Contribution of Mössbauer spectroscopy to the investigation of Fe/S biogenesis

Structural aspects of iron‑sulfur protein biogenesis: An NMR view

Over the last decade, structural aspects involving iron‑sulfur (Fe/S) protein biogenesis have played an increasingly important role in understanding the high mechanistic complexity of mitochondrial and cytosolic machineries maturing Fe/S proteins. In this respect, solution NMR has had a significant impact because of its ability to monitor transient protein-protein interactions, which are abundant in the networks of pathways leading to Fe/S cluster biosynthesis and transfer, as well as thanks to the developments of paramagnetic NMR in both terms of new methodologies and accurate data interpretation. Here, we review the use of solution NMR in characterizing the structural aspects of human Fe/S proteins and their interactions in the framework of Fe/S protein biogenesis. We will first present a summary of the recent advances that have been achieved by paramagnetic NMR and then we will focus our attention on the role of solution NMR in the field of human Fe/S protein biogenesis.

The Intriguing mitoNEET: Functional and Spectroscopic Properties of a Unique [2Fe-2S] Cluster Coordination Geometry

Despite the number of cellular and pathological mitoNEET-related processes, very few details are known about the mechanism of action of the protein. The recently discovered existence of a link between NEET proteins and cancer pave the way to consider mitoNEET and its Fe-S clusters as suitable targets to inhibit cancer cell proliferation. Here, we will review the variety of spectroscopic techniques that have been applied to study mitoNEET in an attempt to explain the drastic difference in clusters stability and reactivity observed for the two redox states, and to elucidate the cellular function of the protein. In particular, the extensive NMR assignment and the characterization of first coordination sphere provide a molecular fingerprint helpful to assist the design of drugs able to impair cellular processes or to directly participate in redox reactions or protein-protein recognition mechanisms.

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.

Bioanalytical applications of Mössbauer spectroscopy

Data on the applications of Mössbauer spectroscopy in the transmission (mainly on 57Fe nuclei) and emission (on 57Co nuclei) variants for analytical studies at the molecular level of metal-containing components in a wide range of biological objects (from biocomplexes and biomacromolecules to supramolecular structures, cells, tissues and organisms) and of objects that are participants or products of biological processes, published in the last 15 years are discussed and systematized. The prospects of the technique in its biological applications, including the developing fields (emission variant, use of synchrotron radiation), are formulated.

The bibliography includes 248 references.

Characterization of Paramagnetic Iron-Sulfur Clusters Using Electron Paramagnetic Resonance Spectroscopy

Continuous-wave (CW) electron paramagnetic resonance (EPR) spectroscopy is a powerful ally in characterizing the multitude of redox-active iron-sulfur cluster-containing ([Fe-S]) species present in biological samples. The technique detects only those clusters that are paramagnetic-having a nonzero total electron spin (S > 0)-thus, it can discriminate between clusters in different oxidation states. The low-temperature CW-EPR spectrum of an [Fe-S] yields the three magnetic g-values that serve as a fingerprint of its electronic structure. This chapter briefly describes the underlying theory that defines this electronic structure and provides a recipe for the acquisition and analysis of EPR spectra of [Fe-S] proteins.

The long-standing relationship between paramagnetic NMR and iron-sulfur proteins: the mitoNEET example. An old method for new stories or the other way around?

Paramagnetic NMR spectroscopy and iron-sulfur (Fe-S) proteins have maintained a synergic relationship for decades. Indeed, the hyperfine shifts with their temperature dependencies and the relaxation rates of nuclei of cluster-bound residues have been extensively used as a fingerprint of the type and of the oxidation state of the Fe-S cluster within the protein frame. The identification of NMR signals from residues surrounding the metal cofactor is crucial for understanding the structure-function relationship in Fe-S proteins, but it is generally impaired in standard NMR experiments by paramagnetic relaxation enhancement due to the presence of the paramagnetic cluster(s). On the other hand, the availability of systems of different sizes and stabilities has, over the years, stimulated NMR spectroscopists to exploit iron-sulfur proteins as paradigmatic cases to develop experiments, models, and protocols. Here, the cluster-binding properties of human mitoNEET have been investigated by 1D and 2D 1 H diamagnetic and paramagnetic NMR, in its oxidized and reduced states. The NMR spectra of both oxidation states of mitoNEET appeared to be significantly different from those reported for previously investigated [ Fe 2 S 2 ] 2 + / + proteins. The protocol we have developed in this work conjugates spectroscopic information arising from "classical" paramagnetic NMR with an extended mapping of the signals of residues around the cluster which can be taken, even before the sequence-specific assignment is accomplished, as a fingerprint of the protein region constituting the functional site of the protein. We show how the combined use of 1D NOE experiments, 13 C direct-detected experiments, and double- and triple-resonance experiments tailored using R1 - and/or R2 -based filters significantly reduces the "blind" sphere of the protein around the paramagnetic cluster. This approach provided a detailed description of the unique electronic properties of mitoNEET, which are responsible for its biological function. Indeed, the NMR properties suggested that the specific electronic structure of the cluster possibly drives the functional properties of different [ Fe 2 S 2 ] proteins.

PRE-driven protein NMR structures: an alternative approach in highly paramagnetic systems

Metalloproteins play key roles across biology, and knowledge of their structure is essential to understand their physiological role. For those metalloproteins containing paramagnetic states, the enhanced relaxation caused by the unpaired electrons often makes signal detection unfeasible near the metal center, precluding adequate structural characterization right where it is more biochemically relevant. Here, we report a protein structure determination by NMR where two different sets of restraints, one containing Nuclear Overhauser Enhancements (NOEs) and another containing Paramagnetic Relaxation Enhancements (PREs), are used separately and eventually together. The protein PioC from Rhodopseudomonas palustris TIE-1 is a High Potential Iron-Sulfur Protein (HiPIP) where the [4Fe-4S] cluster is paramagnetic in both oxidation states at room temperature providing the source of PREs used as alternative distance restraints. Comparison of the family of structures obtained using NOEs only, PREs only, and the combination of both reveals that the pairwise root-mean-square deviation (RMSD) between them is similar and comparable with the precision within each family. This demonstrates that, under favorable conditions in terms of protein size and paramagnetic effects, PREs can efficiently complement and eventually replace NOEs for the structural characterization of small paramagnetic metalloproteins and de novo-designed metalloproteins by NMR. DATABASES: The 20 conformers with the lowest target function constituting the final family obtained using the full set of NMR restraints were deposited to the Protein Data Bank (PDB ID: 6XYV). The 20 conformers with the lowest target function obtained using NOEs only (PDB ID: 7A58) and PREs only (PDB ID: 7A4L) were also deposited to the Protein Data Bank. The chemical shift assignments were deposited to the BMRB (code 34487).

UVA irradiation increases ferrous iron release from human skin fibroblast and endothelial cell ferritin: Consequences for cell senescence and aging

UVA irradiation of human dermal fibroblasts and endothelial cells induces an immediate transient increase in cytosolic Fe(II), as monitored by the fluorescence Fe(II) reporters, FeRhonox1 in cytosol and MitoFerroGreen in mitochondria. Both superoxide dismutase (SOD) inhibition by tetrathiomolybdate (ATM) and catalase inhibition by 3-amino-1, 2, 4-triazole (ATZ) increase and prolong the cytosolic Fe(II) signal after UVA irradiation. SOD inhibition with ATM also increases mitochondrial Fe(II). Thus, mitochondria do not source the UV-dependent increase in cytosolic Fe(II), but instead reflect and amplify raised cytosolic labile Fe(II) concentration. Hence control of cytosolic ferritin iron release is key to preventing UVA-induced inflammation. UVA irradiation also increases dermal endothelial cell H₂O₂, as monitored by the adenovirus vector Hyper-DAAO-NES(HyPer). These UVA-dependent changes in intracellular Fe(II) and H₂O₂ are mirrored by increases in cell superoxide, monitored with the luminescence probe L-012. UV-dependent increases in cytosolic Fe(II), H₂O₂ and L-012 chemiluminescence are prevented by ZnCl₂ (10 μM), an effective inhibitor of Fe(II) transport via ferritin's 3-fold channels. Quercetin (10 μM), a potent membrane permeable Fe(II) chelator, abolishes the cytosolic UVA-dependent FeRhonox1, Fe(II) and HyPer, H₂O₂ and increase in MitoFerroGreen Fe(II) signals. The time course of the quercetin-dependent decrease in endothelial H₂O₂ correlates with the decrease in FeRhox1 signal and both signals are fully suppressed by preloading cells with ZnCl₂. These results confirm that antioxidant enzyme activity is the key factor in controlling intracellular iron levels, and hence maintenance of cell antioxidant capacity is vitally important in prevention of skin aging and inflammation initiated by labile iron and UVA.

Biophysical approaches for the study of metal-protein interactions

Protein-protein interactions play important roles for a variety of cell functions, often involving metal ions; in fact, metal-ion binding mediates and regulates the activity of a wide range of biomolecules. Enlightening all of the specific features of metal-protein and metal-mediated protein-protein interactions can be a very challenging task; a detailed knowledge of the thermodynamic and spectroscopic parameters and the structural changes of the protein is normally required. For this purpose, many experimental techniques are employed, embracing all fields of Analytical and Bioinorganic Chemistry. In addition, the use of peptide models, reproducing the primary sequence of the metal-binding sites, is also proved to be useful. In this paper, a review of the most useful techniques for studying ligand-protein interactions with a special emphasis on metal-protein interactions is provided, with a critical summary of their strengths and limitations.