Synergy of native mass spectrometry and other biophysical techniques in studies of iron‑sulfur cluster proteins and their assembly

The application of mass spectrometric methodologies has revolutionised biological chemistry, from identification through to structural and conformational studies of proteins and other macromolecules. Native mass spectrometry (MS), in which proteins retain their native structure, is a rapidly growing field. This is particularly the case for studies of metalloproteins, where non-covalently bound cofactors remain bound following ionisation. Such metalloproteins include those that contain an iron‑sulfur (FeS) cluster and, despite their fragility and O2 sensitivity, they have been a particular focus for applications of native MS because of its capacity to accurately monitor mass changes that reveal chemical changes at the cluster. Here we review recent advances in these applications of native MS, which, together with data from more traditionally applied biophysical methods, have yielded a remarkable breadth of information about the FeS species present, and provided key mechanistic insight not only for FeS cluster proteins themselves, but also their assembly.

Partial Deoxygenative CO Homocoupling by a Diiron Complex

One route to address climate change is converting carbon dioxide to synthetic carbon-neutral fuels. Whereas carbon dioxide to CO conversion has precedent in homo- and heterogeneous catalysis, deoxygenative coupling of CO to products with C-C bonds-as in liquid fuels-remains challenging. Here, we report coupling of two CO molecules by a diiron complex. Reduction of Fe2 (CO)2 L (2), where L2- is a bis(β-diketiminate) cyclophane, gives [K(THF)5 ][Fe2 (CO)2 L] (3), which undergoes silylation to Fe2 (CO)(COSiMe3 )L (4). Subsequent C-OSiMe3 bond cleavage and C=C bond formation occurs upon reduction of 4, yielding Fe2 (μ-CCO)L. CO derived ligands in this series mediate weak exchange interactions with the ketenylidene affording the smallest J value, with changes to local metal ion spin states and coupling schemes (ferro- vs. antiferromagnetism) based on DFT calculations, Mössbauer and EPR spectroscopy. Finally, reaction of 5 with KEt3 BH or methanol releases the C2 O2- ligand with retention of the diiron core.

Isostructural bridging diferrous chalcogenide cores [FeII(μ-E)FeII] (E = O, S, Se, Te) with decreasing antiferromagnetic coupling down the chalcogenide series

Iron compounds containing a bridging oxo or sulfido moiety are ubiquitous in biological systems, but substitution with the heavier chalcogenides selenium and tellurium, however, is much rarer, with only a few examples reported to date. Here we show that treatment of the ferrous starting material [(^tBupyrpyrr₂)Fe(OEt₂)] (1-OEt₂) (^tBupyrpyrr₂ = 3,5-^tBu₂-bis(pyrrolyl)pyridine) with phosphine chalcogenide reagents E = PR₃ results in the neutral phosphine chalcogenide adduct series [(^tBupyrpyrr₂)Fe(EPR₃)] (E = O, S, Se; R = Ph; E = Te; R = ^tBu) (1-E) without any electron transfer, whereas treatment of the anionic starting material [K]₂[(^tBupyrpyrr₂)Fe₂(μ-N₂)] (2-N₂) with the appropriate chalcogenide transfer source yields cleanly the isostructural ferrous bridging mono-chalcogenide ate complexes [K]₂[(^tBupyrpyrr₂)Fe₂(μ-E)] (2-E) (E = O, S, Se, and Te) having significant deviation in the Fe-E-Fe bridge from linear in the case of E = O to more acute for the heaviest chalcogenide. All bridging chalcogenide complexes were analyzed using a variety of spectroscopic techniques, including ¹H NMR, UV-Vis electronic absorbtion, and ⁵⁷Fe Mössbauer. The spin-state and degree of communication between the two ferrous ions were probed via SQUID magnetometry, where it was found that all iron centers were high-spin (S = 2) Fe^II, with magnetic exchange coupling between the Fe^II ions. Magnetic studies established that antiferromagnetic coupling between the ferrous ions decreases as the identity of the chalcogen is tuned from O to the heaviest congener Te.

Reversible Alkyl-Group Migration between Iron and Sulfur in [Fe4S4] Clusters

Synthetic [Fe4S4] clusters with Fe-R groups (R = alkyl/benzyl) are shown to release organic radicals on an [Fe4S4]3+-R/[Fe4S4]2+ redox couple, the same that has been proposed for a radical-generating intermediate in the superfamily of radical S-adenosyl-l-methionine (SAM) enzymes. In attempts to trap the immediate precursor to radical generation, a species in which the alkyl group has migrated from Fe to S is instead isolated. This S-alkylated cluster is a structurally faithful model of intermediates proposed in a variety of functionally diverse S transferase enzymes and features an "[Fe4S4]+-like" core that exists as a physical mixture of S = 1/2 and 7/2 states. The latter corresponds to an unusual, valence-localized electronic structure as indicated by distortions in its geometric structure and supported by computational analysis. Fe-to-S alkyl group migration is (electro)chemically reversible, and the preference for Fe vs S alkylation is dictated by the redox state of the cluster. These findings link the organoiron and organosulfur chemistry of Fe-S clusters and are discussed in the context of metalloenzymes that are proposed to make and break Fe-S and/or C-S bonds during catalysis.

A Molecular Low-Coordinate [Fe-S-Fe] Unit in Three Oxidation States

A [Fe-S-Fe] subunit with a single sulfide bridging two low-coordinate iron ions is the supposed active site of the iron-molybdenum co-factor (FeMoco) of nitrogenase. Here we report a dinuclear monosulfido bridged diiron(II) complex with a similar complex geometry that can be oxidized stepwise to diiron(II/III) and diiron(III/III) complexes while retaining the [Fe-S-Fe] core. The series of complexes has been characterized crystallographically, and electronic structures have been studied using, inter alia, 57 Fe Mössbauer spectroscopy and SQUID magnetometry. Further, cleavage of the [Fe-S-Fe] unit by CS2 is presented.

Half-Integer Spin Triangles: Old Dogs, New Tricks

Spin triangles, that is, triangular complexes of half-integer spins, are the oldest molecular nanomagnets (MNMs). Their magnetic properties have been studied long before molecular magnetism was delineated as a research field. This Review presents the history of their study, with references to the parallel development of new experimental investigations and new theoretical ideas used for their interpretation. It then presents an indicative list of spin-triangle families to illustrate their chemical diversity. Finally, it makes reference to recent developments in terms of theoretical ideas and new phenomena, as well as to the relevance of spin triangles to spintronic devices and new physics.

Cleavage of cluster iron-sulfide bonds in cyclophane-coordinated FenSm complexes

Reaction of the tri(μ-sulfido)triiron(iii) tris(β-diketiminate) cyclophane complex, Fe3S3LEt/Me (1), or of the di(μ-sulfido)diiron(iii) complex Fe2S2HLEt/Me (5), with the related tri(bromide)triiron(ii) complex Fe3Br3LEt/Me (2) results in electron and ligand redistribution to yield the mixed-ligand multiiron complexes, including Fe3Br2SLEt/Me (3) and Fe2Br2SHLEt/Me (4). The cleavage and redistribution observed in these complexes is reminiscent of necessary Fe-S bond cleavage for substrate activation in nitrogenase enzymes, and provides a new perspective on the lability of Fe-S bonds in FeS clusters.

Mechanisms of iron- and O2-sensing by the [4Fe-4S] cluster of the global iron regulator RirA

RirA is a global regulator of iron homeostasis in Rhizobium and related α-proteobacteria. In its [4Fe-4S] cluster-bound form it represses iron uptake by binding to IRO Box sequences upstream of RirA-regulated genes. Under low iron and/or aerobic conditions, [4Fe-4S] RirA undergoes cluster conversion/degradation to apo-RirA, which can no longer bind IRO Box sequences. Here, we apply time-resolved mass spectrometry and electron paramagnetic resonance spectroscopy to determine how the RirA cluster senses iron and O2. The data indicate that the key iron-sensing step is the O2-independent, reversible dissociation of Fe2+ from [4Fe-4S]2+ to form [3Fe-4S]0. The dissociation constant for this process was determined as Kd = ~3 µM, which is consistent with the sensing of 'free' iron in the cytoplasm. O2-sensing occurs through enhanced cluster degradation under aerobic conditions, via O2-mediated oxidation of the [3Fe-4S]0 intermediate to form [3Fe-4S]1+. This work provides a detailed mechanistic/functional view of an iron-responsive regulator.

Isolation of chloride- and hydride-bridged tri-iron and -zinc clusters in a tris(β-oxo-δ-diimine) cyclophane ligand

A cyclophane ligand (H6L) bearing three β-oxo-δ-diimine arms and the corresponding tri-iron and -zinc complexes in which the metal ions are bridged by either chlorides, viz. Fe3Cl3(H3L) (1) and Zn3Cl3(H3L) (2), or hydrides, viz. Fe3H3(H3L) (3), Zn3H3(H3L) (4), were synthesized and characterized. 1 adopts a chair-shaped C3v-symmetric [Fe3(μ-Cl)3]3+ cluster wherein only one hemisphere of the ligand is metallated and the other three ketoimine sites remain protonated as evidenced by single crystal X-ray diffraction and vibrational and NMR spectroscopic analyses. 3 and 4 were synthesized by substitution of the bridging chlorides in 1 and 2 using KBEt3H and are accessed with retention of the three protonated ketoimine sites.

Dinitrogen Activation and Functionalization using β-Diketiminate Iron Complexes

Iron catalysts are adept at breaking the N-N bond of N₂, as exemplified by the iron-catalyzed Haber-Bosch process and the iron-containing clusters at the active sites of nitrogenase enzymes. This Minireview summarizes recent work that has identified a well-characterized set of multi-iron complexes that are capable of breaking and functionalizing N₂, and are amenable to detailed mechanistic studies. We discuss the redox balancing, the potential intermediates during N₂ activation, the variation of alkali metal reductant, the reversibility of N₂ cleavage, and the formation of N-H and N-C bonds from N₂.

Redox-Sensing Iron-Sulfur Cluster Regulators

SIGNIFICANCE

Iron-sulfur cluster proteins carry out multiple functions, including as regulators of gene transcription/translation in response to environmental stimuli. In all known cases, the cluster acts as the sensory module, where the inherent reactivity/fragility of iron-sulfur clusters with small/redox-active molecules is exploited to effect conformational changes that modulate binding to DNA regulatory sequences. This promotes an often substantial reprogramming of the cellular proteome that enables the organism or cell to adapt to, or counteract, its changing circumstances. Recent Advances: Significant progress has been made recently in the structural and mechanistic characterization of iron-sulfur cluster regulators and, in particular, the O₂ and NO sensor FNR, the NO sensor NsrR, and WhiB-like proteins of Actinobacteria. These are the main focus of this review.

CRITICAL ISSUES

Striking examples of how the local environment controls the cluster sensitivity and reactivity are now emerging, but the basis for this is not yet fully understood for any regulatory family.

FUTURE DIRECTIONS

Characterization of iron-sulfur cluster regulators has long been hampered by a lack of high-resolution structural data. Although this still presents a major future challenge, recent advances now provide a firm foundation for detailed understanding of how a signal is transduced to effect gene regulation. This requires the identification of often unstable intermediate species, which are difficult to detect and may be hard to distinguish using traditional techniques. Novel approaches will be required to solve these problems.

Selective Synthesis of Site-Differentiated Fe4S4 and Fe6S6 Clusters

Obtaining rational control over the structure and nuclearity of metalloclusters is an ongoing challenge in synthetic Fe-S cluster chemistry. We report a new family of tridentate imidazolin-2-imine ligands L(NIm^R)₃ that can bind [Fe₄S₄]²⁺ or [Fe₆S₆]³⁺ clusters, depending on the steric profile of the ligand and the reaction stoichiometry. A high-yielding synthetic route to L(NIm^R)₃ ligands (where R is the imidazolyl N substituents) from trianiline and 2-chloroimidazolium precursors is described. For L(NIm^Me)₃ (tris(1,3,5-(3-( N, N-dimethyl-4,5-diphenylimidazolin-2-imino)phenylmethyl))benzene), metalation with 1 equiv of [Ph₄P]₂[Fe₄S₄Cl₄] and 3 equiv of NaBPh₄ furnishes a mixture of products, but adjusting the stoichiometry to 1.5 equiv of [Ph₄P]₂[Fe₄S₄Cl₄] provides (L(NIm^Me)₃)Fe₆S₆Cl₆ in high yield. Formation of an [Fe₆S₆]³⁺ cluster using L(NIm^Tol)₃ (tris(1,3,5-(3-( N, N-bis(4-methylphenyl)-4,5-diphenylimidazolin-2-imino)phenylmethyl))benzene) is not observed; instead, the [Fe₄S₄]²⁺ cluster [(L(NIm^Tol)₃)(Fe₄S₄Cl)][BPh₄] is cleanly generated when 1 equiv of [Ph₄P]₂[Fe₄S₄Cl₄] is employed. The selectivity for cluster nuclearity is rationalized by the orientation of the imidazolyl rings whereby long N-imidazolyl substituents preclude formation of [Fe₆S₆]³⁺ clusters but not [Fe₄S₄]²⁺ clusters. Thus, the structure and nuclearity of L(NIm^R)₃-bound Fe-S clusters may be selectively controlled through rational modification the ligand's substituents.

Catalytic Silylation of Dinitrogen by a Family of Triiron Complexes

A series of triiron complexes supported by a tris(β-diketiminate)cyclophane (L ^3- ) catalyze the reduction of dinitrogen to tris(trimethylsilyl)amine using KC₈ and Me₃SiCl. Employing Fe₃Br₃ L affords 83 ± 7 equiv. NH₄ ⁺/complex after protonolysis, which is a 50% yield based on reducing equivalents. The series of triiron compounds tested evidences the subtle effects of ancillary donors, including halides, hydrides, sulfides, and carbonyl ligands, and metal oxidation state on N(SiMe₃)₃ yield, and highlight Fe₃(μ₃-N)L as a common species in product mixtures. These results suggest that ancillary ligands can be abstracted with Lewis acids under reducing conditions.

Redox-sensing iron-sulfur cluster regulators

SIGNIFICANCE

Iron-sulfur cluster proteins carry out a wide range of functions, including as regulators of gene transcription/translation in response to environmental stimuli. In all known cases, the cluster acts as the sensory module, where the inherent reactivity/fragility of iron-sulfur clusters towards small/redox active molecules is exploited to effect conformational changes that modulate binding to DNA regulatory sequences. This promotes an often substantial re-programming of the cellular proteome that enables the organism or cell to adapt to, or counteract, its changing circumstances. Recent Advances. Significant progress has been made recently in the structural and mechanistic characterization of iron-sulfur cluster regulators and, in particular, the O2 and NO sensor FNR, the NO sensor NsrR, and WhiB-like proteins of Actinobacteria. These are the main focus of this review.

CRITICAL ISSUES

Striking examples of how the local environment controls the cluster sensitivity and reactivity are now emerging, but the basis for this is not yet fully understood for any regulatory family.

FUTURE DIRECTIONS

Characterization of iron-sulfur cluster regulators has long been hampered by a lack of high resolution structural data. Though this still presents a major future challenge, recent advances now provide a firm foundation for detailed understanding of how a signal is transduced to effect gene regulation. This requires the identification of often unstable intermediate species, which are difficult to detect and may be hard to distinguish using traditional techniques. Novel approaches will be required to solve these problems.

Correlating Bridging Ligand with Properties of Ligand-Templated [MnII3X3]3+ Clusters (X = Br-, Cl-, H-, MeO-)

Polynuclear manganese compounds have garnered interest as mimics and models of the water oxidizing complex (WOC) in photosystem II and as single molecule magnets. Molecular systems in which composition can be correlated to physical phenomena, such as magnetic exchange interactions, remain few primarily because of synthetic limitations. Here, we report the synthesis of a family of trimanganese(II) complexes of the type Mn₃X₃L (X = Cl^-, H^-, and MeO^-) where L^3- is a tris(β-diketiminate) cyclophane. The tri(chloride) complex (2) is structurally similar to the reported tri(bromide) complex (1) with the Mn₃X₃ core having a ladder-like arrangement of alternating M-X rungs, whereas the tri(μ-hydride) (3) and tri(μ-methoxide) (4) complexes contain planar hexagonal cores. The hydride and methoxide complexes are synthesized in good yield (48% and 56%) starting with the bromide complex employing a metathesis-like strategy. Compounds 2-4 were characterized by combustion analysis, X-ray crystallography, X-band EPR spectroscopy, SQUID magnetometry, and infrared and UV-visible spectroscopy. Magnetic susceptibility measurements indicate that the Mn₃ clusters in 2-4 are antiferromagnetically coupled, and the spin ground state of the compounds (S = 3/2 (1, 2) or S = 1/2 (3, 4)) is correlated to the identity of the bridging ligand and structural arrangement of the Mn₃X₃ core (X = Br, Cl, H, OCH₃). Electrochemical experiments on isobutyronitrile solutions of 3 and 4 display broad irreversible oxidations centered at 0.30 V.

Synthesis and Mechanism of Formation of Hydride-Sulfide Complexes of Iron

Iron-sulfide complexes with hydride ligands provide an experimental precedent for spectroscopically detected hydride species on the iron-sulfur MoFe₇S₉C cofactor of nitrogenase. In this contribution, we expand upon our recent synthesis of the first iron sulfide hydride complex from an iron hydride and a sodium thiolate ( Arnet, N. A.; Dugan, T. R.; Menges, F. S.; Mercado, B. Q.; Brennessel, W. W.; Bill, E.; Johnson, M. A.; Holland, P. L., J. Am. Chem. Soc. 2015 , 137 , 13220 - 13223 ). First, we describe the isolation of an analogous iron sulfide hydride with a smaller diketiminate supporting ligand, which benefits from easier preparation of the hydride precursor and easier isolation of the product. Second, we describe mechanistic studies on the C-S bond cleavage through which the iron sulfide hydride product is formed. In a key experiment, use of cyclopropylmethanethiolate as the sulfur precursor leads to products from cyclopropane ring opening, implicating an alkyl radical as an intermediate. Combined with the results of isotopic labeling studies, the data are consistent with a mechanism in which homolytic C-S bond cleavage is followed by rebound of the alkyl radical to abstract a hydrogen atom from iron to give the observed alkane and iron-sulfide products.

Reactivity of hydride bridges in a high-spin [Fe3(μ-H)3]3+ cluster: reversible H2/CO exchange and Fe-H/B-F bond metathesis

The triiron trihydride complex Fe₃H₃L (1) [where L^3– is a tris(β-diketiminate)cyclophanate] reacts with CO and with BF₃·OEt₂ to afford (Fe^ICO)₂Fe^II(μ₃-H)L (2) and Fe₃F₃L (3), respectively.

The triiron trihydride complex Fe₃H₃L (1) [where L^3– is a tris(β-diketiminate)cyclophanate] reacts with CO and with BF₃·OEt₂ to afford (Fe^ICO)₂Fe^II(μ₃-H)L (2) and Fe₃F₃L (3), respectively. Variable-temperature and applied-field Mössbauer spectroscopy support the assignment of two high-spin (HS) iron(i) centers and one HS iron(ii) ion in 2. Preliminary studies support a CO-induced reductive elimination of H₂ from 1, rather than CO trapping a species from an equilibrium mixture. This complex reacts with H₂ to regenerate 1 under a dihydrogen atmosphere, which represents a rare example of reversible CO/H₂ exchange and the first to occur at high-spin metal centers, as well as the first example of a reversible multielectron redox reaction at a designed high-spin metal cluster. The formation of 3 proceeds through a previously unreported net fluoride-for-hydride substitution, and 3 is surprisingly chemically inert to Si–H bonds and points to an unexpectedly large difference between the Fe–F and Fe–H bonds in this high-spin system.

Mass spectrometric identification of intermediates in the O2-driven [4Fe-4S] to [2Fe-2S] cluster conversion in FNR

The iron-sulfur cluster containing protein Fumarate and Nitrate Reduction (FNR) is the master regulator for the switch between anaerobic and aerobic respiration in Escherichia coli and many other bacteria. The [4Fe-4S] cluster functions as the sensory module, undergoing reaction with O₂ that leads to conversion to a [2Fe-2S] form with loss of high-affinity DNA binding. Here, we report studies of the FNR cluster conversion reaction using time-resolved electrospray ionization mass spectrometry. The data provide insight into the reaction, permitting the detection of cluster conversion intermediates and products, including a [3Fe-3S] cluster and persulfide-coordinated [2Fe-2S] clusters [[2Fe-2S](S) _n , where n = 1 or 2]. Analysis of kinetic data revealed a branched mechanism in which cluster sulfide oxidation occurs in parallel with cluster conversion and not as a subsequent, secondary reaction to generate [2Fe-2S](S) _n species. This methodology shows great potential for broad application to studies of protein cofactor-small molecule interactions.

A three-coordinate Fe(ii) center within a [3Fe-(μ3-S)] cluster that provides an accessible coordination site

A μ3-sulfide bridged triiron cluster(ii,ii,iii) supported by a cyclophane ligand undergoes metal-based reduction to yield an all-ferrous species. The latter complex incorporates a three-coordinate iron center that provides an accessible coordination site to a solvent molecule.

Insights into small molecule activation by multinuclear first-row transition metal cyclophanates

The rational design of trimetallic transition metal clusters supported by a trinucleating cyclophane ligand, L³⁻, and the reactivities of these complexes with dinitrogen and carbon dioxide are discussed.