The Acid-Base Properties, Hydrolytic Mechanism, and Susceptibility to O(2) Oxidation of Fe(4)S(4)(SR)(4) Clusters

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.

Minimal Heterochiral de Novo Designed 4Fe-4S Binding Peptide Capable of Robust Electron Transfer

Ambidoxin is a designed, minimal dodecapeptide consisting of alternating L and D amino acids that binds a 4Fe-4S cluster through ligand-metal interactions and an extensive network of second-shell hydrogen bonds. The peptide can withstand hundreds of oxidation-reduction cycles at room temperature. Ambidoxin suggests how simple, prebiotic peptides may have achieved robust redox catalysis on the early Earth.

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.

Chemical aspects of hydrogen sulfide measurements in physiological samples

BACKGROUND

Owing to recent discoveries of many hydrogen sulfide-mediated physiological processes, sulfide biology is in the focus of scientific research. However, the promiscuous chemical properties of sulfide pose complications for biological studies, which led to accumulation of controversial observations in the literature.

SCOPE OF REVIEW

We intend to provide an overview of fundamental thermodynamic and kinetic features of sulfide redox- and coordination-chemical reactions and protonation equilibria in relation to its biological functions. In light of these chemical properties we review the strengths and limitations of the most commonly used sulfide detection methods and recently developed fluorescent probes. We also give a personal perspective on blood and tissue sulfide measurements based on proposed biomolecule-sulfide interactions and point out important chemical aspects of handling sulfide reagent solutions.

MAJOR CONCLUSIONS

The diverse chemistries of sulfide detection methods resulted in orders of magnitude differences in measured physiological sulfide levels. Investigations that were aimed to dissect the underlying molecular reasons responsible for these controversies made the important recognition that there are large sulfide reserves in biological systems. These sulfide pools are tightly regulated in a dynamic manner and they are likely to play a major role in regulation of endogenous-sulfide-mediated biological functions and avoiding toxic side effects.

GENERAL SIGNIFICANCE

Working with sulfide is challenging, because it requires considerable amounts of chemical knowledge to adequately handle reagent sulfide solutions and interpret biological observations. Therefore, we propose that a rigorous chemical approach could aid the reconciliation of the increasing number of controversies in sulfide biology. This article is part of a Special Issue entitled Current methods to study reactive oxygen species - pros and cons and biophysics of membrane proteins. Guest Editor: Christine Winterbourn.

Formation, spectroscopic characterization, and solution stability of an [Fe4S4]2+ cluster derived from β-cyclodextrin dithiolate

The formation and solution properties, including stability in mixed aqueous-Me(2)SO media, have been investigated for an [Fe(4)S(4)](2+) cluster derived from β-cyclodextrin (CD) dithiolate. Clusters of the type [Fe(4)S(4)(SAr)(4)](2-) (Ar = Ph, C(6)H(4)-3-F) are generated in Me(2)SO by redox reactions of [Fe(4)S(4)(SEt)(4)](2-) with 2 equiv of ArSSAr. An analogous reaction with the intramolecular disulfide of 6(A),6(D)-(3-NHCOC(6)H(4)-1-SH)(2)-6(A),6(D)-dideoxy-β-cyclodextrin (14), whose synthesis is described, affords a completely substituted cluster formulated as [Fe(4)S(4){β-CD-(1,3-NHCOC(6)H(4)S)(2)}(2)](2-) (15). Ligand binding is indicated by a circular dichroism spectrum and also by UV-visible and isotropically shifted (1)H NMR spectra and redox behavior convincingly similar to [Fe(4)S(4)(SPh)(4)](2-). One formulation of 15 is a single cluster to which two dithiolates are bound, each in bidentate coordination. With there being no proven precedent for this binding mode, we show that the cluster [Fe(4)S(4)(S(2)-m-xyl)(2)](2-) is a single cubane whose m-xylyldithiolate ligands are bound in a bidentate arrangement. This same structure type was proposed for a cluster formulated as [Fe(4)S(4){β-CD-(1,3-SC(6)H(4)S)(2)}(2)](2-) (16; Kuroda et al. J. Am. Chem. Soc.1988, 110, 4049-4050) and reported to be water-stable. Clusters 15 and 16 are derived from similar ligands differing only in the spacer group between the thiolate binding site and the CD platform. In our search for clusters stable in aqueous or organic-aqueous mixed solvents that are potential candidates for the reconstitution of scaffold proteins implicated in cluster biogenesis, 15 is the most stable cluster that we have thus far encountered under anaerobic conditions in the absence of added ligand.

Cubane-type Fe4S4 clusters with chiral thiolate ligation: formation by ligand substitution, detection of intermediates by 1H NMR, and solid state structures including spontaneous resolution upon crystallization

Cubane-type clusters [Fe(4)S(4)(SR*)(4)](2-) containing chiral thiolate ligands with R* = CH(Me)Ph (1), CH(2)CH(Me)Et (2), and CH(2)CH(OH)CH(2)OH (3) have been prepared by ligand substitution in the reaction systems [Fe(4)S(4)(SEt)(4)]/R*SH (1-3, acetonitrile) and [Fe(4)S(4)Cl(4)](2-)/NaSR*(3, Me(2)SO). Reactions with successive equivalents of thiol or thiolate generate the species [Fe(4)S(4)L(4-n)(SR*)(n)](2-) (L = SEt, Cl) with n = 1-4. Clusters 1 and 2 were prepared with racemic thiols leading to the possible formation of one enantiomeric pair (n = 1) and seven diastereomers and their enantiomers (n = 2-4). Reactions were monitored by isotropically shifted (1)H NMR spectra in acetonitrile or Me(2)SO. In systems affording 1 and 2 as final products, individual mixed-ligand species could not be detected. However, crystallization of (Et(4)N)(2)[1] afforded 1-[SS(RS)(RS)] in which two sites are disordered because of occupancy of R and S ligands. Similarly, (Et(4)N)(2)[2] led to 2-[SSSS], a consequence of spontaneous resolution upon crystallization. The clusters 3-[RRRR] and 3-[SSSS] were obtained from enantiomerically pure thiols. Successive reactions lead to detection of species with n = 1-4 by appearance of four pairs of diastereotopic SCH(2) signals in both acetonitrile and Me(2)SO reaction systems. Identical spectra were obtained with racemic, R-(-), and S-(+) thiols, indicating that ligand-ligand interactions are too weak to allow detection of diastereomers (e.g., [SSSS] vs [SSRR]). The stability of 3 in Me(2)SO/H(2)O media is described.

Stabilities of cubane type [Fe₄S₄(SR)₄](2-) clusters in partially aqueous media

The stability of cubane-type [Fe₄S₄(SR)₄](2-) clusters in mixed organic/aqueous solvents was examined as an initial step in the development of stable water-soluble cluster compounds possibly suitable for reconstitution of scaffold proteins in protein biosynthesis. The research involves primarily spectrophotometric assessment of stability in 20-80% Me₂SO/aqueous media (v/v), from which it was found that conventional clusters tend to be stable for up to 12h in 60% Me₂SO but are much less stable at higher aqueous content. α-Cyclodextrin mono- and dithioesters and thiols were prepared as ligand precursors for cluster binding, which was demonstrated by spectroscopic methods. A potentially bidentate cyclodextrin dithiolate was found to be relatively effective for cluster stabilization in 40% Me₂SO, suggesting (together with earlier results) that other exceptionally large thiolate ligands may promote cluster stability in aqueous media.

Iron-sulfur clusters II: Kinetics of ligand exchange studied on a water-soluble Fe(4)S(4)(SR)(4) cluster

The water-soluble tetranuclear iron-sulfur cluster ion Fe(4)S(4)(SCH(2)CH(2)CO(2) (-))(4) (6-) (II) has been prepared. The stability of II in water is sufficient to allow the spectrotitrimetric determination of the pK(a) of its Fe(4)S(4) core as 7.4. In our hands the one-electron reductions of compounds I [Fe(4)S(4)(SR)(4) (2-), R = alkyl or aryl,] are thermodynamically irreversible with associated E(1/2) values greater than those for one-electron reduction of ferredoxins. In contrast, the one-electron reduction of II is thermodynamically reversible and the associated potential (-0.58 V versus hydrogen electrode) approaches closely that of the ferredoxins. The kinetics for ligand exchange of II as a function of pH and thiol concentration are in accord with four reversible mercaptan/lyate species exchange reactions followed by product formation via specific acid and base catalysis. Preliminary experiments indicate the nucleophilic order towards II to be Cl(-) [unk] Br(-) < HO(-) < CN(-).

Structure and Properties of [Fe(4)S(4){2,6-bis(acylamino)benzenethiolato-S}(4)](2)(-) and [Fe(2)S(2){2,6-bis(acylamino)benzenethiolato-S}(4)](2)(-): Protection of the Fe-S Bond by Double NH.S Hydrogen Bonds

Iron-sulfur clusters containing a singly or doubly NH.S hydrogen-bonded arenethiolate ligand, [Fe(4)S(4)(S-2-RCONHC(6)H(4))(4)](2)(-) (R = CH(3), t-Bu, CF(3)), [Fe(4)S(4){S-2,6-(RCONH)(2)C(6)H(3)}(4)](2)(-), [Fe(2)S(2)(S-2-RCONHC(6)H(4))(4)](2)(-) (R = CH(3), t-Bu, CF(3)), and [Fe(2)S(2){S-2,6-(RCONH)(2)C(6)H(3)}(4)](2)(-), were synthesized as models of bacterial [4Fe-4S] and plant-type [2Fe-2S] ferredoxins. The X-ray structures and IR spectra of (PPh(4))(2)[Fe(4)S(4){S-2,6-(CH(3)CONH)(2)C(6)H(3)}(4)].2CH(3)CN and (NEt(4))(2)[Fe(2)S(2){S-2,6-(t-BuCONH)(2)C(6)H(3)}(4)] indicate that the two amide NH groups at the o,o'-positions are directed to the thiolate sulfur atom and form double NH.S hydrogen bonds. The NH.S hydrogen bond contributes to the positive shift of the redox potential of not only (Fe(4)S(4))(+)/(Fe(4)S(4))(2+) but also (Fe(4)S(4))(2+)/(Fe(4)S(4))(3+) in the [4Fe-4S] clusters as well as (Fe(2)S(2))(2+)/(Fe(2)S(2))(3+) in the [2Fe-2S] clusters. The doubly NH.S hydrogen-bonded thiolate ligand effectively prevents the ligand exchange reaction by benzenethiol because the two amide NH groups stabilize the thiolate by protection from dissociation.

Inhibition by iodoacetamide and acetylene of the H-D-exchange reaction catalyzed by Thiocapsa roseopersicina hydrogenase

The kinetics of H-D isotope exchange catalyzed by the thermostable hydrogenase from Thiocapsa roseopersicina have been studied by analysis of the exchange between D2 and H2O. The pH dependence of the exchange reaction was examined between pH 2.5 and pH 11. Over the whole pH range, HD was produced at a higher initial velocity than H2, with a marked optimum at pH 5.5; a second peak in the pH profile was observed at around pH 8.5. The rapid formation of H2 with respect to HD in the D2/H2O system is consistent with a heterolytic cleavage of D2 into D+ and an enzyme hydride that can both exchange with the solvent. The H-D-exchange activity was lower in the H2/D2O system than in the D2/H2O system. The other reactions catalyzed by the hydrogenase, H2 oxidation and H2 evolution, are pH dependent; the optimal pH were 9.5 for H2 uptake and 4.0 for H2 production. Treatment of the active form of hydrogenase by iodoacetamide led to a slow and irreversible inhibition of the H-D exchange. When iodo[1-14C]acetamide was incubated with hydrogenase, the radioactive labeling of the large subunit was higher for the enzyme activated under H2 than for the inactive oxidized form. Cysteine residues were identified as the alkylated derivative by amino acid analysis. Acetylene, which inhibits H-D exchange and abolishes the Ni-C EPR signal, protected the enzyme from irreversible inhibition by iodoacetamide. These data indicate that iodoacetamide can reach the active site of the H2-activated hydrogenase from T. roseopersicina. This was not found to be the case with the seleno hydrogenase from Desulfovibrio baculatus (now Desulfomicrobium baculatus). Cysteine modification by iodoacetamide upon activation of the enzyme concomitant with loss of H-D exchange indicates that reductive activation makes at least one Cys residue of the active site available for alkylation.

Evaluation of Solvent Accessibility to the [Fe(4)S(4)] Binding Pocket in Native and Tyr19 Mutant High Potential Iron Proteins by (1)H-(15)N HMQC and (19)F NMR Experiments

The solvent accessibility of Chromatium vinosumhigh potential iron protein (HiPIP) has been investigated by use of (1)H-(15)N HMQC, and (19)F NMR spectroscopy. These NMR experiments indicate that solvent accessibility to the cluster core is similar, and minimal, for the reduced and oxidized states of native HiPIP, but increases significantly for mutant proteins (Tyr19Leu and Tyr19His). These results support a proposed role [Agarwal, A.; Li, D.; Cowan, J. A. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 9440-9444] for Tyr19 in maintaining hydrolytic stability of the [Fe(4)S(4)] cluster, and demonstrate a general strategy for mapping out the solvent accessibility of protein-bound metalloredox prosthetic centers.

Role of aromatic residues in stabilization of the [Fe4S4] cluster in high-potential iron proteins (HiPIPs): physical characterization and stability studies of Tyr-19 mutants of Chromatium vinosum HiPIP

The functional role of residue Tyr-19 of Chromatium vinosum HiPIP has been evaluated by site-directed mutagenesis experiments. The stability of the [Fe4S4] cluster prosthetic center is sensitive to side-chain replacements. Polar residues result in significant instability, while nonpolar residues (especially with aromatic side chains) maintain cluster stability. Two-dimensional NMR data of native and mutant HiPIPs are consistent with a model where Tyr-19 serves to preserve the structural rigidity of the polypeptide backbone, thereby maintaining a hydrophobic barrier for exclusion of water from the cluster cavity. Solvent accessibility results in more facile oxidation of the cluster by atmospheric oxygen, with subsequent rapid hydrolysis of the [Fe4S4]3+ core.

A comparative study of DAPI, DIPI, and Hoechst 33258 and 33342 as chromosomal DNA stains

A comparison of four DNA stains considered to be AT-specific with chromosomes from a clonal Chinese hamster cell line B14F28-C5 have been made. The flow karyotype histograms indicate that DAPI, DIPI, and Hoechst 33258 and 33342 do stain similarly in the same preparation. DAPI staining is specific and highly reproducible in this line. We, therefore, recommend this dye as a single chromosome DNA stain for high-resolution flow cytometric measurements in cytogenetics and mutation research.

Dependence of the rates of dissolution of the Fe4S4 clusters of Chromatium vinosum high-potential iron protein and ferredoxin on cluster oxidation state

The influence of oxidation state on the pH dependence of the dissolution of the Fe(4)S(4) clusters of Chromatium vinosum ferredoxin and high-potential iron protein (HIPIP) has been studied. The first-order rate constants (k(obs)) for dissolution of both the Fe(4)S(4)(S-Cys)(4) (2-) and Fe(4)S(4)(S-Cys)(4) (3-) clusters of the ferredoxin follow the same overall kinetic equation but with differing specific rate and equilibrium constants. The dependence of rate and equilibrium constants upon oxidation state may be rationalized on the basis of the accompanying change in electrostatic affinity of a cluster toward H(+) and HO(-). A more drastic change in the pH dependence of the kinetics of dissolution of the Fe(4)S(4) cluster of the HIPIP accompanies its change in oxidation state. Whereas the values of k(obs) for dissolution of HIPIP containing the Fe(4)S(4)(S-Cys)(4) (2-) cluster are strictly second order to [H(+)] and [HO(-)], the pH dependence for dissolution of the HIPIP Fe(4)S(4)(S-Cys)(4) (1-) cluster indicates a first-order dependence upon [H(+)], a second-order dependence upon [HO(-)], and a spontaneous or water rate. These reactivity differences may be related to changes in cluster charge density. Mechanisms of dissolution involve preequilibrium protonation at acidic pH and preequilibrium ligand exchange at basic pH.