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Relevant bibliographies by topics / Cluster [Fe-S]

Academic literature on the topic 'Cluster [Fe-S]'

Author: Grafiati

Published: 25 May 2024

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Journal articles on the topic "Cluster [Fe-S]"

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Rydz, Leszek, Maria Wróbel, and Halina Jurkowska. "Sulfur Administration in Fe–S Cluster Homeostasis." Antioxidants 10, no. 11 (October 29, 2021): 1738. http://dx.doi.org/10.3390/antiox10111738.

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Mitochondria are the key organelles of Fe–S cluster synthesis. They contain the enzyme cysteine desulfurase, a scaffold protein, iron and electron donors, and specific chaperons all required for the formation of Fe–S clusters. The newly formed cluster can be utilized by mitochondrial Fe–S protein synthesis or undergo further transformation. Mitochondrial Fe–S cluster biogenesis components are required in the cytosolic iron–sulfur cluster assembly machinery for cytosolic and nuclear cluster supplies. Clusters that are the key components of Fe–S proteins are vulnerable and prone to degradation whenever exposed to oxidative stress. However, once degraded, the Fe–S cluster can be resynthesized or repaired. It has been proposed that sulfurtransferases, rhodanese, and 3-mercaptopyruvate sulfurtransferase, responsible for sulfur transfer from donor to nucleophilic acceptor, are involved in the Fe–S cluster formation, maturation, or reconstitution. In the present paper, we attempt to sum up our knowledge on the involvement of sulfurtransferases not only in sulfur administration but also in the Fe–S cluster formation in mammals and yeasts, and on reconstitution-damaged cluster or restoration of enzyme’s attenuated activity.

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Frazzon, J., J. R. Fick, and D. R. Dean. "Biosynthesis of iron-sulphur clusters is a complex and highly conserved process." Biochemical Society Transactions 30, no. 4 (August 1, 2002): 680–85. http://dx.doi.org/10.1042/bst0300680.

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Iron-sulphur ([Fe-S]) clusters are simple inorganic prosthetic groups that are contained in a variety of proteins having functions related to electron transfer, gene regulation, environmental sensing and substrate activation. In spite of their simple structures, biological [Fe-S] clusters are not formed spontaneously. Rather, a consortium of highly conserved proteins is required for both the formation of [Fe-S] clusters and their insertion into various protein partners. Among the [Fe-S] cluster biosynthetic proteins are included a pyridoxal phosphate-dependent enzyme (NifS) that is involved in the activation of sulphur from L-cysteine, and a molecular scaffold protein (NifU) upon which [Fe-S] cluster precursors are formed. The formation or transfer of [Fe-S] clusters appears to require an electron-transfer step. Another complexity is that molecular chaperones homologous to DnaJ and DnaK are involved in some aspect of the maturation of [Fe-S]-cluster-containing proteins. It appears that the basic biochemical features of [Fe-S] cluster formation are strongly conserved in Nature, since organisms from all three life Kingdoms contain the same consortium of homologous proteins required for [Fe-S] cluster formation that were discovered in the eubacteria.

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Bandyopadhyay, Sibali, Kala Chandramouli, and Michael K. Johnson. "Iron–sulfur cluster biosynthesis." Biochemical Society Transactions 36, no. 6 (November 19, 2008): 1112–19. http://dx.doi.org/10.1042/bst0361112.

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Iron–sulfur (Fe–S) clusters are present in more than 200 different types of enzymes or proteins and constitute one of the most ancient, ubiquitous and structurally diverse classes of biological prosthetic groups. Hence the process of Fe–S cluster biosynthesis is essential to almost all forms of life and is remarkably conserved in prokaryotic and eukaryotic organisms. Three distinct types of Fe–S cluster assembly machinery have been established in bacteria, termed the NIF, ISC and SUF systems, and, in each case, the overall mechanism involves cysteine desulfurase-mediated assembly of transient clusters on scaffold proteins and subsequent transfer of pre-formed clusters to apo proteins. A molecular level understanding of the complex processes of Fe–S cluster assembly and transfer is now beginning to emerge from the combination of in vivo and in vitro approaches. The present review highlights recent developments in understanding the mechanism of Fe–S cluster assembly and transfer involving the ubiquitous U-type scaffold proteins and the potential roles of accessory proteins such as Nfu proteins and monothiol glutaredoxins in the assembly, storage or transfer of Fe–S clusters.

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La, Ping, Valentina Ghiaccio, Jianbing Zhang, and Stefano Rivella. "An Orchestrated Balance between Mitochondria Biogenesis, Iron-Sulfur Cluster Synthesis and Cellular Iron Acquisition." Blood 132, Supplement 1 (November 29, 2018): 1048. http://dx.doi.org/10.1182/blood-2018-99-112198.

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Abstract Fe-S clusters are essential cofactors for mitochondria functions, and mitochondria are required for Fe-S cluster synthesis. Additionally, mitochondria biogenesis demands cellular iron uptake, which is negatively regulated by Fe-S clusters. Fe-S clusters are synthesized in the mitochondria and cytosol by two different machineries. However, cytosolic Fe-S cluster synthesis necessitates the mitochondrial Fe-S cluster assembly machinery. PGC-1α is a transcriptional coactivator and a master regulator of mitochondria biogenesis. We confirmed that overexpression of PGC-1α in adipocytes and hepatocytes stimulated mitochondria biogenesis, as measured by Mitotrack Green and Deep Red staining, which label total and alive mitochondria, respectively. We further measured Fe-S cluster synthesis by monitoring the gene expression of Fe-S cluster assembly machinery. By using RT-qPCR and Western Blot analyses, we confirmed that PGC-1α expression increases expression of ABCB7, ISCA1, ISCA2, ISD11, Nfu1 and ISCU, components of the Fe-S assembly machinery, suggesting a coordination between mitochondria biogenesis and Fe-S cluster synthesis. Iron Regulatory Proteins (IRP1 and IRP2) control iron metabolism by binding to specific non-coding sequences within an mRNA, known as iron-responsive elements (IRE). In the absence of Fe-S clusters, IRP1 acts as an aconitase (aka ACO1), while IRP2 is degraded by ubiquitination. Aconitases, represented by the cytosolic form ACO1 and mitochondrial form ACO2, catalyze the isomerization of citrate to isocitrate and require Fe-S clusters to be enzymatically active. PGC-1α overexpression enhanced aconitase activity but not their protein levels, corroborating the notion that Fe-S cluster synthesis was increased. To explore whether this coordination solely depends on PGC-1α, we evaluated the Fe-S cluster synthesis status during brown adipocyte maturation, which is characterized by enhanced mitochondria biogenesis and has been suggested to be PGC-1α-independent. We found that the synthesis of Fe-S cluster assembly machinery increased during maturation in both wild-type and PGC-1α-knockout brown adipocytes, indicating that Fe-S cluster synthesis coordinates with mitochondria biogenesis even in the absence of PGC-1α. To explore the impact of Fe-S cluster synthesis on iron acquisition under enhanced mitochondria biogenesis, we evaluated the expression of the iron importer transferrin receptor 1 (TfR1). TfR1 mRNA contains IREs in the 3' untranslated region (UTR). These 3'UTR IREs can be bound by IRPs and responsible for the subsequent stabilization of TfR1 mRNA. Therefore, if IRP1 associates with Fe-S cluster and converted into ACO1, it is expected that both TfR1 mRNA and protein levels would decrease. In contrast, we found that stimulated Fe-S cluster synthesis increased levels of the TfR1 protein, despite reduced IRP1 activity and destabilized TfR1 mRNA. This suggests that Fe-S cluster synthesis coordinates with mitochondria biogenesis but does not block iron uptake. Moreover, we extended our work to erythropoiesis by using murine erythroleukemia (MEL) cells. Stimulated mitochondria biogenesis enhanced expression of the Fe-S cluster assembly machinery and Fe-S cluster synthesis in these cells. TfR1 protein levels were increased despite elevated Fe-S cluster synthesis and reduced IRP activity. We also found increases in heme levels and the expression of aminolevulinic acid synthase 2 (ALAS2), the rate-limiting enzyme for erythroid heme synthesis. Of note, the ALAS2 mRNA contains IRE at the 5'UTR; binding of IRPs to the IRE inhibits translation while high Fe-S cluster levels lead to release. Moreover, as α- and β-globins chain expression is stimulated by increased heme availability, we also observed that mitochondria biogenesis was associated with increased synthesis of these two proteins and hemoglobinization. These data suggests that erythroid heme synthesis, hemoglobin expression and hemoglobinization coordinates with mitochondria biogenesis via Fe-S cluster synthesis. In conclusion, our data show that Fe-S cluster synthesis coordinates with mitochondria biogenesis but does not block cellular iron uptake, thus suggesting a potential unidentified iron regulator to ensure adequate iron for mitochondria biogenesis. Moreover, our work suggests a mechanism underlying the essential role of mitochondria biogenesis in erythropoiesis. Disclosures Rivella: Disc Medicine: Consultancy; MeiraGTx: Other: SAB; Ionis Pharmaceuticals, Inc: Consultancy; Protagonist: Consultancy.

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Zhang, Yan, Elise R. Lyver, Eiko Nakamaru-Ogiso, Heeyong Yoon, Boominathan Amutha, Dong-Woo Lee, Erfei Bi, et al. "Dre2, a Conserved Eukaryotic Fe/S Cluster Protein, Functions in Cytosolic Fe/S Protein Biogenesis." Molecular and Cellular Biology 28, no. 18 (July 14, 2008): 5569–82. http://dx.doi.org/10.1128/mcb.00642-08.

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ABSTRACT In a forward genetic screen for interaction with mitochondrial iron carrier proteins in Saccharomyces cerevisiae, a hypomorphic mutation of the essential DRE2 gene was found to confer lethality when combined with Δmrs3 and Δmrs4. The dre2 mutant or Dre2-depleted cells were deficient in cytosolic Fe/S cluster protein activities while maintaining mitochondrial Fe/S clusters. The Dre2 amino acid sequence was evolutionarily conserved, and cysteine motifs (CX2CXC and twin CX2C) in human and yeast proteins were perfectly aligned. The human Dre2 homolog (implicated in blocking apoptosis and called CIAPIN1 or anamorsin) was able to complement the nonviability of a Δdre2 deletion strain. The Dre2 protein with triple hemagglutinin tag was located in the cytoplasm and in the mitochondrial intermembrane space. Yeast Dre2 overexpressed and purified from bacteria was brown and exhibited signature absorption and electron paramagnetic resonance spectra, indicating the presence of both [2Fe-2S] and [4Fe-4S] clusters. Thus, Dre2 is an essential conserved Fe/S cluster protein implicated in extramitochondrial Fe/S cluster assembly, similar to other components of the so-called CIA (cytoplasmic Fe/S cluster assembly) pathway although partially localized to the mitochondrial intermembrane space.

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Mendel, Ralf R., Thomas W. Hercher, Arkadiusz Zupok, Muhammad A. Hasnat, and Silke Leimkühler. "The Requirement of Inorganic Fe-S Clusters for the Biosynthesis of the Organometallic Molybdenum Cofactor." Inorganics 8, no. 7 (July 16, 2020): 43. http://dx.doi.org/10.3390/inorganics8070043.

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Iron-sulfur (Fe-S) clusters are essential protein cofactors. In enzymes, they are present either in the rhombic [2Fe-2S] or the cubic [4Fe-4S] form, where they are involved in catalysis and electron transfer and in the biosynthesis of metal-containing prosthetic groups like the molybdenum cofactor (Moco). Here, we give an overview of the assembly of Fe-S clusters in bacteria and humans and present their connection to the Moco biosynthesis pathway. In all organisms, Fe-S cluster assembly starts with the abstraction of sulfur from l-cysteine and its transfer to a scaffold protein. After formation, Fe-S clusters are transferred to carrier proteins that insert them into recipient apo-proteins. In eukaryotes like humans and plants, Fe-S cluster assembly takes place both in mitochondria and in the cytosol. Both Moco biosynthesis and Fe-S cluster assembly are highly conserved among all kingdoms of life. Moco is a tricyclic pterin compound with molybdenum coordinated through its unique dithiolene group. Moco biosynthesis begins in the mitochondria in a Fe-S cluster dependent step involving radical/S-adenosylmethionine (SAM) chemistry. An intermediate is transferred to the cytosol where the dithiolene group is formed, to which molybdenum is finally added. Further connections between Fe-S cluster assembly and Moco biosynthesis are discussed in detail.

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Ayala-Castro, Carla, Avneesh Saini, and F. Wayne Outten. "Fe-S Cluster Assembly Pathways in Bacteria." Microbiology and Molecular Biology Reviews 72, no. 1 (March 2008): 110–25. http://dx.doi.org/10.1128/mmbr.00034-07.

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SUMMARY Iron-sulfur (Fe-S) clusters are required for critical biochemical pathways, including respiration, photosynthesis, and nitrogen fixation. Assembly of these iron cofactors is a carefully controlled process in cells to avoid toxicity from free iron and sulfide. Multiple Fe-S cluster assembly pathways are present in bacteria to carry out basal cluster assembly, stress-responsive cluster assembly, and enzyme-specific cluster assembly. Although biochemical and genetic characterization is providing a partial picture of in vivo Fe-S cluster assembly, a number of mechanistic questions remain unanswered. Furthermore, new factors involved in Fe-S cluster assembly and repair have recently been identified and are expanding the complexity of current models. Here we attempt to summarize recent advances and to highlight new avenues of research in the field of Fe-S cluster assembly.

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Johnson, D. C., P. C. Dos Santos, and D. R. Dean. "NifU and NifS are required for the maturation of nitrogenase and cannot replace the function of isc-gene products in Azotobacter vinelandii." Biochemical Society Transactions 33, no. 1 (February 1, 2005): 90–93. http://dx.doi.org/10.1042/bst0330090.

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In recent years, it has become evident that [Fe-S] proteins, such as hydrogenase, nitrogenase and aconitase, require a complex machinery to assemble and insert their associated [Fe-S] clusters. So far, three different types of [Fe-S] cluster biosynthetic systems have been identified and these have been designated nif, isc and suf. In the present work, we show that the nif-specific [Fe-S] cluster biosynthetic system from Azotobacter vinelandii, which is required for nitrogenase maturation, cannot functionally replace the isc [Fe-S] cluster system used for the maturation of other [Fe-S] proteins, such as aconitase. The results indicate that, in certain cases, [Fe-S] cluster biosynthetic machineries have evolved to perform only specialized functions.

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Srour, Batoul, Sylvain Gervason, Beata Monfort, and Benoit D’Autréaux. "Mechanism of Iron–Sulfur Cluster Assembly: In the Intimacy of Iron and Sulfur Encounter." Inorganics 8, no. 10 (October 3, 2020): 55. http://dx.doi.org/10.3390/inorganics8100055.

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Iron–sulfur (Fe–S) clusters are protein cofactors of a multitude of enzymes performing essential biological functions. Specialized multi-protein machineries present in all types of organisms support their biosynthesis. These machineries encompass a scaffold protein on which Fe–S clusters are assembled and a cysteine desulfurase that provides sulfur in the form of a persulfide. The sulfide ions are produced by reductive cleavage of the persulfide, which involves specific reductase systems. Several other components are required for Fe–S biosynthesis, including frataxin, a key protein of controversial function and accessory components for insertion of Fe–S clusters in client proteins. Fe–S cluster biosynthesis is thought to rely on concerted and carefully orchestrated processes. However, the elucidation of the mechanisms of their assembly has remained a challenging task due to the biochemical versatility of iron and sulfur and the relative instability of Fe–S clusters. Nonetheless, significant progresses have been achieved in the past years, using biochemical, spectroscopic and structural approaches with reconstituted system in vitro. In this paper, we review the most recent advances on the mechanism of assembly for the founding member of the Fe–S cluster family, the [2Fe2S] cluster that is the building block of all other Fe–S clusters. The aim is to provide a survey of the mechanisms of iron and sulfur insertion in the scaffold proteins by examining how these processes are coordinated, how sulfide is produced and how the dinuclear [2Fe2S] cluster is formed, keeping in mind the question of the physiological relevance of the reconstituted systems. We also cover the latest outcomes on the functional role of the controversial frataxin protein in Fe–S cluster biosynthesis.

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Dos Santos, Patricia C., Archer D. Smith, Jeverson Frazzon, Valerie L. Cash, Michael K. Johnson, and Dennis R. Dean. "Iron-Sulfur Cluster Assembly." Journal of Biological Chemistry 279, no. 19 (March 1, 2004): 19705–11. http://dx.doi.org/10.1074/jbc.m400278200.

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The NifU protein is a homodimer that is proposed to provide a molecular scaffold for the assembly of [Fe-S] clusters uniquely destined for the maturation of the nitrogenase catalytic components. There are three domains contained within NifU, with the N-terminal domain exhibiting a high degree of primary sequence similarity to a related family of [Fe-S] cluster biosynthetic scaffolds designated IscU. The C-terminal domain of NifU exhibits sequence similarity to a second family of proposed [Fe-S] cluster biosynthetic scaffolds designated Nfu. Genetic experiments described here involving amino acid substitutions within the N-terminal and C-terminal domains of NifU indicate that both domains can separately participate in nitrogenase-specific [Fe-S] cluster formation, although the N-terminal domain appears to have the dominant function. Thesein vivoexperiments were supported byin vitro[Fe-S] cluster assembly and transfer experiments involving the activation of an apo-form of the nitrogenase Fe protein.

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Dissertations / Theses on the topic "Cluster [Fe-S]"

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Bian, Shumin. "Fe-S proteins : cluster assembly and degradation /." The Ohio State University, 1998. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487952208109007.

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Islam, Shams Tania Afroza. "The catalytic properties of Fe-S cluster containing enzymes." Thesis, University of Oxford, 2017. https://ora.ox.ac.uk/objects/uuid:eba9a2de-52fb-4da8-88e2-1fb0c2f69998.

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Many enzymes contain iron- sulfur (Fe-S) clusters which have a huge impact on their catalytic properties. These clusters may form part of the active site or form an electron relay system from the surface of the protein to the active site. Protein film electrochemistry (PFE) was utilized to elucidate the properties of some Fe-S cluster enzymes, namely, Hyd-1(a hydrogenase with an Fe-S electron relay), PceA (a reductive dehalogenase containing Fe-S clusters to facilitate electron transfer with redox partner) and CODH I_Ch and CODH II_Ch (carbon monoxide dehydrogenases with Fe-S electron relay systems and Ni-incorporated Fe-S clusters as active sites). The role of a proline residue at the active site in Hyd-1 was investigated and it was concluded that some local instability and adverse effect on H₂ activation were introduced upon replacement of proline with an alanine residue. The PceA dehalogenase was studied with PFE in terms of their interactions with various substrates and inhibitors. Furthermore, a method for performing 'film correction' for liquid substrates as that of the dehalogenase was established. Aspects of the catalytic cycle and effects of oxygen (O₂), peroxide (H₂O₂) and hydroxylamine (NH₂OH), a nitrogen-containing peroxide analogue on CODH ICh and CODH IICh were investigated with PFE. Finally, Electrochemical Impedance Spectroscopy (EIS), a technique involving application of alternating current (AC), was added to the portfolio was PFE techniques to compare CpI and CrHydA1 (hydrogenases with and without Fe-S electron relay system, respectively) in terms of time-dependent and time-independent processes within them. A novel term, exchange catalytic rate, for expressing inherent proficiency of the enzyme at zero-current potential was proposed and quantified. A means for measuring electroactive coverage and theoretical turnover during catalysis in PFE experiments was developed.

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Luo, Wen-I. "The Role of Chaperones in Iron-Sulfur Cluster Biogenesis." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1325168796.

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Puglisi, Rita. "Structural and functional characterization of chaperones in Fe-S cluster biogenesis and regulation." Thesis, King's College London (University of London), 2017. https://kclpure.kcl.ac.uk/portal/en/theses/structural-and-functional-characterization-of-chaperones-in-fes-cluster-biogenesis-and-regulation(b2e55aa5-c7b3-4113-8222-7e856a26a36b).html.

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Dysfunctions in Fe-S protein biogenesis and mitochondrial iron accumulation in heart and neurones are part of the phenotype of a genetic neurodegenerative disease called Friedreich's ataxia. This pathology is caused by the deficiency of a mitochondrial protein, frataxin, highly conserved throughout species and currently thought to be a regulator of Fe-S cluster biosynthesis. The study of the mechanism of Fe-S cluster assembly in mitochondria is important to provide insights and valuable information potentially relevant for the study of iron-storage diseases. The biogenesis of iron sulfur clusters involves a complex molecular machine with macromolecular structures containing multiple subunits with specific functions. The high level of conservation of the components suggests the bacterial system as excellent model because of its inherent lower complexity. Isc is one of the operons that encodes proteins responsible for Fe-S cluster biogenesis in bacteria, including the desulfurase IscS, the scaffold protein IscU on which the Fe-S cluster is assembled, the two chaperones HscA and HscB, the trascription regulator IscR, a ferredoxin and two other proteins called IscA and YfhJ, whose role is still unclear. The function of the chaperones HscA and HscB is thought to assist the transfer of the cluster from the scaffold protein to the final acceptors. The main objective of this project was to get new evidence to understand the functions of the chaperones and the mechanisms by which they are involved in Fe-S cluster biogenesis and regulation through the application of structural biology and biochemistry. In particular, I focused on the structural and functional characterization of co-chaperone HscB and the analysis of its interactions with other members of the machinery through NMR and other biophysical techniques. My main findings are that HscB has an unprecedently reported interaction with IscS and that this interaction slows down cluster formation explaining a large plethora of evidence. These findings provide an entirely new perspective to the comprehension of the role of HscB and propose this protein as partner of central components of the Isc machine.

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Ramirez, Melissa V. "Probing Plant Metabolism: The Machineries of [Fe-S] Cluster Assembly and Flavonoid Biosynthesis." Diss., Virginia Tech, 2008. http://hdl.handle.net/10919/77167.

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The organization of metabolism is an essential feature of cellular biochemistry. Metabolism does not occur as a linear assembly of freely diffusing enzymes, but as a complex web in which multiple interactions are possible. Because of the crowded environment of the cell, there must be structured and ordered mechanisms that control metabolic pathways. The following work will examine two metabolic pathways, one that is ubiquitous among living organisms and another that is entirely unique to plants, and examine the organization of each in an attempt to further define mechanisms that are fundamental features of metabolic control. One study offers some of the first characterizations of genes involved in [Fe-S] cluster assembly in Arabidopsis. The other explores the mechanisms that control localization of an enzyme that is part of the well-characterized flavonoid biosynthetic pathway. These two distinct pathways serve as unique models for genetic and biochemical studies that contribute to our overall understanding of plant metabolism.
Ph. D.

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Nuth, Manunya. "Mechanism of Fe-S cluster biosynthesis the [2Fe-2S] IscU as a model scaffold /." Connect to this title online, 2004. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1092856116.

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Thesis (Ph. D.)--Ohio State University, 2004.
Document formatted into pages. Includes bibliographical references. Abstract available online via OhioLINK's ETD Center; full text release delayed at author's request until 2005 Aug. 18.

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Johnson, Deborah Cumaraswamy. "Controlled Expression and Functional Analysis of the Iron-Sulfur Cluster Biosynthetic Machinery in Azotobacter vinelandii." Diss., Virginia Tech, 2006. http://hdl.handle.net/10919/27755.

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A system was developed for the controlled expression of genes in Azotobacter vinelandii by using genomic fusions to the sucrose catabolic regulon. This system was used for the functional analysis of the A. vinelandii isc genes, whose products are involved in the maturation of [Fe-S] proteins. For this analysis the scrX gene, contained within the sucrose catabolic regulon, was replaced by the A. vinelandii iscS, iscU, iscA, hscB, hscA, fdx, iscX gene cluster, resulting in duplicate genomic copies of these genes, one whose expression is directed by the normal isc regulatory elements (Pisc) and the other whose expression is directed by the scrX promoter (PscrX). Functional analysis of [Fe-S] protein maturation components was achieved by placing a mutation within a particular Pisc-controlled gene with subsequent repression of the corresponding PscrX-controlled component by growth on glucose as the carbon source. This experimental strategy was used to show that IscS, IscU, HscBA and Fdx are essential in A. vinelandii and that their depletion results in a deficiency in the maturation of aconitase, an enzyme that requires a [4Fe-4S] cluster for its catalytic activity. Depletion of IscA results in null growth only when cells are cultured under conditions of elevated oxygen, marking the first null phenotype associated with the loss of a bacterial IscA-type protein. Furthermore, the null growth phenotype of cells depleted for HscBA could be partially reversed by culturing cells under conditions of low oxygen. These results are interpreted to indicate that HscBA and IscA could have functions related to the protection or repair of the primary IscS/IscU machinery when grown under aerobic conditions. Conserved amino acid residues within IscS, IscU, and IscA that are essential for their respective functions and/or display a partial or complete dominant-negative growth phenotype were also identified using this system. Inactivation of the IscR repressor protein resulted in a slow growth phenotype that could be specifically attributed to the elevated expression of an intact [Fe-S] cluster biosynthetic system. This system was also used to investigate the extent to which the two [Fe-S] biosynthetic systems in A. vinelandii, Nif and Isc, can perform overlapping functions. Under normal laboratory growth conditions, no cross-talk between the two systems could be detected. However, elevated expression of Isc components as a consequence of inactivation of the IscR repressor protein results in a modest ability of the Isc [Fe-S] protein maturation components to replace the function of Nif-specific [Fe-S] protein maturation components. Similarly, when expressed at very high levels the Nif-specific [Fe-S] protein maturation components could functionally replace the Isc components. Oxygen levels were also found to affect the ability of the Nif and Isc systems to perform common functions. Nevertheless, the lack of significant reciprocal cross-talk between the Nif and Isc systems when they are produced only at levels necessary to satisfy their respective physiological functions, indicates a high level of target specificity with respect to [Fe-S] protein maturation.
Ph. D.

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Beilschmidt, Lena Kristina. "Evidences for the non-redundant function of A-type proteins ISCA1 and ISCA2 in iron-sulfur cluster biogenesis." Thesis, Strasbourg, 2014. http://www.theses.fr/2014STRAJ031/document.

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Les centres fer-soufre (Fe-S) sont des cofacteurs protéiques essentiels qui participent à un nombre important de fonctions cellulaires allant du métabolisme de l’ADN à la respiration mitochondriale. L’assemblage des centres Fe-S et leur insertion dans des protéines acceptrices requièrent l’activité d’une machinerie protéique dédiée. Bien que les protéines de la biogenèse des centres Fe-S soient conservées, plusieurs aspects fonctionnels et mécanistiques restent inconnus. Notre travail de thèse a consisté à caractériser les protéines mammifères de type A, ISCA1 et ISCA2, qui sont impliquées dans la biogenèse mitochondriales des centres Fe-S. En utilisant une approche couplant l’immunoprécipitation avec une analyse protéomique par spectrométrie de masse, plusieurs interactions protéiques d’ISCA1 et ISCA2 ont pu être identifiées. En plus d’une interaction entre ISCA1 et ISCA2, nous avons ainsi montré l’existence d’interactions spécifiques à chacune de ces protéines. Une approche de knockdown dans la souris via l’injection de virus adéno-associés, a permis de montrer l’absence de redondance fonctionnelle entre ISCA1 et ISCA2 puisque seul ISCA1 se trouve être nécessaire dans la maturation d’une catégorie de protéines à centre Fe-S
Iron-sulfur clusters (Fe-S) are essential cofactors involved in different cellular processes ranging from DNA metabolism to respiration. Assembly of Fe-S clusters and their insertion into acceptor proteins is performed by dedicated protein machineries. Despite the high conservation from bacteria to man, different functional and mechanistic aspects of the Fe-S biogenesis remain elusive. In the present work, the function of the two mammalian A-type proteins ISCA1 and ISCA2 that are implicated in Fe-S biogenesis was investigated in vivo. First, an extensive analysis coupling immunoprecipitations and mass spectrometry led to the identification of a direct binding between ISCA1 and ISCA2 as well as specific protein partners of each protein. Furthermore, knockdown experiments in the mouse using adeno-associated virus provided clear evidence of the non-redundant function of ISCA1 and ISCA2, since only ISCA1 was shown to be required for a specific subset of mitochondrial Fe-S proteins

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Jayawardhana, W. Geethamala Dhananjalee. "Investigation of the Influence of Transition Metal Ions on the Fe-S Cluster Biosynthesis Protein SufU." Bowling Green State University / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1448034834.

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Selvaraj, Brinda. "Biochemical and structural studies of 4-hydroxyphenylacetate decarboxylase and its activating enzyme." Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, 2014. http://dx.doi.org/10.18452/17052.

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Strikt anaerobe Bakterien wie Clostridium difficile und C. scatologenes verwenden GRE, um die chemisch ungünstige Decarboxylierung von 4-Hydroxyphenylacetat zu p-Cresol zu katalysieren. Das Enzymsystem besteht aus einer Decarboxylase und dem zugehörigen Aktivierungsenzym. Die 4-Hydroxyphenylacetat-Decarboxylase (4Hpad) besitzt zusätzlich zum Protein-basierten Glycinradikal eine weitere Untereinheit mit bis zu zwei [4Fe-4S] Clustern und repräsentiert hierdurch eine neue Klasse von Fe/S-Cluster-haltigen GREs, die aromatische Verbindungen umsetzen. Das Aktivierungsenzym (4Hpad-AE) weicht vom Standardtypus ab, indem es zusätzlich zum S-Adenosylmethionin(SAM)-bindenden [4Fe-4S]-Cluster (RS-Cluster) mindestens einen weiteren [4Fe-4S]-Cluster bindet. In dieser Studie wurden heterologe Expressions- und Reinigungsprotokolle für 4Hpad und 4Hpad-AE entwickelt. Kristallstrukturen von 4Hpad cokristallisiert mit den Substraten (4-Hydroxyphenylacetat, 3,4-Dihydroxyphenylacetat) und dem Inhibitor (4-Hydroxyphenylacetamid) zeigten geringe strukturelle Änderungen im aktiven Zentrum des Proteins. Die Radikalbildung am 4Hpad-AE wurde durch die Überprüfung einer klassischen reduktiven Spaltung von SAM zu den Reaktionsprodukten 5’-Deoxyadenosin und Methionin bestätigt. EPR- und Mössbauer-Spektroskopische Analysen zeigten, dass 4Hpad-AE mindestens einen zusätzlichen [4Fe-4S] Cluster neben dem einzelnen RS-Cluster enthält. Die katalytische Notwendigkeit eines zusätzlichen Clusters wurde durch eine Mutationsanalyse untersucht, wobei eine verkürzte Version des Enzyms ohne die zusätzliche Cystein-reiche Insertion konstruiert wurde. Das verkürzte Mutante ohne die Bindungsmotive für die zusätzlichen Cluster gekennzeichnet, die Konfiguration, Stöchiometrie und die Funktion der zusätzlichen Cluster diagnostizieren.
4-hydroxyphenylacetate decarboxylase (4Hpad) is a two [4Fe-4S] cluster containing glycyl radical enzyme proposed to use a glycyl/thiyl radical dyad to catalyze the last step of tyrosine fermentation in Clostridium difficile and C. scatologenes by a Kolbe-type decarboxylation. The decarboxylation product p-cresol is a virulence factor of the human pathogen C. difficile. The small subunit of 4Hpad may have a regulatory function with the Fe/S clusters involved in complex formation and radical dissipation in the absence of substrate. The respective activating enzyme (4Hpad-AE) has one or two [4Fe-4S] cluster(s) in addition to the SAM-binding [4Fe-4S] cluster (RS cluster). The role of these auxiliary clusters is still under debate with proposed functions including structural integrity and conduit for electron transfer to the RS cluster. This study shows the optimized expression and purification protocols for the decarboxylase and the co-crystallization experiments and binding studies with 4-hydroxy-phenylacetate and 3,4-dihydroxyphenylacetate and with the inhibitor 4-hydroxy-phenylacetamide. The purification and characterization of active site mutants of decarboxylase are also done. Concerning 4-HPAD-AE, we report on the purification of code-optimized variants, and on spectroscopic and kinetic studies to characterize the respective i) SAM binding enthalpies, ii) rates for reductive cleavage of SAM and iii) putative functions of the additional Fe/S clusters. The truncated mutant lacking the binding motifs for the auxiliary clusters is characterized to diagnose the configuration, stoichiometry and function of the auxiliary clusters.

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Books on the topic "Cluster [Fe-S]"

1

David, Sheila S. Fe-S Cluster Enzymes. Elsevier Science & Technology Books, 2017.

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David, Sheila S. Fe-S Cluster Enzymes Part B. Elsevier Science & Technology Books, 2018.

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Fe-S Cluster Enzymes Part A. Elsevier, 2017. http://dx.doi.org/10.1016/s0076-6879(17)x0012-8.

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Fe-S Cluster Enzymes Part B. Elsevier, 2018. http://dx.doi.org/10.1016/s0076-6879(17)x0016-5.

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David, Sheila S. Fe-S Cluster Enzymes Part A. Elsevier Science & Technology Books, 2017.

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Fe-S Cluster Enzymes Part B, Volume 599. Academic Press, 2018.

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Book chapters on the topic "Cluster [Fe-S]"

1

Crain, Adam V., Kaitlin S. Duschene, John W. Peters, and Joan B. Broderick. "Iron-Sulfur Cluster Proteins, Fe/S-S-adenosylmethionine Enzymes and Hydrogenases." In Encyclopedia of Metalloproteins, 1034–44. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4614-1533-6_355.

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Nishio, K., M. Nakai, and T. Hase. "Fe-S Cluster Formation of Ferredoxin in Chloroplast Stroma." In Photosynthesis: Mechanisms and Effects, 3155–58. Dordrecht: Springer Netherlands, 1998. http://dx.doi.org/10.1007/978-94-011-3953-3_739.

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Tang, Au-chin, Qian-shu Li, and Chia-chung Sun. "The Structural Rule of Mo-Fe-S Cluster Compounds." In Applied Quantum Chemistry, 213–22. Dordrecht: Springer Netherlands, 1986. http://dx.doi.org/10.1007/978-94-009-4746-7_13.

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Molé, Christa N., Kinjal Dave, and Deborah L. Perlstein. "Methods to Unravel the Roles of ATPases in Fe-S Cluster Biosynthesis." In Methods in Molecular Biology, 155–71. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1605-5_9.

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Zhao, Cuiping, Christina A. Roberts, Ian J. Drake, and Yuchen Liu. "Study of Fe-S Cluster Proteins in Methanococcus maripaludis, a Model Archaeal Organism." In Methods in Molecular Biology, 37–50. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1605-5_2.

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Carter, Terrell D., and F. Wayne Outten. "Ni-NTA Affinity Chromatography to Characterize Protein–Protein Interactions During Fe-S Cluster Biogenesis." In Methods in Molecular Biology, 125–36. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1605-5_7.

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Dos Santos, Patricia C., and Dennis R. Dean. "1 A retrospective on the discovery of [Fe-S] cluster biosynthetic machineries in Azotobacter vinelandii." In Biochemistry, Biosynthesis and Human Diseases, edited by Tracey Rouault, 1–30. Berlin, Boston: De Gruyter, 2017. http://dx.doi.org/10.1515/9783110479850-001.

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Pagel, B. E. J., and G. Tautvaišienė. "S/α/Fe Abundance Ratios in Halo Field Stars: Is There a Globular Cluster Connection?" In The Evolution of The Milky Way, 27–33. Dordrecht: Springer Netherlands, 2000. http://dx.doi.org/10.1007/978-94-010-0938-6_3.

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Duverger, Yohann, and Béatrice Py. "Molecular Biology and Genetic Tools to Investigate Functional Redundancy Among Fe-S Cluster Carriers in E. coli." In Methods in Molecular Biology, 3–36. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1605-5_1.

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Ueda, Chie, Michelle Langton, and Maria-Eirini Pandelia. "Characterization of Fe-S Clusters in Proteins by." In Methods in Molecular Biology, 281–305. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1605-5_15.

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Conference papers on the topic "Cluster [Fe-S]"

1

Tong, Wing-Hang, Nunziata Maio, and Tracey A. Rouault. "Abstract B08: Metabolic adaption in inflammatory macrophages through the modulation of Fe-S cluster biogenesis factors." In Abstracts: AACR Special Conference: Metabolism and Cancer; June 7-10, 2015; Bellevue, WA. American Association for Cancer Research, 2016. http://dx.doi.org/10.1158/1557-3125.metca15-b08.

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Das, Nishith K., and T. Shoji. "First-Principles Study of Atomic Hydrogen and Oxygen Adsorption on Doped-Iron Nanoclusters." In 2016 24th International Conference on Nuclear Engineering. American Society of Mechanical Engineers, 2016. http://dx.doi.org/10.1115/icone24-60516.

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Density functional theory calculations have been used to calculate the ground state structure and oxygen and hydrogen adsorption properties of the pure and doped-iron nanoclusters. Small atomic clusters containing two to six atoms have been considered and a single Fe atom has replaced by a minor element i.e. Zr, Ti, and Sc. Doping of a minor element increases the cluster stability and octahedron Fe5Zr is the most stable structure within this study. Zr- and Sc-doped clusters have the highest oxygen and hydrogen adsorption energy. The electronic structure shows a strong hybridization between the metal 3d and oxygen 2p orbitals with a small contribution from metal 4s and 3p orbitals. Additionally, H s and metal 4s states form a new peak below the Fermi energy and a small modification is observed for 3d orbitals near the Fermi level. A small amount of Zr- and Sc-doping into the Fe-based alloys might improve the oxide film adherence.

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Rafikova, O., M. Niihori, C. A. Eccles, M. Vasilyev, and R. Rafikov. "Pulmonary Hypertension and Metabolic Disease in Rats with Human Mutation in Fe-S Cluster Scaffold Protein NFU1." In American Thoracic Society 2019 International Conference, May 17-22, 2019 - Dallas, TX. American Thoracic Society, 2019. http://dx.doi.org/10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a5870.

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Barua, Bipul, Subhasish Mohanty, Saurindranath Majumdar, and Krishnamurti Natesan. "Implementation and Validation of a Fully Mechanistic Fatigue Modeling Approach in a High Performance Computing Framework." In ASME 2019 Pressure Vessels & Piping Conference. American Society of Mechanical Engineers, 2019. http://dx.doi.org/10.1115/pvp2019-93954.

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Abstract Current approaches of fatigue evaluation of nuclear reactor components or other safety critical structural systems use S∼N curve based empirical relations which may have large uncertainty. This uncertainty may be reduced by using a more mechanistic approach. In the proposed mechanistic approach, material models are developed based on the evolution of material behavior under uniaxial fatigue experiments and implement those models into 3D finite element (FE) calculations for fatigue evaluation under multiaxial loading. However, this approach requires simulating structures under thousands of fatigue cycles which necessitates the use of high performance computing (HPC) to determine fatigue life of a large component/system within reasonable time frame. Speeding up the FE simulation of large systems requires the use of a higher number of cores, which is extremely costly, particularly when a commercial FE code is used. Also, commercial software is not necessarily optimized for use in an HPC environment. In this work, an open source parallel computing solver along with a multi-core cluster is used to scale up the number of cores. The HPC-based mechanistic fatigue modeling framework is validated through evaluating fatigue life of a pressurized water reactor surge line pipe under idealistic loading cycles and comparing the simulation results with observations from uniaxial fatigue experiment of 316 stainless steel specimen.

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Sakata, K., K. Tagomori, N. Sugiyama, S. Sasaki, Y. Shinya, M. Yasuki, H. Sasaki, T. Nanbu, K. Takashima, and H. Katanoda. "Development of Velocity Measurement Methods for Cold Sprayed Particle Clusters Using Particle Image Velocimetry Techniques." In ITSC 2014, edited by R. S. Lima, A. Agarwal, M. M. Hyland, Y. C. Lau, G. Mauer, A. McDonald, and F. L. Toma. DVS Media GmbH, 2014. http://dx.doi.org/10.31399/asm.cp.itsc2014p0648.

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Abstract In this investigation, particle image velocimetry (PIV) and direct imaging are used to measure particle velocities during cold spraying. Four feedstock powders were sprayed, including Ni, WC-Co, carbonyl Fe, and Cr steel. Multiple exposures at 500 ns intervals were used to measure in-flight particle velocities via direct imaging with a high shutter speed camera. Velocimetry measurements were made with a double-pulse laser and a high-resolution camera. With the minimum frame straddling time set to 100 ns, a maximum particle velocity of 1052 m/s was measured.

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Reports on the topic "Cluster [Fe-S]"

1

Choudhary, Ruplal, Victor Rodov, Punit Kohli, Elena Poverenov, John Haddock, and Moshe Shemesh. Antimicrobial functionalized nanoparticles for enhancing food safety and quality. United States Department of Agriculture, January 2013. http://dx.doi.org/10.32747/2013.7598156.bard.

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Original objectives The general goal of the project was to utilize the bactericidal potential of curcumin- functionalizednanostructures (CFN) for reinforcement of food safety by developing active antimicrobial food-contact surfaces. In order to reach the goal, the following secondary tasks were pursued: (a) further enhancement of the CFN activity based on understanding their mode of action; (b) preparing efficient antimicrobial surfaces, investigating and optimizing their performance; (c) testing the efficacy of the antimicrobial surfaces in real food trials. Background to the topic The project dealt with reducing microbial food spoilage and safety hazards. Cross-contamination through food-contact surfaces is one of the major safety concerns, aggravated by bacterial biofilm formation. The project implemented nanotech methods to develop novel antimicrobial food-contact materials based on natural compounds. Food-grade phenylpropanoidcurcumin was chosen as the most promising active principle for this research. Major conclusions, solutions, achievements In agreement with the original plan, the following research tasks were performed. Optimization of particles structure and composition. Three types of curcumin-functionalizednanostructures were developed and tested: liposome-type polydiacetylenenanovesicles, surface- stabilized nanoparticles and methyl-β-cyclodextrin inclusion complexes (MBCD). The three types had similar minimal inhibitory concentration but different mode of action. Nanovesicles and inclusion complexes were bactericidal while the nanoparticlesbacteriostatic. The difference might be due to different paths of curcumin penetration into bacterial cell. Enhancing the antimicrobial efficacy of CFN by photosensitization. Light exposure strengthened the bactericidal efficacy of curcumin-MBCD inclusion complexes approximately three-fold and enhanced the bacterial death on curcumin-coated plastic surfaces. Investigating the mode of action of CFN. Toxicoproteomic study revealed oxidative stress in curcumin-treated cells of E. coli. In the dark, this effect was alleviated by cellular adaptive responses. Under light, the enhanced ROS burst overrode the cellular adaptive mechanisms, disrupted the iron metabolism and synthesis of Fe-S clusters, eventually leading to cell death. Developing industrially-feasible methods of binding CFN to food-contact surfaces. CFN binding methods were developed for various substrates: covalent binding (binding nanovesicles to glass, plastic and metal), sonochemical impregnation (binding nanoparticles to plastics) and electrostatic layer-by-layer coating (binding inclusion complexes to glass and plastics). Investigating the performance of CFN-coated surfaces. Flexible and rigid plastic materials and glass coated with CFN demonstrated bactericidal activity towards Gram-negative (E. coli) and Gram-positive (Bac. cereus) bacteria. In addition, CFN-impregnated plastic material inhibited bacterial attachment and biofilm development. Testing the efficacy of CFN in food preservation trials. Efficient cold pasteurization of tender coconut water inoculated with E. coli and Listeriamonocytogeneswas performed by circulation through a column filled with CFN-coated glass beads. Combination of curcumin coating with blue light prevented bacterial cross contamination of fresh-cut melons through plastic surfaces contaminated with E. coli or Bac. licheniformis. Furthermore, coating of strawberries with CFN reduced fruit spoilage during simulated transportation extending the shelf life by 2-3 days. Implications, both scientific and agricultural BARD Report - Project4680 Page 2 of 17 Antimicrobial food-contact nanomaterials based on natural active principles will preserve food quality and ensure safety. Understanding mode of antimicrobial action of curcumin will allow enhancing its dark efficacy, e.g. by targeting the microbial cellular adaptation mechanisms.

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