Sulfur Cluster Research Articles

Mitochondrial De Novo Assembly of Iron–Sulfur Clusters in Mammals: Complex Matters in a Complex That Matters

Iron–sulfur clusters (Fe–S or ISC) are essential cofactors that function in a wide range of biological pathways. In mammalian cells, Fe–S biosynthesis primarily relies on mitochondria and involves a concerted group of evolutionary-conserved proteins forming the ISC pathway. In the early stage of the ISC pathway, the Fe–S core complex is required for de novo assembly of Fe–S. In humans, the Fe–S core complex comprises the cysteine desulfurase NFS1, the scaffold protein ISCU2, frataxin (FXN), the ferredoxin FDX2, and regulatory/accessory proteins ISD11 and Acyl Carrier Protein (ACP). In recent years, the field has made significant advances in unraveling the structure of the Fe–S core complex and the mechanism underlying its function. Herein, we review the key recent findings related to the Fe–S core complex and its components. We highlight some of the unanswered questions and provide a model of the Fe–S assembly within the complex. In addition, we briefly touch on the genetic diseases associated with mutations in the Fe–S core complex components.

Structure and electron transfer pathways of an electron-bifurcating NiFe-hydrogenase.

Electron bifurcation enables thermodynamically unfavorable biochemical reactions. Four groups of bifurcating flavoenzyme are known and three use FAD to bifurcate. FeFe-HydABC hydrogenase represents the fourth group, but its bifurcation site is unknown. We report cryo-EM structures of the related NiFe-HydABCSL hydrogenase that reversibly oxidizes H2 and couples endergonic reduction of ferredoxin with exergonic reduction of NAD. FMN surrounded by a unique arrangement of iron sulfur clusters forms the bifurcating center. NAD binds to FMN in HydB, and electrons from H2 via HydA to a HydB [4Fe-4S] cluster enable the FMN to reduce NAD. Low-potential electron transfer from FMN to the HydC [2Fe-2S] cluster and subsequent reduction of a uniquely penta-coordinated HydB [2Fe-2S] cluster require conformational changes, leading to ferredoxin binding and reduction by a [4Fe-4S] cluster in HydB. This work clarifies the electron transfer pathways for a large group of hydrogenases underlying many essential functions in anaerobic microorganisms.

Computational Approach for Probing Redox Potential for Iron-Sulfur Clusters in Photosystem I.

Simple SummaryMany biological systems contain iron–sulfur clusters, which are typically found as components of electron transport proteins. Continuum electrostatic calculations were used to investigate the effect of protein environment on the redox properties of the three iron–sulfur clusters in the cyanobacterial photosystem I. Our results show a good correlation between the estimated and the measured reduction potential. Moreover, the results indicate that the low potential of FX is shown to be due to the interactions with the surrounding residues and ligating sulfurs. Our results will help in understanding the electron transfer reaction in photosystem I.Photosystem I is a light-driven electron transfer device. Available X-ray crystal structure from Thermosynechococcus elongatus showed that electron transfer pathways consist of two nearly symmetric branches of cofactors converging at the first iron–sulfur cluster FX, which is followed by two terminal iron–sulfur clusters FA and FB. Experiments have shown that FX has lower oxidation potential than FA and FB, which facilitates the electron transfer reaction. Here, we use density functional theory and Multi-Conformer Continuum Electrostatics to explain the differences in the midpoint potentials of the FX, FA and FB clusters. Our calculations show that FX has the lowest oxidation potential compared to FA and FB due to strong pairwise electrostatic interactions with surrounding residues. These interactions are shown to be dominated by the bridging sulfurs and cysteine ligands, which may be attributed to the shorter average bond distances between the oxidized Fe ion and ligating sulfurs for FX compared to FA and FB. Moreover, the electrostatic repulsion between the 4Fe-4S clusters and the positive potential of the backbone atoms is lowest for FX compared to both FA and FB. These results agree with the experimental measurements from the redox titrations of low-temperature EPR signals and of room temperature recombination kinetics.

Structural Insights into a Fusion Protein between a Glutaredoxin-like and a Ferredoxin-Disulfide Reductase Domain from an Extremophile Bacterium

In eukaryotic photosynthetic organisms, ferredoxin–thioredoxin reductases (FTRs) are key proteins reducing several types of chloroplastic thioredoxins (TRXs) in light conditions. The electron cascade necessary to reduce oxidized TRXs involves a pair of catalytic cysteines and a [4Fe–4S] cluster present at the level of the FTR catalytic subunit, the iron–sulfur cluster receiving electrons from ferredoxins. Genomic analyses revealed the existence of FTR orthologs in non-photosynthetic organisms, including bacteria and archaea, referred to as ferredoxin-disulfide reductase (FDR) as they reduce various types of redoxins. In this study, we describe the tridimensional structure of a natural hybrid protein formed by an N-terminal glutaredoxin-like domain fused to a FDR domain present in the marine bacterium Desulfotalea psychrophila Lsv54. This structure provides information on how and why the absence of the variable subunit present in FTR heterodimer which normally protects the Fe–S cluster is dispensable in FDR proteins. In addition, modelling of a tripartite complex based on the existing structure of a rubredoxin (RBX)–FDR fusion present in anaerobic methanogen archaea allows recapitulating the electron flow involving these RBX, FDR and GRX protein domains.

Iron-sulfur clusters as inhibitors and catalysts of viral replication.

A virus hijacks host cellular machineries and metabolites in order to reproduce. In response, the innate immune system activates different processes to fight back. Although many aspects of these processes have been well investigated, the key roles played by iron-sulfur [FeS] clusters, which are among the oldest classes of bio-inorganic cofactors, have barely been considered. Here we discuss how several [FeS] cluster-containing proteins activate, support and modulate the innate immune response to restrict viral infections, and how some of these proteins simultaneously support the replication of viruses. We also propose models of function of some proteins in the innate immune response and argue that [FeS] clusters in many of these proteins act as biological 'fuses' to control the response. We hope this overview helps to inspire future research in the emerging field of bio-inorganic virology/immunology and that such studies may reveal new molecular insight into the links between viral infections and diseases like cancer and neurodegeneration.

Metal-Porphyrin Frameworks Supported by Carbon Nanotubes: Efficient Polysulfide Electrocatalysts for Lithium-Sulfur Batteries

Lithium-sulfide batteries (LSBs) are highly appealing for the next-generation energy storage systems due to their high theoretical energy density and low cost. However, practical applications of LSBs are still largely hindered by the complicated sulfur redox reactions and the fatal polysulfide shuttling. In nature, cytochrome c reductase works as an efficient biocatalyst for oxidative phosphorylation benefiting from the synergistic electron transfer between porphyrins and sulfur clusters. Inspired by this, herein, two porphyrin-based metal-organic frameworks (Hf-H2DPBP and Hf-CoDPBP) supported by carbon nanotubes (CNTs) were demonstrated to be efficient electrocatalysts for accelerating polysulfide redox kinetics when as separator coatings for LSBs. Consequently, the cells exhibited high initial specific capacities of 1345 mAh g-1 (Hf-H2DPBP/CNT) and 1325 mAh g-1 (Hf-CoDPBP/CNT) at 0.1 C, and maintained outstanding stability with capacities of 582 mAh g-1 (Hf-H2DPBP/CNT) and 513 mAh g-1 (Hf-CoDPBP/CNT) after 500 cycles at 2 C with a decay rate of only 0.079% and 0.086% per cycle, respectively. Even at a high sulfur loading up to 6.2 mg/cm2, the cells still demonstrated excellent performances with an initial specific capacity of 911 mAh g-1 (Hf-H2DPBP/CNT) and 952 mAh g-1 (Hf-CoDPBP/CNT) at 0.1 C, and retained the specific capacities of 745 mAh g-1 (Hf-H2DPBP/CNT) and 818 mAh g-1 (Hf-CoDPBP/ CNT) after 60 cycles, respectively. Furthermore, the high and comparable electrochemical performances can be attributed to the remarkable redox kinetics of both free-base and Co porphyrins toward polysulfides, as supported by DFT calculations.

Mammalian iron sulfur cluster biogenesis and human diseases.

IUBMB LifeEarly View SPECIAL ISSUE Mammalian iron sulfur cluster biogenesis and human diseases Nunziata Maio, Corresponding Author Nunziata Maio maion@mail.nih.gov orcid.org/0000-0002-6225-6058 Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA Correspondence Nunziata Maio, Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 9000 Rockville Pike, 20892 Bethesda, MD, USA. Email: maion@mail.nih.govSearch for more papers by this authorTracey A. Rouault, Tracey A. Rouault Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USASearch for more papers by this author Nunziata Maio, Corresponding Author Nunziata Maio maion@mail.nih.gov orcid.org/0000-0002-6225-6058 Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA Correspondence Nunziata Maio, Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 9000 Rockville Pike, 20892 Bethesda, MD, USA. Email: maion@mail.nih.govSearch for more papers by this authorTracey A. Rouault, Tracey A. Rouault Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USASearch for more papers by this author First published: 31 January 2022 https://doi.org/10.1002/iub.2597 Funding information: Intramural Research Program of the National Institutes of Health Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Early ViewOnline Version of Record before inclusion in an issue RelatedInformation

Methods to identify and characterize iron–sulfur oligopeptides in water

Iron–sulfur clusters are ubiquitous cofactors that mediate central biological processes. However, despite their long history, these metallocofactors remain challenging to investigate when coordinated to small (≤ six amino acids) oligopeptides in aqueous solution. In addition to being often unstable in vitro, iron–sulfur clusters can be found in a wide variety of forms with varied characteristics, which makes it difficult to easily discern what is in solution. This difficulty is compounded by the dynamics of iron–sulfur peptides, which frequently coordinate multiple types of clusters simultaneously. To aid investigations of such complex samples, a summary of data from multiple techniques used to characterize both iron–sulfur proteins and peptides is provided. Although not all spectroscopic techniques are equally insightful, it is possible to use several, readily available methods to gain insight into the complex composition of aqueous solutions of iron–sulfur peptides.

Mammalian iron sulfur cluster biogenesis: From assembly to delivery to recipient proteins with a focus on novel targets of the chaperone and co-chaperone proteins.

The authors declare no conflict of interest.

Effect of Oriented Electric Fields on Biologically Relevant Iron-Sulfur Clusters: Tuning Redox Reactivity for Catalysis.

Enzyme-based iron-sulfur clusters, exemplified in families such as hydrogenases, nitrogenases, and radical S-adenosylmethionine enzymes, feature in many essential biological processes. The functionality of biological iron-sulfur clusters extends beyond simple electron transfer, relying primarily on the redox activity of the clusters, with a remarkable diversity for different enzymes. The active-site structure and the electrostatic environment in which the cluster resides direct this redox reactivity. Oriented electric fields in enzymatic active sites can be significantly strong, and understanding the extent of their effect on iron-sulfur cluster reactivity can inform first steps toward rationally engineering their reactivity. An extensive systematic density functional theory-based screening approach using OPBE/TZP has afforded a simple electric field-effect representation. The results demonstrate that the orientation of an external electric field of strength 28.8 MV cm-1 at the center of the cluster can have a significant effect on its relative stability in the order of 35 kJ mol-1. This shows clear implications for the reactivity of iron-sulfur clusters in enzymes. The results also demonstrate that the orientation of the electric field can alter the most stable broken-symmetry state, which further has implications on the directionality of initiated electron-transfer reactions. These insights open the path for manipulating the enzymatic redox reactivity of iron-sulfur cluster-containing enzymes by rationally engineering oriented electric fields within the enzymes.

Expanding the phenotypic and molecular spectrum of NFS1-related disorders that cause functional deficiencies in mitochondrial and cytosolic iron-sulfur cluster containing enzymes.

Iron-sulfur cluster proteins are involved in critical functions for gene expression regulation and mitochondrial bioenergetics including the oxidative phosphorylation system. The c.215G>A p.(Arg72Gln) variant in NFS1 has been previously reported to cause infantile mitochondrial complex II and III deficiency. We describe three additional unrelated patients with the same missense variant. Two infants with the same homozygous variant presented with hypotonia, weakness and lactic acidosis, and one patient with compound heterozygous p.(Arg72Gln) and p.(Arg412His) variants presented as a young adult with gastrointestinal symptoms and fatigue. Skeletal muscle biopsy from patients 1 and 3 showed abnormal mitochondrial morphology, and functional analyses demonstrated decreased activity in respiratory chain complex II and variably in complexes I and III. We found decreased mitochondrial and cytosolic aconitase activities but only mildly affected lipoylation of pyruvate dehydrogenase and 2-oxoglutarate dehydrogenase enzymes. Our studies expand the phenotypic spectrum and provide further evidence for the pathogenicity and functional sequelae of NFS1-related disorders with disturbances in both mitochondrial and cytosolic iron-sulfur cluster containing enzymes.

The Redox Active [2Fe-2S] Clusters: Key-Components of a Plethora of Enzymatic Reactions—Part I: Archaea

The earliest forms of life (i.e., Archaea, Bacteria, and Eukarya) appeared on our planet about ten billion years after its formation. Although Archaea do not seem to possess the multiprotein machinery constituted by the NIF (Nitrogen Fixation), ISC (Iron Sulfur Cluster), SUF (sulfur mobilization) enzymes, typical of Bacteria and Eukarya, some of them are able to encode Fe-S proteins. Here we discussed the multiple enzymatic reactions triggered by the up-to-date structurally characterized members of the archaeal family that require the crucial presence of structurally characterized [2Fe-2S] assemblies, focusing on their biological functions and, when available, on their electrochemical behavior.

During FeS cluster biogenesis, ferredoxin and frataxin use overlapping binding sites on yeast cysteine desulfurase Nfs1

In mitochondria, cysteine desulfurase (Nfs1) plays a central role in the biosynthesis of iron–sulfur (FeS) clusters, cofactors critical for activity of many cellular proteins. Nfs1 functions both as a sulfur donor for cluster assembly and as a binding platform for other proteins functioning in the process. These include not only the dedicated scaffold protein (Isu1) on which FeS clusters are synthesized but also accessory FeS cluster biogenesis proteins frataxin (Yfh1) and ferredoxin (Yah1). Yfh1 has been shown to activate cysteine desulfurase enzymatic activity, whereas Yah1 supplies electrons for the persulfide reduction. While Yfh1 interaction with Nfs1 is well understood, the Yah1–Nfs1 interaction is not. Here, based on the results of biochemical experiments involving purified WT and variant proteins, we report that in Saccharomyces cerevisiae, Yah1 and Yfh1 share an evolutionary conserved interaction site on Nfs1. Consistent with this notion, Yah1 and Yfh1 can each displace the other from Nfs1 but are inefficient competitors when a variant with an altered interaction site is used. Thus, the binding mode of Yah1 and Yfh1 interacting with Nfs1 in mitochondria of S. cerevisiae resembles the mutually exclusive binding of ferredoxin and frataxin with cysteine desulfurase reported for the bacterial FeS cluster assembly system. Our findings are consistent with the generally accepted scenario that the mitochondrial FeS cluster assembly system was inherited from bacterial ancestors of mitochondria.

Acid–base resistant ligand-modified molybdenum–sulfur clusters with enhanced photocatalytic activity towards hydrogen evolution

The first trimeric [MoIV3S7] cluster of MoS-MBTZ containing both S and N coordination sites, obtained by ligand-modification engineering, displays high acid–base stability and excellent photocatalytic activity towards H2evolution.

An unexpected all-metal aromatic tetranuclear silver cluster in human copper chaperone Atox1.

Metal clusters, such as iron–sulfur clusters, play key roles in sustaining life and are intimately involved in the functions of metalloproteins. Herein we report the formation and crystal structure of a planar square tetranuclear silver cluster when silver ions were mixed with human copper chaperone Atox1. Quantum chemical studies reveal that two Ag 5s1 electrons in the tetranuclear silver cluster fully occupy the one bonding molecular orbital, with the assumption that this Ag4 cluster is Ag42+, leading to extensive electron delocalization over the planar square and significant stabilization. This bonding pattern of the tetranuclear silver cluster represents an aromatic all-metal structure that follows a 4n + 2 electron counting rule (n = 0). This is the first time an all-metal aromatic silver cluster was observed in a protein.

A site-differentiated [4Fe-4S] cluster controls electron transfer reactivity of Clostridium acetobutylicum [FeFe]-hydrogenase I.

One of the many functions of reduction–oxidation (redox) cofactors is to mediate electron transfer in biological enzymes catalyzing redox-based chemical transformation reactions. There are numerous examples of enzymes that utilize redox cofactors to form electron transfer relays to connect catalytic sites to external electron donors and acceptors. The compositions of relays are diverse and tune transfer thermodynamics and kinetics towards the chemical reactivity of the enzyme. Diversity in relay design is exemplified among different members of hydrogenases, enzymes which catalyze reversible H2 activation, which also couple to diverse types of donor and acceptor molecules. The [FeFe]-hydrogenase I from Clostridium acetobutylicum (CaI) is a member of a large family of structurally related enzymes where interfacial electron transfer is mediated by a terminal, non-canonical, His-coordinated, [4Fe–4S] cluster. The function of His coordination was examined by comparing the biophysical properties and reactivity to a Cys substituted variant of CaI. This demonstrated that His coordination strongly affected the distal [4Fe–4S] cluster spin state, spin pairing, and spatial orientations of molecular orbitals, with a minor effect on reduction potential. The deviations in these properties by substituting His for Cys in CaI, correlated with pronounced changes in electron transfer and reactivity with the native electron donor–acceptor ferredoxin. The results demonstrate that differential coordination of the surface localized [4Fe–4S]His cluster in CaI is utilized to control intermolecular and intramolecular electron transfer where His coordination creates a physical and electronic environment that enables facile electron exchange between electron carrier molecules and the iron–sulfur cluster relay for coupling to reversible H2 activation at the catalytic site.

Synthesis of atomic platinum with high loading on metal-organic sulfide

Synthesis of ultrafine noble metal with sizes down to nanoscale and even atomic scale is of great significance for heterogeneous catalysis. However, the metal loading is usually kept below 2 wt% due to the aggregation tendency at higher metal contents. Herein, by mimicking the multicentered metal sulfur cluster of metalloenzyme, a bioinspired synthesis of isolated noble metal atoms on the metal-organic sulfide (MOS) framework was reported. The sulfur-rich framework featuring [Mo3S7Br6]2− cluster as the building block and dithiol as the linking node was constructed via chemical bonding and employed to support atomic metal species. Remarkably, highly dispersed platinum atoms with a loading amount as high as 18.5 wt% on the underlying sulfur-rich framework could be obtained after reduction. By increasing the number of benzene rings in the dithiol, the pore size and even the wettability of the MOS frameworks could be modulated. The general applicability of the synthesis could also be extended to the synthesis of atomic Pd. Furthermore, the Pt-loaded MOS could serve as the catalyst for selective hydrogenation of phenylacetylene to styrene in both organic solvent and pure water. Density function theory calculation demonstrated that the atomic Pt sites in the sulfur-rich coordination environment could activate H2 molecules and chemoselectively catalyze the semi-hydrogenation of phenylacetylene to styrene through moderately low energy barriers. The metalation of such a versatile MOS framework will shed light on the synthesis of bioinspired catalytic materials with well-defined structures for more diverse applications.

Using a chemical genetic screen to enhance our understanding of the antimicrobial properties of copper.

The competitive toxic and stress-inducing nature of copper necessitates systems that sequester and export this metal from the cytoplasm of bacterial cells. Several predicted mechanisms of toxicity include the production of reactive oxygen species, thiol depletion, DNA, and iron-sulfur cluster disruption. Accompanying these mechanisms include pathways of homeostasis such as chelation, oxidation, and transport. Still, the mechanisms of copper resistance and sensitivity are not fully understood. Furthermore, studies fail to recognize that the response to copper is likely a result of numerous mechanisms, as in the case for homeostasis, in which proteins and enzymes work as a collective to maintain appropriate copper concentrations. In this study, we used the Keio collection, an array of 3985 Escherichia coli mutants, each with a deleted non-essential gene, to gain a better understanding of the effects of prolonged exposure to copper. In short, we recovered two copper homeostatic genes involved in transporting and assembling that are required in mediating prolonged copper stress under the conditions assessed. The gene coding for the protein TolC was uncovered as a sensitive hit, and we demonstrated that tolC, an outer membrane efflux channel, is key in mitigating copper sensitivity. Additionally, the activity of tRNA processing was enriched along with the deletion of several proteins involved in importing generated copper tolerance. Lastly, key genes belonging to central carbon metabolism and nicotinamide adenine dinucleotide biosynthesis were uncovered as tolerant hits. Overall, this study shows that copper sensitivity and tolerance are a result of numerous mechanisms acting in combination within the cell.

Numerical Investigation of Cathode Structure Influence on Electrochemical Behavior of Lithium-Sulfur Battery

Nowadays, Lithium-Sulfur batteries are often considered as the next generation technology for energy storage systems. This article investigates the influence of the size of sulfur clusters present in the cathode on the battery overall electrochemical behavior. The properties of the cathode are studied by cyclic voltammetry simulations using a custom numerical model implemented into Ansys Fluent. The simulation is supplemented by experimental cyclic voltammetry measurements and images from a scanning electron microscope.

Substitutional oxygen activated photoluminescence enhancement in monolayer transition metal dichalcogenides

Atomically thin transition metal dichalcogenides (TMDCs) are intriguing semiconductors for photonics and optoelectronics, and therefore enhancing their photoluminescence (PL) efficiency is crucial for these applications. Many efforts have been contributed to enhancing the PL performance of monolayer TMDCs, yet the complexity between the microstructure and the PL efficiency has hindered the manipulation of their PL properties. Here we demonstrate that the PL intensity of the monolayer TMDC can be enhanced by nearly one order of magnitude with a ∼20% narrower spectral linewidth after a pre-activation plateau using laser irradiation in ambient environment. Combined experimental and theoretical studies reveal that low-power laser irradiation generates many sulfur vacancy clusters, which are subsequently filled up by oxygen, and the lattice substitutional oxygen clusters induce the dramatic PL enhancement of monolayer WS2. Such PL enhancement phenomenon is found to be universal for other monolayer TMDCs, and thus would benefit their versatile optical applications.