and three feasible mechanisms for associative exchange and three for dissociative exchange are identified. Consistent electronic structures and potential energy surfaces are maintained throughout. Changes in the spin populations of Fe2 and Fe6 connected with cluster deformation and with metal-ligand bond formation are identified.

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.

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

Rigorous substrate selectivity is a hallmark of enzyme catalysis. This selectivity is generally ascribed to a thermodynamically favorable process of substrate binding to the enzyme active site based upon complementary physiochemical characteristics, which allows both acquisition and orientation. However, this chemical selectivity is more difficult to rationalize for diminutive molecules that possess too narrow a range of physical characteristics to allow either precise positioning or discrimination between a substrate and an inhibitor. Foremost among these small molecules are dissolved gases such as H₂, N₂, O₂, CO, CO₂, NO, N₂O, NH₃, and CH₄ so often encountered in metalloenzyme catalysis. Nevertheless, metalloenzymes have evolved to metabolize these small-molecule substrates with high selectivity and efficiency.The soluble methane monooxygenase enzyme (sMMO) acts upon two of these small molecules, O₂ and CH₄, to generate methanol as part of the C1 metabolic pathway of methanotrophic organisms. sMMO is capable of oxidizing many alternative hydrocarbon substrates. Remarkably, however, it will preferentially oxidize methane, the substrate with the fewest discriminating physical characteristics and the strongest C-H bond. Early studies led us to broadly attribute this specificity to the formation of a "molecular sieve" in which a methane- and oxygen-sized tunnel provides a size-selective route from bulk solvent to the completely buried sMMO active site. Indeed, recent cryogenic and serial femtosecond ambient temperature crystallographic studies have revealed such a route in sMMO. A detailed study of the sMMO tunnel considered here in the context of small-molecule tunnels identified in other metalloenzymes reveals three discrete characteristics that contribute to substrate selectivity and positioning beyond that which can be provided by the active site itself. Moreover, the dynamic nature of many tunnels allows an exquisite coordination of substrate binding and reaction phases of the catalytic cycle. Here we differentiate between the highly selective molecular tunnel, which allows only the one-dimensional transit of small molecules, and the larger, less-selective channels found in typical enzymes. Methods are described to identify and characterize tunnels as well as to differentiate them from channels. In metalloenzymes which metabolize dissolved gases, we posit that the contribution of tunnels is so great that they should be considered to be extensions of the active site itself. A full understanding of catalysis by these enzymes requires an appreciation of the roles played by tunnels. Such an understanding will also facilitate the use of the enzymes or their synthetic mimics in industrial or pharmaceutical applications.

CowN sustains nitrogenase turnover in the presence of the inhibitor carbon monoxide

Nitrogenase is the only enzyme capable of catalyzing nitrogen fixation, the reduction of dinitrogen gas (N₂) to ammonia (NH₃). Nitrogenase is tightly inhibited by the environmental gas carbon monoxide (CO). Nitrogen-fixing bacteria rely on the protein CowN to grow in the presence of CO. However, the mechanism by which CowN operates is unknown. Here, we present the biochemical characterization of CowN and examine how CowN protects nitrogenase from CO. We determine that CowN interacts directly with nitrogenase and that CowN protection observes hyperbolic kinetics with respect to CowN concentration. At a CO concentration of 0.001 atm, CowN restores nearly full nitrogenase activity. Our results further indicate that CowN's protection mechanism involves decreasing the binding affinity of CO to nitrogenase's active site approximately tenfold without interrupting substrate turnover. Taken together, our work suggests CowN is an important auxiliary protein in nitrogen fixation that engenders CO tolerance to nitrogenase.

Reactivity, Mechanism, and Assembly of the Alternative Nitrogenases

Biological nitrogen fixation is catalyzed by the enzyme nitrogenase, which facilitates the cleavage of the relatively inert triple bond of N2. Nitrogenase is most commonly associated with the molybdenum-iron cofactor called FeMoco or the M-cluster, and it has been the subject of extensive structural and spectroscopic characterization over the past 60 years. In the late 1980s and early 1990s, two "alternative nitrogenase" systems were discovered, isolated, and found to incorporate V or Fe in place of Mo. These systems are regulated by separate gene clusters; however, there is a high degree of structural and functional similarity between each nitrogenase. Limited studies with the V- and Fe-nitrogenases initially demonstrated that these enzymes were analogously active as the Mo-nitrogenase, but more recent investigations have found capabilities that are unique to the alternative systems. In this review, we will discuss the reactivity, biosynthetic, and mechanistic proposals for the alternative nitrogenases as well as their electronic and structural properties in comparison to the well-characterized Mo-dependent system. Studies over the past 10 years have been particularly fruitful, though key aspects about V- and Fe-nitrogenases remain unexplored.

Bond-valence analyses of the crystal structures of FeMo/V cofactors in FeMo/V proteins

The bond-valence method has been used for valence calculations of FeMo/V cofactors in FeMo/V proteins using 51 crystallographic data sets of FeMo/V proteins from the Protein Data Bank. The calculations show molybdenum(III) to be present in MoFe₇S₉C(Cys)(HHis)[R-(H)homocit] (where H₄homocit is homocitric acid, HCys is cysteine and HHis is histidine) in FeMo cofactors, while vanadium(III) with a more reduced iron complement is obtained for FeV cofactors. Using an error analysis of the calculated valences, it was found that in FeMo cofactors Fe1, Fe6 and Fe7 can be unambiguously assigned as iron(III), while Fe2, Fe3, Fe4 and Fe5 show different degrees of mixed valences for the individual Fe atoms. For the FeV cofactors in PDB entry 5n6y, Fe4, Fe5 and Fe6 correspond to iron(II), iron(II) and iron(III), respectively, while Fe1, Fe2, Fe3 and Fe7 exhibit strongly mixed valences. Special situations such as CO-bound and selenium-substituted FeMo cofactors and O(N)H-bridged FeV cofactors are also discussed and suggest rearrangement of the electron configuration on the substitution of the bridging S atoms.

Characterization of the Earliest Intermediate of Fe-N2 Protonation: CW and Pulse EPR Detection of an Fe-NNH Species and Its Evolution to Fe-NNH2

Iron diazenido species (Fe(NNH)) have been proposed as the earliest intermediates of catalytic N₂-to-NH₃ conversion (N₂RR) mediated by synthetic iron complexes and relatedly as intermediates of N₂RR by nitrogenase enzymes. However, direct identification of such iron species, either during or independent of catalysis, has proven challenging owing to their high degree of instability. The isolation of more stable silylated diazenido analogues, Fe(NNSiR₃), and also of further downstream intermediates (e.g., Fe(NNH₂)), nonetheless points to Fe(NNH) as the key first intermediate of protonation in synthetic systems. Herein we show that low-temperature protonation of a terminally bound Fe-N₂^- species, supported by a bulky trisphosphinoborane ligand (^ArP₃^B), generates an S = 1/2 terminal Fe(NNH) species that can be detected and characterized by continuous-wave (CW) and pulse EPR techniques. The ¹H-hyperfine for ^ArP₃^BFe(NNH) derived from the presented ENDOR studies is diagnostic for the distally bound H atom ( a_iso = 16.5 MHz). The Fe(NNH) species evolves further to cationic [Fe(NNH₂)]⁺ in the presence of additional acid, the latter being related to a previously characterized [Fe(NNH₂)]⁺ intermediate of N₂RR mediated by a far less encumbered iron tris(phosphine)borane catalyst. While catalysis is suppressed in the present sterically very crowded system, N₂-to-NH₃ conversion can nevertheless be demonstrated. These observations in sum add support to the idea that Fe(NNH) plays a central role as the earliest intermediate of Fe-mediated N₂RR in a synthetic system.

How feasible is the reversible S-dissociation mechanism for the activation of FeMo-co, the catalytic site of nitrogenase?

The active site of the enzyme nitrogenase (N₂→ NH₃) is a Fe₇MoS₉C cluster that contains three doubly-bridging μ-S atoms around a central belt. A vanadium nitrogenase variant has a slightly different cluster, containing two μ-S atoms. Recent crystal structures have revealed substitution of one μ-S (S2B, bridging Fe2 and Fe6), by CO in Mo-nitrogenase and an uncertain light atom in V-nitrogenase. These systems retained catalytic activity, and were able to recover the lost μ-S atom. Electron density attributed to the dissociated S is displaced by 7 Å in the crystal structure of the non-standard V-protein. The hypothesis arising from these observations is that the chemical mechanism of nitrogenase involves reversible dissociation of S2B, leaving Fe2 and Fe6 seriously under-coordinated and reactive in trapping N₂ and binding reaction intermediates. Accumulated experimental evidence points to the Fe2-S2B-Fe6 domain as the centre of catalytic hydrogenation of N₂. Using DFT simulations of a large model (>488 atoms) containing all relevant surrounding protein residues, I have investigated the chemical steps that could allow dissociation of S2B. The participation of H atoms is crucial, as is involvement of the nearby side chain of His195 that can function as proton donor to S2B and hydrogen-bonding supporter of displaced S2B. A significant result is that after ingress and binding of N₂ at Fe2 the breaking of the Fe2-S2B bond can be strongly exergonic with negligible kinetic barrier. Subsequent extension of the Fe6-S2B bond and dissociation as H₂S (or SH^-) is endergonic by 20-25 kcal mol^-1, partly because the separating H₂S is restricted by surrounding amino-acids. I present a number of reaction sequences and energy landscapes, and derive thirteen chemical principles relevant to the postulated S-dissociation mechanism. A key conclusion is that unhooking of S2BH or S2BH₂ from Fe2 is favourable, likely, and propitious for subsequent H transfer to bound N₂ or reaction intermediates. The space between Fe2 and Fe6 supports two bridging ligands, and another H atom on Fe6 can move without kinetic barrier to occupy the bridging position vacated by S2B.

A Structural Basis for 129 Xe Hyper-CEST Signal in TEM-1 β-Lactamase

Genetically encoded (GE) contrast agents detectable by magnetic resonance imaging (MRI) enable non-invasive visualization of gene expression and cell proliferation at virtually unlimited penetration depths. Using hyperpolarized ¹²⁹ Xe in combination with chemical exchange saturation transfer, an MR contrast approach known as hyper-CEST, enables ultrasensitive protein detection and biomolecular imaging. GE MRI contrast agents developed to date include nanoscale proteinaceous gas vesicles as well as the monomeric bacterial proteins TEM-1 β-lactamase (bla) and maltose binding protein (MBP). To improve understanding of hyper-CEST NMR with proteins, structural and computational studies were performed to further characterize the Xe-bla interaction. X-ray crystallography validated the location of a high-occupancy Xe binding site predicted by MD simulations, and mutagenesis experiments confirmed this Xe site as the origin of the observed CEST contrast. Structural studies and MD simulations with representative bla mutants offered additional insight regarding the relationship between local protein structure and CEST contrast.

Rewiring of Cyanobacterial Metabolism for Hydrogen Production: Synthetic Biology Approaches and Challenges

With the demand for renewable energy growing, hydrogen (H₂) is becoming an attractive energy carrier. Developing H₂ production technologies with near-net zero carbon emissions is a major challenge for the "H₂ economy." Certain cyanobacteria inherently possess enzymes, nitrogenases, and bidirectional hydrogenases that are capable of H₂ evolution using sunlight, making them ideal cell factories for photocatalytic conversion of water to H₂. With the advances in synthetic biology, cyanobacteria are currently being developed as a "plug and play" chassis to produce H₂. This chapter describes the metabolic pathways involved and the theoretical limits to cyanobacterial H₂ production and summarizes the metabolic engineering technologies pursued.

Comparison of hydroxycarboxylato imidazole molybdenum(iv) complexes and nitrogenase protein structures: indirect evidence for the protonation of homocitrato FeMo-cofactors

Glycolato and lactato imidazole molybdenum(iv) complexes are used for structural comparison with FeMo-cofactors of MoFe-protein structures.

Mapping Hydrophobic Tunnels and Cavities in Neuroglobin with Noble Gas under Pressure

Internal cavities are crucial for conformational flexibility of proteins and can be mapped through noble gas diffusion and docking. Here we investigate the hydrophobic cavities and tunnel network in neuroglobin (Ngb), a hexacoordinated heme protein likely to be involved in neuroprotection, using crystallography under noble gas pressure, mostly at room temperature. In murine Ngb, a large internal cavity is involved in the heme sliding mechanism to achieve binding of gaseous ligands through coordination to the heme iron. In this study, we report that noble gases are hosted by two major sites within the internal cavity. We propose that these cavities could store oxygen and allow its relay in the heme proximity, which could correspond to NO location in the nitrite-reductase function of Ngb. Thanks to a recently designed pressurization cell using krypton at high pressure, a new gas binding site has been characterized that reveals an alternate pathway for gaseous ligands. A new gas binding site on the proximal side of the heme has also been characterized, using xenon pressure on a Ngb mutant (V140W) that binds CO with a similar rate and affinity to the wild-type, despite a reshaping of the internal cavity. Moreover, this study, to our knowledge, provides new insights into the determinants of the heme sliding mechanism, suggesting that the shift at the beginning of helix G precedes and drives this process.

Inert Gas Deactivates Protein Activity by Aggregation

Biologically inert gases play important roles in the biological functionality of proteins. However, researchers lack a full understanding of the effects of these gases since they are very chemically stable only weakly absorbed by biological tissues. By combining X-ray fluorescence, particle sizing and molecular dynamics (MD) simulations, this work shows that the aggregation of these inert gases near the hydrophobic active cavity of pepsin should lead to protein deactivation. Micro X-ray fluorescence spectra show that a pepsin solution can contain a high concentration of Xe or Kr after gassing, and that the gas concentrations decrease quickly with degassing time. Biological activity experiments indicate a reversible deactivation of the protein during this gassing and degassing. Meanwhile, the nanoparticle size measurements reveal a higher number of “nanoparticles” in gas-containing pepsin solution, also supporting the possible interaction between inert gases and the protein. Further, MD simulations indicate that gas molecules can aggregate into a tiny bubble shape near the hydrophobic active cavity of pepsin, suggesting a mechanism for reducing their biological function.

Structural Characterization of Poised States in the Oxygen Sensitive Hydrogenases and Nitrogenases

The crystallization of FeS cluster-containing proteins has been challenging due to their oxygen sensitivity, and yet these enzymes are involved in many critical catalytic reactions. The last few years have seen a wealth of innovative experiments designed to elucidate not just structural but mechanistic insights into FeS cluster enzymes. Here, we focus on the crystallization of hydrogenases, which catalyze the reversible reduction of protons to hydrogen, and nitrogenases, which reduce dinitrogen to ammonia. A specific focus is given to the different experimental parameters and strategies that are used to trap distinct enzyme states, specifically, oxidants, reductants, and gas treatments. Other themes presented here include the recent use of Cryo-EM, and how coupling various spectroscopies to crystallization is opening up new approaches for structural and mechanistic analysis.

Reversible Protonated Resting State of the Nitrogenase Active Site

Protonated states of the nitrogenase active site are mechanistically significant since substrate reduction is invariably accompanied by proton uptake. We report the low pH characterization by X-ray crystallography and EPR spectroscopy of the nitrogenase molybdenum iron (MoFe) proteins from two phylogenetically distinct nitrogenases (Azotobacter vinelandii, Av, and Clostridium pasteurianum, Cp) at pHs between 4.5 and 8. X-ray data at pHs of 4.5–6 reveal the repositioning of side chains along one side of the FeMo-cofactor, and the corresponding EPR data shows a new S = 3/2 spin system with spectral features similar to a state previously observed during catalytic turnover. The structural changes suggest that FeMo-cofactor belt sulfurs S3A or S5A are potential protonation sites. Notably, the observed structural and electronic low pH changes are correlated and reversible. The detailed structural rearrangements differ between the two MoFe proteins, which may reflect differences in potential protonation sites at the active site among nitrogenase species. These observations emphasize the benefits of investigating multiple nitrogenase species. Our experimental data suggest that reversible protonation of the resting state is likely occurring, and we term this state “E₀H⁺”, following the Lowe–Thorneley naming scheme.

Ligand Field Strength Mediates Electron Delocalization in Octahedral [((H)L)2Fe6(L')m](n+) Clusters

To assess the impact of terminal ligand binding on a variety of cluster properties (redox delocalization, ground-state stabilization, and breadth of redox state accessibility), we prepared three electron-transfer series based on the hexanuclear iron cluster [((H)L)2Fe6(L')m](n+) in which the terminal ligand field strength was modulated from weak to strong (L' = DMF, MeCN, CN). The extent of intracore M-M interactions is gauged by M-M distances, spin ground state persistence, and preference for mixed-valence states as determined by electrochemical comproportionation constants. Coordination of DMF to the [((H)L)2Fe6] core leads to weaker Fe-Fe interactions, as manifested by the observation of ground states populated only at lower temperatures (<100 K) and by the greater evidence of valence trapping within the mixed-valence states. Comproportionation constants determined electrochemically (Kc = 10(4)-10(8)) indicate that the redox series exhibits electronic delocalization (class II-III), yet no intervalence charge transfer (IVCT) bands are observable in the near-IR spectra. Ligation of the stronger σ donor acetonitrile results in stabilization of spin ground states to higher temperatures (∼300 K) and a high degree of valence delocalization (Kc = 10(2)-10(8)) with observable IVCT bands. Finally, the anionic cyanide-bound series reveals the highest degree of valence delocalization with the most intense IVCT bands (Kc = 10(12)-10(20)) and spin ground state population beyond room temperature. Across the series, at a given formal oxidation level, the capping ligand on the hexairon cluster dictates the overall properties of the aggregate, modulating the redox delocalization and the persistence of the intracore coupling of the metal sites.

Docking and migration of carbon monoxide in nitrogenase: the case for gated pockets from infrared spectroscopy and molecular dynamics

Evidence of a CO docking site near the FeMo cofactor in nitrogenase has been obtained by Fourier transform infrared spectroscopy-monitored low-temperature photolysis. We investigated the possible migration paths for CO from this docking site using molecular dynamics calculations. The simulations support the notion of a gas channel with multiple internal pockets from the active site to the protein exterior. Travel between pockets is gated by the motion of protein residues. Implications for the mechanism of nitrogenase reactions with CO and N2 are discussed.

The pathway for serial proton supply to the active site of nitrogenase: enhanced density functional modeling of the Grotthuss mechanism

Proton translocation along a chain of eight waters to the active site of nitrogenase is described in detail, using density functional simulations with a 269 atom system that includes surrounding amino acids.