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Transition Metal Ions in Biology
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Transition Metal Ions in Biology

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 14489

Special Issue Editor

Dr. Pedro Tavares

E-Mail Website
Guest Editor
1. UCIBIO-Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
2. Associate Laboratory i4HB, Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
Interests: transition metal; metalloproteins; metalloenzymes; bioinorganic chemistry; metal ion homeostasis; transition metal catalysts; electron transfer; enzyme cofactors

Special Issue Information

Dear Colleagues,

Transition metal ions are fundamental for life as we know it. They are present in all essential biological processes and pathways, such as nitrogen fixation, photosynthesis, cellular respiration, cell proliferation, stress response, biomineralization, among others. While iron is the most abundant of these elements, manganese, zinc, copper, molybdenum, cobalt, chromium, vanadium, nickel and tungsten also play a substantial role in biological systems. The successful use of transition metal ions is certainly due to the fundamental ability to exist in different oxidation states and in a multitude of coordination structures with three of the five most abundant elements in life (oxygen, nitrogen and sulfur). With the application of up-to-date methodologies to study biological and biochemical systems, new and sophisticated roles of metal ions in living systems can be revealed in articles in this Special Issue that aims to highlight some of the recent advances. We would like to invite experts in the field to contribute both original research papers, as well as review articles, covering basic aspects and future directions in the field.

Dr. Pedro Tavares
Guest Editor

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Keywords

  • transition metal
  • metalloproteins
  • metalloenzymes
  • bioinorganic chemistry
  • metal ion homeostasis
  • transition metal catalysts
  • electron transfer
  • enzyme cofactors

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Published Papers (6 papers)

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Research

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17 pages, 3216 KiB  
Article
A Comparative Multi-Frequency EPR Study of Dipolar Interaction in Tetra-Heme Cytochromes
by Wilfred R. Hagen and Ricardo O. Louro
Int. J. Mol. Sci. 2023, 24(16), 12713; https://doi.org/10.3390/ijms241612713 - 12 Aug 2023
Cited by 2 | Viewed by 1013
Abstract
Distances between Fe ions in multiheme cytochromes are sufficiently short to make the intramolecular dipole-dipole interaction between hemes probable. In the analysis of EPR data from cytochromes, this interaction has thus far been ignored under the assumption that spectra are the simple sum [...] Read more.
Distances between Fe ions in multiheme cytochromes are sufficiently short to make the intramolecular dipole-dipole interaction between hemes probable. In the analysis of EPR data from cytochromes, this interaction has thus far been ignored under the assumption that spectra are the simple sum of non-interacting components. Here, we use a recently developed low-frequency broadband EPR spectrometer to establish the extent of dipolar interaction in the example cytochromes, characterize its spectral signatures, and identify present limitations in the analysis. Broadband EPR spectra of Shewanella oneidensis MR-1 small tetraheme cytochrome (STC) have been collected over the frequency range of 0.45 to 13.11 GHz, and they have been compared to similar data from Desulfovibrio vulgaris Hildenborough cytochrome c3. The two cases are representative examples of two very different heme topologies and corresponding electron-transfer properties in tetraheme proteins. While in cytochrome c3, the six Fe-Fe distances can be sorted into two well-separated groups, those in STC are diffuse. Since the onset of dipolar interaction between Fe-Fe pairs is already observed in the X-band, the g values are determined in the simulation of the 13.11 GHz spectrum. Low-frequency spectra are analyzed with the inclusion of dipolar interaction based on available structural data on mutual distances and orientations between all hemes. In this procedure, all 24 possible assignments of individual heme spectra to heme topologies are sampled. The 24 configurations can be reduced to a few, but inspection falls short of a unique assignment, due to a remaining lack of understanding of the fine details of these complex spectra. In general, the EPR analysis suggests the four-heme system in c3 to be more rigid than that in STC, which is proposed to be related to different physiological roles in electron transfer. Full article
(This article belongs to the Special Issue Transition Metal Ions in Biology)
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14 pages, 3241 KiB  
Article
Dye Decolorization by a Miniaturized Peroxidase Fe-MimochromeVI*a
by Marco Chino, Salvatore La Gatta, Linda Leone, Maria De Fenza, Angela Lombardi, Vincenzo Pavone and Ornella Maglio
Int. J. Mol. Sci. 2023, 24(13), 11070; https://doi.org/10.3390/ijms241311070 - 4 Jul 2023
Cited by 7 | Viewed by 1805
Abstract
Oxidases and peroxidases have found application in the field of chlorine-free organic dye degradation in the paper, toothpaste, and detergent industries. Nevertheless, their widespread use is somehow hindered because of their cost, availability, and batch-to-batch reproducibility. Here, we report the catalytic proficiency of [...] Read more.
Oxidases and peroxidases have found application in the field of chlorine-free organic dye degradation in the paper, toothpaste, and detergent industries. Nevertheless, their widespread use is somehow hindered because of their cost, availability, and batch-to-batch reproducibility. Here, we report the catalytic proficiency of a miniaturized synthetic peroxidase, Fe-Mimochrome VI*a, in the decolorization of four organic dyes, as representatives of either the heterocyclic or triarylmethane class of dyes. Fe-Mimochrome VI*a performed over 130 turnovers in less than five minutes in an aqueous buffer at a neutral pH under mild conditions. Full article
(This article belongs to the Special Issue Transition Metal Ions in Biology)
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14 pages, 1989 KiB  
Article
Influence of Cupric (Cu2+) Ions on the Iron Oxidation Mechanism by DNA-Binding Protein from Starved Cells (Dps) from Marinobacter nauticus
by João P. L. Guerra, Daniela Penas, Pedro Tavares and Alice S. Pereira
Int. J. Mol. Sci. 2023, 24(12), 10256; https://doi.org/10.3390/ijms241210256 - 17 Jun 2023
Cited by 2 | Viewed by 2065
Abstract
Dps proteins (DNA-binding proteins from starved cells) are multifunctional stress defense proteins from the Ferritin family expressed in Prokarya during starvation and/or acute oxidative stress. Besides shielding bacterial DNA through binding and condensation, Dps proteins protect the cell from reactive oxygen species by [...] Read more.
Dps proteins (DNA-binding proteins from starved cells) are multifunctional stress defense proteins from the Ferritin family expressed in Prokarya during starvation and/or acute oxidative stress. Besides shielding bacterial DNA through binding and condensation, Dps proteins protect the cell from reactive oxygen species by oxidizing and storing ferrous ions within their cavity, using either hydrogen peroxide or molecular oxygen as the co-substrate, thus reducing the toxic effects of Fenton reactions. Interestingly, the interaction between Dps and transition metals (other than iron) is a known but relatively uncharacterized phenomenon. The impact of non-iron metals on the structure and function of Dps proteins is a current topic of research. This work focuses on the interaction between the Dps from Marinobacter nauticus (a marine facultative anaerobe bacterium capable of degrading petroleum hydrocarbons) and the cupric ion (Cu2+), one of the transition metals of greater biological relevance. Results obtained using electron paramagnetic resonance (EPR), Mössbauer and UV/Visible spectroscopies revealed that Cu2+ ions bind to specific binding sites in Dps, exerting a rate-enhancing effect on the ferroxidation reaction in the presence of molecular oxygen and directly oxidizing ferrous ions when no other co-substrate is present, in a yet uncharacterized redox reaction. This prompts additional research on the catalytic properties of Dps proteins. Full article
(This article belongs to the Special Issue Transition Metal Ions in Biology)
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16 pages, 4999 KiB  
Article
A Biochemical Deconstruction-Based Strategy to Assist the Characterization of Bacterial Electric Conductive Filaments
by Marta A. Silva, Ana P. Fernandes, David L. Turner and Carlos A. Salgueiro
Int. J. Mol. Sci. 2023, 24(8), 7032; https://doi.org/10.3390/ijms24087032 - 11 Apr 2023
Cited by 2 | Viewed by 1640
Abstract
Periplasmic nanowires and electric conductive filaments made of the polymeric assembly of c-type cytochromes from Geobacter sulfurreducens bacterium are crucial for electron storage and/or extracellular electron transfer. The elucidation of the redox properties of each heme is fundamental to the understanding of [...] Read more.
Periplasmic nanowires and electric conductive filaments made of the polymeric assembly of c-type cytochromes from Geobacter sulfurreducens bacterium are crucial for electron storage and/or extracellular electron transfer. The elucidation of the redox properties of each heme is fundamental to the understanding of the electron transfer mechanisms in these systems, which first requires the specific assignment of the heme NMR signals. The high number of hemes and the molecular weight of the nanowires dramatically decrease the spectral resolution and make this assignment extremely complex or unattainable. The nanowire cytochrome GSU1996 (~42 kDa) is composed of four domains (A to D) each containing three c-type heme groups. In this work, the individual domains (A to D), bi-domains (AB, CD) and full-length nanowire were separately produced at natural abundance. Sufficient protein expression was obtained for domains C (~11 kDa/three hemes) and D (~10 kDa/three hemes), as well as for bi-domain CD (~21 kDa/six hemes). Using 2D-NMR experiments, the assignment of the heme proton NMR signals for domains C and D was obtained and then used to guide the assignment of the corresponding signals in the hexaheme bi-domain CD. This new biochemical deconstruction-based procedure, using nanowire GSU1996 as a model, establishes a new strategy to functionally characterize large multiheme cytochromes. Full article
(This article belongs to the Special Issue Transition Metal Ions in Biology)
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9 pages, 2746 KiB  
Article
Tracking W-Formate Dehydrogenase Structural Changes During Catalysis and Enzyme Reoxidation
by Guilherme Vilela-Alves, Rita Rebelo Manuel, Ana Rita Oliveira, Inês Cardoso Pereira, Maria João Romão and Cristiano Mota
Int. J. Mol. Sci. 2023, 24(1), 476; https://doi.org/10.3390/ijms24010476 - 28 Dec 2022
Cited by 7 | Viewed by 2626
Abstract
Metal-dependent formate dehydrogenases (Fdh) catalyze the reversible conversion of CO2 to formate, with unrivalled efficiency and selectivity. However, the key catalytic aspects of these enzymes remain unknown, preventing us from fully benefiting from their capabilities in terms of biotechnological applications. Here, we [...] Read more.
Metal-dependent formate dehydrogenases (Fdh) catalyze the reversible conversion of CO2 to formate, with unrivalled efficiency and selectivity. However, the key catalytic aspects of these enzymes remain unknown, preventing us from fully benefiting from their capabilities in terms of biotechnological applications. Here, we report a time-resolved characterization by X-ray crystallography of the Desulfovibrio vulgaris Hildenborough SeCys/W-Fdh during formate oxidation. The results allowed us to model five different intermediate structures and to chronologically map the changes occurring during enzyme reduction. Formate molecules were assigned for the first time to populate the catalytic pocket of a Fdh. Finally, the redox reversibility of DvFdhAB in crystals was confirmed by reduction and reoxidation structural studies. Full article
(This article belongs to the Special Issue Transition Metal Ions in Biology)
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Review

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22 pages, 1926 KiB  
Review
Vanadium Compounds with Antidiabetic Potential
by Luísa M. P. F. Amaral, Tânia Moniz, André M. N. Silva and Maria Rangel
Int. J. Mol. Sci. 2023, 24(21), 15675; https://doi.org/10.3390/ijms242115675 - 27 Oct 2023
Cited by 11 | Viewed by 4329
Abstract
Over the last four decades, vanadium compounds have been extensively studied as potential antidiabetic drugs. With the present review, we aim at presenting a general overview of the most promising compounds and the main results obtained with in vivo studies, reported from 1899–2023. [...] Read more.
Over the last four decades, vanadium compounds have been extensively studied as potential antidiabetic drugs. With the present review, we aim at presenting a general overview of the most promising compounds and the main results obtained with in vivo studies, reported from 1899–2023. The chemistry of vanadium is explored, discussing the importance of the structure and biochemistry of vanadate and the impact of its similarity with phosphate on the antidiabetic effect. The spectroscopic characterization of vanadium compounds is discussed, particularly magnetic resonance methodologies, emphasizing its relevance for understanding species activity, speciation, and interaction with biological membranes. Finally, the most relevant studies regarding the use of vanadium compounds to treat diabetes are summarized, considering both animal models and human clinical trials. An overview of the main hypotheses explaining the biological activity of these compounds is presented, particularly the most accepted pathway involving vanadium interaction with phosphatase and kinase enzymes involved in the insulin signaling cascade. From our point of view, the major discoveries regarding the pharmacological action of this family of compounds are not yet fully understood. Thus, we still believe that vanadium presents the potential to help in metabolic control and the clinical management of diabetes, either as an insulin-like drug or as an insulin adjuvant. We look forward to the next forty years of research in this field, aiming to discover a vanadium compound with the desired therapeutic properties. Full article
(This article belongs to the Special Issue Transition Metal Ions in Biology)
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