Purification, composition, charge, and molecular weight of the FeMo cofactor from Azotobacter vinelandii nitrogenase

Assignment of protonated R-homocitrate in extracted FeMo-cofactor of nitrogenase via vibrational circular dichroism spectroscopies

Protonation of FeMo-cofactor is important for the process of substrate hydrogenation. Its structure has been clarified as Δ-Mo*Fe₇S₉C(R-homocit*)(cys)(Hhis) for the efforts of nearly 30 years, while it remains controversial whether FeMo-cofactor is protonated or deprotonated with chelated ≡C-O(H) homocitrate. We have used protonated molybdenum(V) lactates 1 and its enantiomer as model compounds for R-homocitrate in FeMo-cofactor of nitrogenase. Vibrational circular dichroism (VCD) spectrum of 1 at 1051 cm^-1 is attributed to ≡C-O_H vibration, and molybdenum(VI) R-lactate at 1086 cm^-1 is assigned as ≡C-O _α-alkoxy vibration. These vibrations set up labels for the protonation state of coordinated α-hydroxycarboxylates. The characteristic VCD band of NMF-extracted FeMo-cofactor is assigned to ν(C-O_H), which is based on the comparison of molybdenum(VI) R-homocitrate. Density Functional Theory calculations are in consistent with these assignments. To the best of our knowledge, this is the first time that protonated R-homocitrate in FeMo-cofactor is confirmed by VCD spectra.

Preparation and representation of recombinant Mn-ferritin flower-like spherical aggregates from marine invertebrates

Ferritin has important functions in the transition and storage of toxic metal ions, but its regulation and function in many invertebrate species are still largely unknown. In our previous work, the cDNA sequence of Sinonovacula constricta, Apostichopus japonicas and Acaudina leucoprocta were constructed and efficiently expressed in E. Coli BL21 under IPTG induction. In this follow-up study, the recombinant ferritins were exposed to heavy metal manganese. The manganese concentration levels in three recombinant ferritins were greater than horse spleen ferritin (HSF). Compared with HSF, the amount of manganese enrichment in the three recombinant ferritins was 1.75-fold, 3.25-fold and 2.42-fold increases in ScFER, AjFER, and AlFER, respectively. After phosphate stimulation, the concentration of manganese increased and was higher than the ordinary dialysis control groups. The ScFER was four times its baseline value. The AjFER and AlFER were 1.4- and 8-fold higher, respectively. The AlFER sample stimulated by phosphate was 22-fold that of HSF. The morphologies of the resulting Mn-Ferritin from different marine invertebrates were characterized with scanning electron microscopy. Surface morphologies were lamella flower-like and are consistent with changes in surface morphologies of the standard Mn-HSF. Invertebrate recombinant ferritin and HSF both can uptake manganese. We found that the structure of A. leucoproctarecombinant Mn-Ferritin aggregate changed over time. The surface formed lamella flower-like aggregate, but gradually merged to create a relatively uniform plate-like phase of aggregate spherically and fused without clear boundaries.

Comparative assessment of the composition and charge state of nitrogenase FeMo-cofactor

A significant limitation in our understanding of the molecular mechanism of biological nitrogen fixation is the uncertain composition of the FeMo-cofactor (FeMo-co) of nitrogenase. In this study we present a systematic, density functional theory-based evaluation of spin-coupling schemes, iron oxidation states, ligand protonation states, and interstitial ligand composition using a wide range of experimental criteria. The employed functionals and basis sets were validated with molecular orbital information from X-ray absorption spectroscopic data of relevant iron-sulfur clusters. Independently from the employed level of theory, the electronic structure with the greatest number of antiferromagnetic interactions corresponds to the lowest energy state for a given charge and oxidation state distribution of the iron ions. The relative spin state energies of resting and oxidized FeMo-co already allowed exclusion of certain iron oxidation state distributions and interstitial ligand compositions. Geometry-optimized FeMo-co structures of several models further eliminated additional states and compositions, while reduction potentials indicated a strong preference for the most likely charge state of FeMo-co. Mössbauer and ENDOR parameter calculations were found to be remarkably dependent on the employed training set, density functional, and basis set. Overall, we found that a more oxidized [Mo(IV)-2Fe(II)-5Fe(III)-9S(2-)-C(4-)] composition with a hydroxyl-protonated homocitrate ligand satisfies all of the available experimental criteria and is thus favored over the currently preferred composition of [Mo(IV)-4Fe(II)-3Fe(III)-9S(2-)-N(3-)] from the literature.

Nitrogenase structure and function relationships by density functional theory

Modern density functional theory has tremendous potential with matching popularity in metalloenzymology to reveal the unseen atomic and molecular details of structural data, spectroscopic measurements, and biochemical experiments by providing insights into unobservable structures and states, while also offering theoretical justifications for observed trends and differences. An often untapped potential of this theoretical approach is to bring together diverse experimental structural and reactivity information and allow for these to be critically evaluated at the same level. This is particularly applicable for the tantalizingly complex problem of the structure and molecular mechanism of biological nitrogen fixation. In this chapter we provide a review with extensive practical details of the compilation and evaluation of experimental data for an unbiased and systematic density functional theory analysis that can lead to remarkable new insights about the structure-function relationships of the iron-sulfur clusters of nitrogenase.

Cooperativity and intermediates in the equilibrium reactions of Fe(II,III) with ethanethiolate in N-methylformamide solution

The reaction of FeCl(2) or FeCl(3) with sodium ethanethiolate (SEt) in N-methylformamide (NMF) has been reevaluated to rectify a previous Fe(II) oxidation artifact. On titrating Fe(II) with EtS(-) concentrations up to 12 mol Eq, new features in the UV/vis spectrum (epsilon(344)=(3.1+/-0.2)x10(3) M(-1) cm(-1); epsilon(486)=(4.5+/-0.1)x10(2) M(-1) cm(-1)) indicated that the first observable step was the formation of a single complex different from the known tetrahedral tetrathiolate, [Fe(SEt)(4)](2-) . As the EtS(-) concentration increased past 12.5 mol Eq the UV/vis spectrum gradually transformed to that of [Fe(SEt)(4)](2-) (lambda(max)=314 nm). A Hill-formalism fit to the titration data of the initially formed complex indicated cooperative ligation by three ethanethiolate ions, with K(coop)=(1.7+/-0.1)x10(3) M(-3) and Hill "n"=2.4+/-0.1 (r=0.997). The 3:1 EtS(-)-Fe(II) complex is proposed to be [Fe(2)(SEt)(6)](2-). Titration of Fe(III) with EtS(-) showed direct cooperative formation of [Fe(SEt)(4)](-) [epsilon(340)=(3.4+/-0.5)x10(3) M(-1) cm(-1)] with a Hill-formalism K(coop)=(4.3+/-0.1)x10(2) M(-4) and a Hill coefficient "n"=3.7+/-0.2 (r=0.996). Further ligation past [Fe(SEt)(4)](-) was observed at EtS(-) concentrations above 35 mol Eq. The Fe(III) Hill constants are at variance with our previous report. However, the UV/vis spectrum of Fe(III) in NMF solution was found to change systematically over time, consistent with a slow progressive deprotonation of [Fe(nmf)](3+). The observed time-to-time differences in the equilibrium chemistry of Fe(III) with ethanethiolate in NMF thus reflect variation in the microscopic solution composition of FeCl(3) in alkaline NMF solvent. These results are related to the chemistry of nitrogenase FeMo cofactor in alkaline NMF solution.

Characteristics of Trapping Various Organophosphorus Pesticides with a Ferritin Reactor of Shark Liver (Sphyrna zygaena)

A reactor is composed of liver ferritin of Sphyrna zygaena (SZLF) and an oscillating bag. A reactive procedure for trapping various organphosphorus pesticides (OPs) with the SZLF reactor in the flowing water is described in detail, showing the maximal trapping numbers of 28 +/-1.0 dichlorovos/SZLF, 42 +/- 1.0 dimethoate/SZLF, and 55 +/- 1.0 methamido-phos/SZLF determined by a improved spectrophotometric method in 12 h. In addition, it is found that the OP numbers trapped by the reactor increase along with the incubation time and its concentration increment in the flowing water (or seawater), respectively. This trapping capacity is considered to depend on the composition of amino acids on the surface of the ferritin shell interior rather than the available volume within the shell. A novel pathway for trapping various OPs with the ferritin is suggested in reference to unstable characteristics of the protein subunits. We claim that the ferritin reactor will be employed to monitor the contamination level of various OPs in the flowing water continuously.

Characteristics of trapping copper ions with scrolled ferritin reactor in the flowing seawater

Native liver ferritin of Dasyatis akajei (DALF), apoDALF, and reconstituted DALF were employed to construct a ferritin reactor, respectively. An apparatus consisting of a mixer, a ferritin reactor, and a magnetic stirrer was constructed to study capacity and feasibility of trapping Cu2+ in the flowing seawater. The experimental results showed that the numbers of trapping Cu2+ with DALF reactor were higher than these with the reactors of apoDALF and reconstituted DALF, respectively, giving the maximal numbers of 98 +/- 5 Cu2+ per molecular DALF in 120 h. We found that the iron layer with a high ratio of phosphate to ion on the surface of the ferritin core played an important role in increasing numbers of trapping Cu2+. In addition, we found two positive relations of dependence of trapping Cu2+ numbers with the reactor on the incubation time and on the Cu2+ concentration in the flowing seawater. Another apparatus consisting of a buoyage, an isolation basket equipped with griddling, and a scrolled ferritin reactor was constructed to study the feasibility of trapping Cu2+ in the sea area. Moreover, the present studies indicated that this apparatus had been used to not only analyze and evaluate the concentration variety of various heavy metal ions such as Cu2+ and Pb2+ diluting by the seawater but also monitor the formation of pollution degree by various small organic molecules during the climax and the neap.

Binding sites of nitrogenase: kinetic and theoretical studies of cyanide binding to extracted FeMo-cofactor derivatives

The first kinetic study of a substrate (CN(-)) binding to the isolated active site (extracted FeMo-cofactor) of nitrogenase is described. The kinetics of the reactions between CN(-) and various derivatives of extracted FeMo-cofactor [FeMoco-L; where L is bound to Mo, and is NMF, Bu(t)NC, or imidazole (ImH)] have been followed using a stopped-flow, sequential-mix method in which the course of the reaction is followed indirectly, by monitoring the change in the rate of the reaction of the cofactor with PhS(-). The kinetic results, together with DFT calculations, indicate that the initial site of CN(-) binding to FeMoco-L is controlled by a combination of the electron-richness of the cluster core and lability of the Mo-L bond. Ultimately, the reactions between FeMoco-L and CN(-) involve displacement of L and binding of CN(-) to Mo. These reactions occur with a variety of rates and rate laws dependent on the nature of L. For FeMoco-NMF, the reaction with CN(-) is complete within the dead-time of the apparatus (ca. 4 ms), while with FeMoco-CNBu(t) the reaction is much slower and exhibits first order dependences on the concentrations of both FeMoco-CNBu(t) and CN(-) (k = 2.5 +/- 0.5 x 10(4) dm(3) mol(-1) s(-1)). The reaction of FeMoco-ImH with CN(-) occurs at a rate which exhibits a first order dependence on FeMoco-ImH but is independent of the concentration of CN(-) (k = 50 +/- 10 s(-1)). The results are interpreted in terms of CN(-) binding directly to the Mo site for FeMoco-NMF and FeMoco-ImH, but with FeMoco-CNBu(t) initial binding at an Fe site is followed by movement of CN(-) to Mo. Complementary DFT calculations are consistent with this interpretation, indicating that, in FeMoco-L, the Mo-L bond is stronger for L = ImH than for L = CNBu(t) and the binding of CN(-) to Mo is stronger than to any Fe atom in the cofactor.

Density functional study of the electric hyperfine interactions and the redox-structural correlations in the cofactor of nitrogenase. Analysis of general trends in (57)Fe isomer shifts

The influence of the interstitial atom, X, discovered in a recent crystallographic study of the MoFe protein of nitrogenase, on the electric hyperfine interactions of (57)Fe has been investigated with density functional theory. A semiempirical theory for the isomer shift, delta, is formulated and applied to the cofactor. The values of delta for the relevant redox states of the cofactor are predicted to be higher in the presence of X than in its absence. The analysis strongly suggests a [Mo(4+)4Fe(2+)3Fe(3+)] oxidation state for the S = 3/2 state M(N). Among C(4-), N(3-), and O(2-), oxide is found to be the least likely candidate for X. The analysis suggests that X should be present in the cofactor states M(OX) and M(R) as well as in the alternative nitrogenases. The calculations of the electric field gradients (EFGs) indicate that the small values for DeltaE(Q) in M(N) result from an extensive cancellation between valence and ligand contributions. X emerges from the analysis of the hyperfine interactions as an ionically bonded species. Its major effect is on the asymmetry parameters for the EFGs at the six equatorial sites, Fe(Eq). A spin-coupling scheme is proposed for the state [Mo(4+)4Fe(2+)3Fe(3+)] that is consistent with the measured (57)Fe A-tensors and DeltaE(Q) values for M(N) and identifies the unique site exhibiting the small A value with the terminal Fe site, Fe(T). The optimized structure of a cofactor model has been calculated for several oxidation states. The study reveals a contraction in the average Fe-Fe distance upon increasing the number of electrons stored in the cluster, in accord with extended X-ray absorption fine structure studies. The reliability of the adopted methodology for predicting redox-structural correlations is tested for cuboidal [4Fe-4S] clusters. The calculations reveal a systematic increase in the S...S sulfide distances, in quantitative agreement with the available data. These trends are rationalized by a simple electrostatic model.

Effect of redox mediators on nitrogenase and hydrogenase activities in Azotobacter vinelandii

In bioelectrochemical studies, redox mediators such as methylene blue, natural red, and thionine are used to studying the redox characteristics of enzymes in the living cell. Here we show that nitrogenase activity in Azotobacter vinelandii is completely inhibited by oxidized methylene blue (MBo) when the concentration of this mediator in the medium is increased up to 72 microM. This activity in A. vinelandii is somewhat inhibited by a coenzyme, ascorbic acid (AA). However, the nitrogenase activity within the A. vinelandii cell is unchanged even for a high concentration of oxidized natural red (NRo) alone. Interestingly, these mediators and AA do not have the capacity to inhibit the H2 uptake activity of the hydrogenase in A. vinelandii. Average active rates of 66 nM H2 evolved/mg cell protein/min from the nitrogenase and 160 nM H2-uptake/mg cell protein/min from the hydrogenase in A. vinelandii are found in aid of the activities of the enzymes for H2 evolution and for H2 uptake are compared. The activities of both enzymes in A. vinelandii are strongly inhibited by thionine having high oxidative potential. Mechanisms of various mediators acting in vivo for both enzymes in A. vinelandii are discussed.

Catalytic Reduction of Hydrazine to Ammonia with MoFe(3)S(4)-Polycarboxylate Clusters. Possible Relevance Regarding the Function of the Molybdenum-Coordinated Homocitrate in Nitrogenase

The catalytic function of the previously synthesized and characterized [(L)MoFe(3)S(4)Cl(3)](2)(-)(,3)(-) clusters (L = tetrachlorocatecholate, citrate, citramalate, methyliminodiacetate, nitrilotriacetate, thiodiglycolate) and of the [MoFe(3)S(4)Cl(3)(thiolactate)](2)(4)(-) and [(MoFe(3)S(4)Cl(4))(2)(&mgr;-oxalate)](4)(-) clusters in the reduction of N(2)H(4) to NH(3) is reported. In the catalytic reduction, which is carried out at ambient temperature and pressure, cobaltocene and 2,6-lutidinium chloride are supplied externally as electron and proton sources, respectively. In experiments where the N(2)H(4) to the [(L)MoFe(3)S(4)Cl(3)](n)()(-) catalyst ratio is 100:1, and over a period of 30 min, the reduction proceeds to 92% completion for L = citrate, 66% completion for L = citramalate, and 34% completion for L = tetrachlorocatecholate. The [Fe(4)S(4)Cl(4)](2)(-) cluster is totally inactive and gives only background ammonia measurements. Inhibition studies with PEt(3) and CO as inhibitors show a dramatic decrease in the catalytic efficiency. These results are consistent with results obtained previously in our laboratory and strongly suggest that N(2)H(4) activation and reduction occur at the Mo site of the [(L)MoFe(3)S(4)Cl(3)](2)(-)(, 3)(-) clusters. A possible pathway for the N(2)H(4) reduction on a single metal site (Mo) and a possible role for the carboxylate ligand are proposed. The possibility that the Mo-bound polycarboxylate ligand acts as a proton delivery "shuttle" during hydrazine reduction is considered.