Circular dichroism and x-ray spectroscopies of Azotobacter vinelandii nitrogenase iron protein. MgATP and MgADP induced protein conformational changes affecting the [4Fe-4S] cluster and characterization of a [2Fe-2S] form

Automated Fast-Flow Synthesis of Chromosome 9 Open Reading Frame 72 Dipeptide Repeat Proteins

An expansion of the hexanucleotide (GGGGCC) repeat sequence in chromosome 9 open frame 72 (c9orf72) is the most common genetic mutation in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The mutation leads to the production of toxic dipeptide repeat proteins (DPRs) that induce neurodegeneration. However, the fundamental physicochemical properties of DPRs remain largely unknown due to their limited availability. Here, we synthesized the c9orf72 DPRs poly-glycine-arginine (poly-GR), poly-proline-arginine (poly-PR), poly-glycine-proline (poly-GP), poly-proline-alanine (poly-PA), and poly-glycine-alanine (poly-GA) using automated fast-flow peptide synthesis (AFPS) and achieved single-domain chemical synthesis of proteins with up to 200 amino acids. Circular dichroism spectroscopy of the synthetic DPRs revealed that proline-containing poly-PR, poly-GP, and poly-PA could adopt polyproline II-like helical secondary structures. In addition, structural analysis by size-exclusion chromatography indicated that longer poly-GP and poly-PA might aggregate. Furthermore, cell viability assays showed that human neuroblastoma cells cultured with poly-GR and poly-PR with longer repeat lengths resulted in reduced cell viability, while poly-GP and poly-PA did not, thereby reproducing the cytotoxic property of endogenous DPRs. This research demonstrates the potential of AFPS to synthesize low-complexity peptides and proteins necessary for studying their pathogenic mechanisms and constructing disease models.

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.

Electron Transfer in Nitrogenase

Nitrogenase is the only enzyme capable of reducing N2 to NH3. This challenging reaction requires the coordinated transfer of multiple electrons from the reductase, Fe-protein, to the catalytic component, MoFe-protein, in an ATP-dependent fashion. In the last two decades, there have been significant advances in our understanding of how nitrogenase orchestrates electron transfer (ET) from the Fe-protein to the catalytic site of MoFe-protein and how energy from ATP hydrolysis transduces the ET processes. In this review, we summarize these advances, with focus on the structural and thermodynamic redox properties of nitrogenase component proteins and their complexes, as well as on new insights regarding the mechanism of ET reactions during catalysis and how they are coupled to ATP hydrolysis. We also discuss recently developed chemical, photochemical, and electrochemical methods for uncoupling substrate reduction from ATP hydrolysis, which may provide new avenues for studying the catalytic mechanism of nitrogenase.

The Spectroscopy of Nitrogenases

Nitrogenases are responsible for biological nitrogen fixation, a crucial step in the biogeochemical nitrogen cycle. These enzymes utilize a two-component protein system and a series of iron-sulfur clusters to perform this reaction, culminating at the FeMco active site (M = Mo, V, Fe), which is capable of binding and reducing N2 to 2NH3. In this review, we summarize how different spectroscopic approaches have shed light on various aspects of these enzymes, including their structure, mechanism, alternative reactivity, and maturation. Synthetic model chemistry and theory have also played significant roles in developing our present understanding of these systems and are discussed in the context of their contributions to interpreting the nature of nitrogenases. Despite years of significant progress, there is still much to be learned from these enzymes through spectroscopic means, and we highlight where further spectroscopic investigations are needed.

Site-Specific Oxidation State Assignments of the Iron Atoms in the [4Fe:4S]2+/1+/0 States of the Nitrogenase Fe-Protein

The nitrogenase iron protein (Fe-protein) contains an unusual [4Fe:4S] iron-sulphur cluster that is stable in three oxidation states: 2+, 1+, and 0. Here, we use spatially resolved anomalous dispersion (SpReAD) refinement to determine oxidation assignments for the individual irons for each state. Additionally, we report the 1.13-Å resolution structure for the ADP bound Fe-protein, the highest resolution Fe-protein structure presently determined. In the dithionite-reduced [4Fe:4S]1+ state, our analysis identifies a solvent exposed, delocalized Fe2.5+ pair and a buried Fe2+ pair. We propose that ATP binding by the Fe-protein promotes an internal redox rearrangement such that the solvent-exposed Fe pair becomes reduced, thereby facilitating electron transfer to the nitrogenase molybdenum iron-protein. In the [4Fe:4S]0 and [4Fe:4S]2+ states, the SpReAD analysis supports oxidation states assignments for all irons in these clusters of Fe2+ and valence delocalized Fe2.5+ , respectively.

Unraveling the interactions of the physiological reductant flavodoxin with the different conformations of the Fe protein in the nitrogenase cycle

Nitrogenase reduces dinitrogen (N₂) to ammonia in biological nitrogen fixation. The nitrogenase Fe protein cycle involves a transient association between the reduced, MgATP-bound Fe protein and the MoFe protein and includes electron transfer, ATP hydrolysis, release of P_i, and dissociation of the oxidized, MgADP-bound Fe protein from the MoFe protein. The cycle is completed by reduction of oxidized Fe protein and nucleotide exchange. Recently, a kinetic study of the nitrogenase Fe protein cycle involving the physiological reductant flavodoxin reported a major revision of the rate-limiting step from MoFe protein and Fe protein dissociation to release of P_i Because the Fe protein cannot interact with flavodoxin and the MoFe protein simultaneously, knowledge of the interactions between flavodoxin and the different nucleotide states of the Fe protein is critically important for understanding the Fe protein cycle. Here we used time-resolved limited proteolysis and chemical cross-linking to examine nucleotide-induced structural changes in the Fe protein and their effects on interactions with flavodoxin. Differences in proteolytic cleavage patterns and chemical cross-linking patterns were consistent with known nucleotide-induced structural differences in the Fe protein and indicated that MgATP-bound Fe protein resembles the structure of the Fe protein in the stabilized nitrogenase complex structures. Docking models and cross-linking patterns between the Fe protein and flavodoxin revealed that the MgADP-bound state of the Fe protein has the most complementary docking interface with flavodoxin compared with the MgATP-bound state. Together, these findings provide new insights into the control mechanisms in protein-protein interactions during the Fe protein cycle.

Design and fine-tuning redox potentials of metalloproteins involved in electron transfer in bioenergetics

Redox potentials are a major contributor in controlling the electron transfer (ET) rates and thus regulating the ET processes in the bioenergetics. To maximize the efficiency of the ET process, one needs to master the art of tuning the redox potential, especially in metalloproteins, as they represent major classes of ET proteins. In this review, we first describe the importance of tuning the redox potential of ET centers and its role in regulating the ET in bioenergetic processes including photosynthesis and respiration. The main focus of this review is to summarize recent work in designing the ET centers, namely cupredoxins, cytochromes, and iron-sulfur proteins, and examples in design of protein networks involved these ET centers. We then discuss the factors that affect redox potentials of these ET centers including metal ion, the ligands to metal center and interactions beyond the primary ligand, especially non-covalent secondary coordination sphere interactions. We provide examples of strategies to fine-tune the redox potential using both natural and unnatural amino acids and native and nonnative cofactors. Several case studies are used to illustrate recent successes in this area. Outlooks for future endeavors are also provided. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.

Frataxin Accelerates [2Fe-2S] Cluster Formation on the Human Fe-S Assembly Complex

Iron-sulfur (Fe-S) clusters function as protein cofactors for a wide variety of critical cellular reactions. In human mitochondria, a core Fe-S assembly complex [called SDUF and composed of NFS1, ISD11, ISCU2, and frataxin (FXN) proteins] synthesizes Fe-S clusters from iron, cysteine sulfur, and reducing equivalents and then transfers these intact clusters to target proteins. In vitro assays have relied on reducing the complexity of this complicated Fe-S assembly process by using surrogate electron donor molecules and monitoring simplified reactions. Recent studies have concluded that FXN promotes the synthesis of [4Fe-4S] clusters on the mammalian Fe-S assembly complex. Here the kinetics of Fe-S synthesis reactions were determined using different electron donation systems and by monitoring the products with circular dichroism and absorbance spectroscopies. We discovered that common surrogate electron donor molecules intercepted Fe-S cluster intermediates and formed high-molecular weight species (HMWS). The HMWS are associated with iron, sulfide, and thiol-containing proteins and have properties of a heterogeneous solubilized mineral with spectroscopic properties remarkably reminiscent of those of [4Fe-4S] clusters. In contrast, reactions using physiological reagents revealed that FXN accelerates the formation of [2Fe-2S] clusters rather than [4Fe-4S] clusters as previously reported. In the preceding paper [Fox, N. G., et al. (2015) Biochemistry 54, DOI: 10.1021/bi5014485], [2Fe-2S] intermediates on the SDUF complex were shown to readily transfer to uncomplexed ISCU2 or apo acceptor proteins, depending on the reaction conditions. Our results indicate that FXN accelerates a rate-limiting sulfur transfer step in the synthesis of [2Fe-2S] clusters on the human Fe-S assembly complex.

The Human Iron-Sulfur Assembly Complex Catalyzes the Synthesis of [2Fe-2S] Clusters on ISCU2 That Can Be Transferred to Acceptor Molecules

Iron-sulfur (Fe-S) clusters are essential protein cofactors for most life forms. In human mitochondria, the core Fe-S biosynthetic enzymatic complex (called SDUF) consists of NFS1, ISD11, ISCU2, and frataxin (FXN) protein components. Few mechanistic details about how this complex synthesizes Fe-S clusters and how these clusters are delivered to targets are known. Here circular dichroism and Mössbauer spectroscopies were used to reveal details of the Fe-S cluster assembly reaction on the SDUF complex. SDUF reactions generated [2Fe-2S] cluster intermediates that readily converted to stable [2Fe-2S] clusters bound to uncomplexed ISCU2. Similar reactions that included the apo Fe-S acceptor protein human ferredoxin (FDX1) resulted in formation of [2Fe-2S]-ISCU2 rather than [2Fe-2S]-FDX1. Subsequent addition of dithiothreitol (DTT) induced transfer of the cluster from ISCU2 to FDX1, suggesting that [2Fe-2S]-ISCU2 is an intermediate. Reactions that initially included DTT rapidly generated [2Fe-2S]-FDX1 and bypassed formation of [2Fe-2S]-ISCU2. In the absence of apo-FDX1, incubation of [2Fe-2S]-ISCU2 with DTT generated [4Fe-4S]-ISCU2 species. Together, these results conflict with a recent report of stable [4Fe-4S] cluster formation on the SDUF complex. Rather, they support a model in which SDUF builds transient [2Fe-2S] cluster intermediates that generate clusters on sulfur-containing molecules, including uncomplexed ISCU2. Additional small molecule or protein factors are required for the transfer of these clusters to Fe-S acceptor proteins or the synthesis of [4Fe-4S] clusters.

Fluorescent probes for tracking the transfer of iron-sulfur cluster and other metal cofactors in biosynthetic reaction pathways

Iron-sulfur (Fe-S) clusters are protein cofactors that are constructed and delivered to target proteins by elaborate biosynthetic machinery. Mechanistic insights into these processes have been limited by the lack of sensitive probes for tracking Fe-S cluster synthesis and transfer reactions. Here we present fusion protein- and intein-based fluorescent labeling strategies that can probe Fe-S cluster binding. The fluorescence is sensitive to different cluster types ([2Fe-2S] and [4Fe-4S] clusters), ligand environments ([2Fe-2S] clusters on Rieske, ferredoxin (Fdx), and glutaredoxin), and cluster oxidation states. The power of this approach is highlighted with an extreme example in which the kinetics of Fe-S cluster transfer reactions are monitored between two Fdx molecules that have identical Fe-S spectroscopic properties. This exchange reaction between labeled and unlabeled Fdx is catalyzed by dithiothreitol (DTT), a result that was confirmed by mass spectrometry. DTT likely functions in a ligand substitution reaction that generates a [2Fe-2S]-DTT species, which can transfer the cluster to either labeled or unlabeled Fdx. The ability to monitor this challenging cluster exchange reaction indicates that real-time Fe-S cluster incorporation can be tracked for a specific labeled protein in multicomponent assays that include several unlabeled Fe-S binding proteins or other chromophores. Such advanced kinetic experiments are required to untangle the intricate networks of transfer pathways and the factors affecting flux through branch points. High sensitivity and suitability with high-throughput methodology are additional benefits of this approach. We anticipate that this cluster detection methodology will transform the study of Fe-S cluster pathways and potentially other metal cofactor biosynthetic pathways.

Characterization of [4Fe-4S] cluster vibrations and structure in nitrogenase Fe protein at three oxidation levels via combined NRVS, EXAFS, and DFT analyses

Azotobacter vinelandii nitrogenase Fe protein (Av2) provides a rare opportunity to investigate a [4Fe-4S] cluster at three oxidation levels in the same protein environment. Here, we report the structural and vibrational changes of this cluster upon reduction using a combination of NRVS and EXAFS spectroscopies and DFT calculations. Key to this work is the synergy between these three techniques as each generates highly complementary information and their analytical methodologies are interdependent. Importantly, the spectroscopic samples contained no glassing agents. NRVS and DFT reveal a systematic 10-30 cm(-1) decrease in Fe-S stretching frequencies with each added electron. The "oxidized" [4Fe-4S](2+) state spectrum is consistent with and extends previous resonance Raman spectra. For the "reduced" [4Fe-4S](1+) state in Fe protein, and for any "all-ferrous" [4Fe-4S](0) cluster, these NRVS spectra are the first available vibrational data. NRVS simulations also allow estimation of the vibrational disorder for Fe-S and Fe-Fe distances, constraining the EXAFS analysis and allowing structural disorder to be estimated. For oxidized Av2, EXAFS and DFT indicate nearly equal Fe-Fe distances, while addition of one electron decreases the cluster symmetry. However, addition of the second electron to form the all-ferrous state induces significant structural change. EXAFS data recorded to k = 21 Å(-1) indicates a 1:1 ratio of Fe-Fe interactions at 2.56 Å and 2.75 Å, a result consistent with DFT. Broken symmetry (BS) DFT rationalizes the interplay between redox state and the Fe-S and Fe-Fe distances as predominantly spin-dependent behavior inherent to the [4Fe-4S] cluster and perturbed by the Av2 protein environment.

Spectroscopic and functional characterization of iron-sulfur cluster-bound forms of Azotobacter vinelandii (Nif)IscA

The mechanism of [4Fe-4S] cluster assembly on A-type Fe-S cluster assembly proteins, in general, and the specific role of (Nif)IscA in the maturation of nitrogen fixation proteins are currently unknown. To address these questions, in vitro spectroscopic studies (UV-visible absorption/CD, resonance Raman and Mössbauer) have been used to investigate the mechanism of [4Fe-4S] cluster assembly on Azotobacter vinelandii(Nif)IscA, and the ability of (Nif)IscA to accept clusters from NifU and to donate clusters to the apo form of the nitrogenase Fe-protein. The results show that (Nif)IscA can rapidly and reversibly cycle between forms containing one [2Fe-2S](2+) and one [4Fe-4S](2+) cluster per homodimer via DTT-induced two-electron reductive coupling of two [2Fe-2S](2+) clusters and O(2)-induced [4Fe-4S](2+) oxidative cleavage. This unique type of cluster interconversion in response to cellular redox status and oxygen levels is likely to be important for the specific role of A-type proteins in the maturation of [4Fe-4S] cluster-containing proteins under aerobic growth or oxidative stress conditions. Only the [4Fe-4S](2+)-(Nif)IscA was competent for rapid activation of apo-nitrogenase Fe protein under anaerobic conditions. Apo-(Nif)IscA was shown to accept clusters from [4Fe-4S] cluster-bound NifU via rapid intact cluster transfer, indicating a potential role as a cluster carrier for delivery of clusters assembled on NifU. Overall the results support the proposal that A-type proteins can function as carrier proteins for clusters assembled on U-type proteins and suggest that they are likely to supply [2Fe-2S] clusters rather than [4Fe-4S] for the maturation of [4Fe-4S] cluster-containing proteins under aerobic or oxidative stress growth conditions.

Insights into [FeFe]-hydrogenase structure, mechanism, and maturation

Hydrogenases are metalloenzymes that are key to energy metabolism in a variety of microbial communities. Divided into three classes based on their metal content, the [Fe]-, [FeFe]-, and [NiFe]-hydrogenases are evolutionarily unrelated but share similar nonprotein ligand assemblies at their active site metal centers that are not observed elsewhere in biology. These nonprotein ligands are critical in tuning enzyme reactivity, and their synthesis and incorporation into the active site clusters require a number of specific maturation enzymes. The wealth of structural information on different classes and different states of hydrogenase enzymes, biosynthetic intermediates, and maturation enzymes has contributed significantly to understanding the biochemistry of hydrogen metabolism. This review highlights the unique structural features of hydrogenases and emphasizes the recent biochemical and structural work that has created a clearer picture of the [FeFe]-hydrogenase maturation pathway.

Biosynthesis of (bacterio)chlorophylls: ATP-dependent transient subunit interaction and electron transfer of dark operative protochlorophyllide oxidoreductase

Dark operative protochlorophyllide oxidoreductase (DPOR) catalyzes the light-independent two-electron reduction of protochlorophyllide a to form chlorophyllide a, the last common precursor of chlorophyll a and bacteriochlorophyll a biosynthesis. During ATP-dependent DPOR catalysis the homodimeric ChlL(2) subunit carrying a [4Fe-4S] cluster transfers electrons to the corresponding heterotetrameric catalytic subunit (ChlN/ChlB)(2), which also possesses a redox active [4Fe-4S] cluster. To investigate the transient interaction of both subcomplexes and the resulting electron transfer reactions, the ternary DPOR enzyme holocomplex comprising subunits ChlN, ChlB, and ChlL from the cyanobacterium Prochlorococcus marinus was trapped as an octameric (ChlN/ChlB)(2)(ChlL(2))(2) complex after incubation with the nonhydrolyzable ATP analogs adenosine 5'-(gamma-thio)triphosphate, adenosine 5'-(beta,gamma-imido)triphosphate, or MgADP in combination with AlF(4)(-). Additionally, a mutant ChlL(2) protein, with a deleted Leu(153) in the switch II region also allowed for the formation of a stable octameric complex. Furthermore, efficient complex formation required the presence of protochlorophyllide. Electron paramagnetic resonance spectroscopy of ternary DPOR complexes revealed a reduced [4Fe-4S] cluster located on ChlL(2), indicating that complete ATP hydrolysis is a prerequisite for intersubunit electron transfer. Circular dichroism spectroscopic experiments indicated nucleotide-dependent conformational changes for ChlL(2) after ATP binding. A nucleotide-dependent switch mechanism triggering ternary complex formation and electron transfer was concluded. From these results a detailed redox cycle for DPOR catalysis was deduced.

Characterization of a modified nitrogenase Fe protein from Klebsiella pneumoniae in which the 4Fe4S cluster has been replaced by a 4Fe4Se cluster

The Azotobacter vinelandii nifS gene product has been used with selenocysteine to reconstitute Klebsiella pneumoniae nitrogenase Fe protein. Chemical analysis and extended X-ray absorption fine structure (EXAFS) spectroscopy show that the 4Fe4S cluster present in the native protein is replaced by a 4Fe4Se cluster. As well, EXAFS spectroscopy shows that the bond lengths to the cysteine thiolate ligands shrink by 0.05 A (from 2.28 to 2.23 A) upon reduction, whereas the Fe-Fe distance is essentially unchanged. Thus, the core of the 4Fe4Se cluster remains essentially static on reduction, whilst the external cysteine thiolate ligands are pulled in towards the cluster. Compared with native (S)-Fe protein, the (Se)-Fe protein has a 20-fold increased rate of MgATP-induced Fe chelation, a sixfold decreased specific activity for acetylene reduction, a fivefold decreased rate of MgATP-dependent electron transfer from (Se)-Fe protein to MoFe protein, and a fourfold increase in the ATP to 2e (-) ratio. The high ATP to 2e (-) ratio and decreased specific activity are consistent with a lower rate of dissociation of oxidized (Se)-Fe protein from reduced MoFe protein. Thus, the relatively small adjustments in the Fe protein structure necessary to accommodate the 4Fe4Se cluster are transmitted both to adjacent residues that dock at the surface of the MoFe protein and to the ATP hydrolysis sites located approximately 19 A away.

Structural analysis of Arabidopsis CnfU protein: an iron-sulfur cluster biosynthetic scaffold in chloroplasts

CnfU, a key iron-sulfur (Fe-S) cluster biosynthetic scaffold that is required for biogenesis of ferredoxin and photosystem I in chloroplasts, consists of two tandemly repeated domains in which only the N-terminal domain contains a conserved CXXC motif. We have determined the crystal structure of the metal-free dimer of AtCnfU-V from Arabidopsis thaliana at 1.35 A resolution. The N-terminal domains of the two monomers are linked together through two intermolecular disulfide bonds between the CXXC motifs. At the dimer interface, a total of four cysteine sulfur atoms provide a Fe-S cluster assembly site surrounded by uncharged but hydrophilic structurally mobile segments. The C-terminal domain of one monomer interacts with the N-terminal domain of the opposing monomer and thereby stabilizes dimer formation. Furthermore, Fe K-edge X-ray absorption spectroscopic analysis of the holo-CnfU dimer in solution suggests the presence of a typical [2Fe-2S]-type cluster coordinated by four thiolate ligands. Based on these data, a plausible model of the holo-AtCnfU-V dimer containing a surface-exposed [2Fe-2S] cluster assembled in the dimer interface was deduced. We propose that such a structural framework is important for CnfU to function as a Fe-S cluster biosynthetic scaffold.

Structural and biochemical implications of single amino acid substitutions in the nucleotide-dependent switch regions of the nitrogenase Fe protein from Azotobacter vinelandii

The structures of nitrogenase Fe proteins with defined amino acid substitutions in the previously implicated nucleotide-dependent signal transduction pathways termed switch I and switch II have been determined by X-ray diffraction methods. In the Fe protein of nitrogenase the nucleotide-dependent switch regions are responsible for communication between the sites responsible for nucleotide binding and hydrolysis and the [4Fe-4S] cluster of the Fe protein and the docking interface that interacts with the MoFe protein upon macromolecular complex formation. In this study the structural characterization of the Azotobacter vinelandii nitrogenase Fe protein with Asp at position 39 substituted by Asn in MgADP-bound and nucleotide-free states provides an explanation for the experimental observation that the altered Fe proteins form a trapped complex subsequent to a single electron transfer event. The structures reveal that the substitution allows the formation of a hydrogen bond between the switch I Asn39 and the switch II Asp125. In the structure of the native enzyme the analogous interaction between the side chains of Asp39 and Asp125 is precluded due to electrostatic repulsion. These results suggest that the electrostatic repulsion between Asp39 and Asp125 is important for dissociation of the Fe protein:MoFe protein complex during catalysis. In a separate study, the structural characterization of the Fe protein with Asp129 substituted by Glu provides the structural basis for the observation that the Glu129-substituted variant in the absence of bound nucleotides has biochemical properties in common with the native Fe protein with bound MgADP. Interactions of the longer Glu side chain with the phosphate binding loop (P-loop) results in a similar conformation of the switch II region as the conformation that results from the binding of the phosphate of ADP to the P-loop.

MECHANISTIC FEATURES OF THE MO-CONTAINING NITROGENASE

Nitrogenase is the complex metalloenzyme responsible for biological dinitrogen reduction. This reaction represents the single largest contributor to the reductive portion of the global nitrogen cycle. Recent developments in understanding the mechanism of the Mo-based nitrogenase are reviewed. Topics include how nucleotide binding and hydrolysis are coupled to electron transfer and substrate reduction, how electrons are accumulated and transferred within the MoFe-protein, and how substrates bind and are reduced at the active site metal cluster.

Thermodynamics of nucleotide interactions with the Azotobacter vinelandii nitrogenase iron protein

The nitrogenase iron (Fe) protein binds two molecules of MgATP or MgADP, which results in protein conformational changes that are important for subsequent steps of the nitrogenase reaction mechanism. In the present work, isothermal titration calorimetry has been used to deconvolute the apparent binding constants (K'a1 and K'a2) and the thermodynamic terms (delta H' degree and delta S' degree) for each of the two binding events of MgATP or MgADP to either the reduced or oxidized states of the Fe protein from Azotobacter vinelandii. The Fe protein was found to bind two nucleotides with positive cooperativity and the oxidation state of the [4Fe-4S] cluster of the Fe protein was found to influence the affinity for binding nucleotides, with the oxidized ([4Fe-4S]2+) state having up to a 15-fold higher affinity for nucleotides when compared to the reduced ([4Fe-4S]1+) state. The first nucleotide binding reaction was found to be driven by a large favorable entropy change (delta S' degree = 10-21 cal mol-1 K-1), with a less favorable or unfavorable enthalpy change (delta H' degree = +1.5 to -3.3 kcal mol-1). In contrast, the second nucleotide binding reaction was found to be driven by a favorable change in enthalpy (delta H' degree = -3.1 to -13.0 kcal mol-1), with generally less favorable entropy changes. A plot of the associated enthalpy (-delta H' degree) and entropy terms (-T delta S' degree) for each nucleotide and protein binding reaction revealed a linear relationship with a slope of 1.12, consistent with strong enthalpy-entropy compensation. These results indicate that the binding of the first nucleotide to the nitrogenase Fe protein results in structural changes accompanied by the reorganization of bound water molecules, whereas the second nucleotide binding reaction appears to result in much smaller structural changes and is probably largely driven by bonding interactions. Evidence is presented that the total free energy change (delta G' degree) derived from the binding of two nucleotides to the Fe protein accounts for the total change in the midpoint potential of the [4Fe-4S] cluster.

The role of methionine 156 in cross-subunit nucleotide interactions in the iron protein of nitrogenase

A variant Fe protein has been created at the completely conserved residue methionine 156 by changing it to cysteine. The Azotobacter vinelandii strain expressing M156C is unable to grow under nitrogen-fixing conditions, and the purified protein cannot support substrate reduction in vitro. This mutation has an effect on the Fe protein's ability to undergo the MgATP-induced conformational change as evidenced by the fact that M156C is chelated in the presence of MgATP with a lower observed rate than wild-type. While the electron paramagnetic resonance spectra of this protein are similar to those of the wild-type Fe protein, the circular dichroism spectrum is markedly different in the presence of MgATP, showing that the conformation adopted by M156C following nucleotide binding is different from the wild-type conformation. Although competition activity and chelation assays show that this Fe protein can still form a complex with the MoFe protein, this altered conformation only supports MgATP hydrolysis at 1% the rate of wild-type Fe protein. A model based on x-ray crystallographic information is presented to explain the importance of Met-156 in stabilization of the correct conformation of the Fe protein via critical interactions of the residue with Asp-43 and nucleotide in the other subunit.

An all-ferrous state of the Fe protein of nitrogenase. Interaction with nucleotides and electron transfer to the MoFe protein

The MoFe protein of nitrogenase catalyzes the six-electron reduction of dinitrogen to ammonia. It has long been believed that this protein receives the multiple electrons it requires one at a time, from the [4Fe-4S]2+/+ couple of the Fe protein. Recently an all-ferrous [4Fe-4S]0 state of the Fe protein was demonstrated suggesting instead a series of two electron steps involving the [4Fe-4S]2+/0 couple. We have examined the interactions of the [4Fe-4S]0 Fe protein with nucleotides and its ability to transfer electrons to the MoFe protein. The [4Fe-4S]0 Fe protein binds both MgATP and MgADP and undergoes the MgATP induced conformational change and then binds properly to the MoFe protein, as evidenced by the fact that the behavior of the 0 and +1 oxidation states in the chelation and chelation protection assays are indistinguishable. Nucleotide binding does not effect the distinctive UV/Vis, CD, or Mössbauer spectra exhibited by the [4Fe-4S]0 Fe protein; however, because the intensity of the g = 16.4 EPR signal of the [4Fe-4S]0 Fe protein is extremely sensitive to minor variations of the rhombicity parameter E/D, the EPR signal is sensitive to the binding of nucleotides. A 50:50 mixture of [4Fe-4S]2+ and [4Fe-4S]0 Fe protein results in electron self-exchange and 100% production of [4Fe-4S]+ Fe protein, demonstrating that the +1/0 couple is fully reversible. MgATP is absolutely required for electron transfer from the [4Fe-4S]0 Fe protein to the reduced state of the MoFe protein. In that reaction both electrons are transferred and are used to reduce substrate.

Characterization of a variant iron protein of nitrogenase that is impaired in its ability to adopt the MgATP-induced conformational change

An Azotobacter vinelandii nitrogenase iron protein mutant has been created which contains an alanine to glycine substitution at amino acid 157. The strain expressing this mutant Fe protein is able to grow under nitrogen-fixing conditions. This contrasts with an A. vinelandii strain described previously which is unable to grow under nitrogen-fixing conditions and which expresses an Fe protein variant that has an alanine to serine mutation at position 157. The A157S Fe protein was unable to support substrate reduction by nitrogenase because of an inability to undergo a required MgATP-induced conformational change. Although the A157G strain grows at 55% of the rate of the wild-type strain, purified A157G Fe protein is only able to support substrate reduction in in vitro assays at a rate that is approximately 20% of the rate supported by the wild-type Fe protein. Electron paramagnetic resonance, circular dichroism spectroscopies, and enzymatic activity data indicate that the A157G Fe protein adopts the correct conformation upon the binding of MgATP. However, kinetic studies using chelation show that this protein undergoes the conformational change more slowly than the wild-type protein. Thus, this mutant has lower activity because of an impaired ability to undergo this conformational change. Comparison of two available x-ray crystal structures of the native Fe protein alone and complexed with the MoFe protein has provided us with a model to explain the change in activity in alanine 157 mutants. Steric interactions with the side chain of residue 157 influence the protein's ability to undergo the initial MgATP-induced conformational change. In the case of the A157G mutant, however, once the correct conformation is attained, the protein can participate in all subsequent reactions including complex formation, electron transfer, and MgATP hydrolysis. Thus, the role of alanine 157 is to stabilize the proper initial conformation upon MgATP binding.

Iron-sulfur clusters: nature's modular, multipurpose structures

Iron-sulfur proteins are found in all life forms. Most frequently, they contain Fe2S2, Fe3S4, and Fe4S4 clusters. These modular clusters undergo oxidation-reduction reactions, may be inserted or removed from proteins, can influence protein structure by preferential side chain ligation, and can be interconverted. In addition to their electron transfer function, iron-sulfur clusters act as catalytic centers and sensors of iron and oxygen. Their most common oxidation states are paramagnetic and present significant challenges for understanding the magnetic properties of mixed valence systems. Iron-sulfur clusters now rank with such biological prosthetic groups as hemes and flavins in pervasive occurrence and multiplicity of function.

Evidence for electron transfer-dependent formation of a nitrogenase iron protein-molybdenum-iron protein tight complex. The role of aspartate 39

Nitrogenase-catalyzed substrate reduction reactions require the association of the iron (Fe) protein and the molybdenum-iron (MoFe) protein, electron transfer from the Fe protein to the MoFe protein coupled to the hydrolysis of MgATP, followed by protein-protein complex dissociation. This work examines the role of MgATP hydrolysis and electron transfer in the dissociation of the Fe protein-MoFe protein complex. Alteration of aspartate 39 to asparagine (D39N) in the nucleotide binding site of Azotobacter vinelandii Fe protein by site-directed mutagenesis resulted in an Fe protein-MoFe protein complex that did not dissociate after electron transfer. While the D39N Fe protein-MoFe protein complex was inactive in all substrate reduction reactions, the complex catalyzed both reductant-dependent and reductant-independent MgATP hydrolysis. Once docked to the MoFe protein, the D39N Fe protein was found to transfer one electron to the MoFe protein requiring MgATP hydrolysis, with an apparent first order rate constant of 0.02 s-1 compared with 140 s-1 for the wild-type Fe protein. Only following electron transfer to the MoFe protein did the D39N Fe protein form a tight complex with the MoFe protein, with no detectable dissociation rate. This was in contrast with the dissociation rate constant of the wild-type Fe protein from the MoFe protein following electron transfer of 5 s-1. Chemically oxidized D39N Fe protein with MgADP-bound did not form a tight complex with the MoFe protein, showing a dissociation rate similar to chemically oxidized wild-type Fe protein (3 s-1 for D39N Fe protein and 6 s-1 for wild-type Fe protein). These results suggest that electron transfer from the Fe protein to the MoFe protein within the protein-protein complex normally induces conformational changes which increase the affinity of the Fe protein for the MoFe protein. A model is presented in which Asp-39 participates in a nucleotide signal transduction pathway involved in component protein-protein dissociation.