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Biomolecules
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Recent Insights into Metal Binding Proteins
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Recent Insights into Metal Binding Proteins

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Biomacromolecules: Proteins, Nucleic Acids and Carbohydrates".

Deadline for manuscript submissions: closed (31 December 2024) | Viewed by 6753

Special Issue Editors

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: metalloproteins; bioinorganic chemistry; spectroscopy; transition metal catalysts; electron transfer; enzyme cofactors
Dr. Alice S. Pereira

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: iron homeostasis; non-heme iron proteins; DNA-binding, protection and condensation in bacteria; molecular dynamics; enzyme kinetics

Special Issue Information

Dear Colleagues,

Metal ions impart important functional and structural diversity to biologic systems. Without metal ions, biochemical processes would be impossible. Only the elemental characteristics of metal ions can support life’s diverse needs in terms of on redox chemistry, energy transduction, molecular transport, cellular detoxification, protection, regulation, and signaling.

Currently, more than 40% of all known protein structures contain metal ions, with characteristic structures ranging from simple mononuclear bound atoms to complex multi- or hetero-metal clusters. With only a handful of amino acids, organic cofactors, small molecules and labile atoms known to contribute metal ion binding in proteins, the known structural plasticity is surprising. Tailored by evolution, binding sites are strongholds that address catalysis or fleeting when metal transport is needed.

Dealing with metal ions also requires us to find solutions that an avoid availability and toxicity problems. Enzymes that contribute to homeostasis are certainly among the most ubiquitous systems in biology. Excellent examples include the protein nanocages that deal with iron storage and the toxicity that can be found to possess the same basic structural features and functions in all living organisms.

This Special Issue aims to publish up-to-date views and highlight recent discoveries in the structural and functional characterization of metal-binding proteins structural and their impact on biology. As such, we would like to invite experts in the field to contribute both original research papers and review articles, covering basic aspects and future directions in the field.

Dr. Pedro Tavares
Dr. Alice S. Pereira
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomolecules is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • metal-binding proteins
  • metalloproteins
  • metalloenzymes
  • metal homeostasis

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Published Papers (4 papers)

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Research

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24 pages, 7946 KiB  
Article
Heterologous Expression of Either Human or Soya Bean Ferritins in Budding Yeast Reveals Common Functions Protecting Against Oxidative Agents and Counteracting Double-Strand Break Accumulation
by Nuria Pujol Carrión and Maria Ángeles de la Torre-Ruiz
Biomolecules 2025, 15(3), 447; https://doi.org/10.3390/biom15030447 - 20 Mar 2025
Viewed by 289
Abstract
Ferritins are globular proteins that, upon self-assembly in nanocages, are capable of bio-safely storing huge concentrations of bioavailable iron. They are present in most cell types and organisms; one of the exceptions is yeast. Heterologous expression of either human or vegetal ferritins in [...] Read more.
Ferritins are globular proteins that, upon self-assembly in nanocages, are capable of bio-safely storing huge concentrations of bioavailable iron. They are present in most cell types and organisms; one of the exceptions is yeast. Heterologous expression of either human or vegetal ferritins in Saccharomyces cerevisiae revealed new and unknown functions for soya bean ferritins; validated this model by confirming previously characterized functions in human ferritins and also demonstrated that, like human H chain, vegetal H1, and H2 chains also shown a tendency to localize in the nucleus when expressed in an eukaryotic cell model lacking plastids and chloroplasts. Furthermore, when expressed in the system budding yeast, the four ferritins (human H and L and soya bean H1 and H2 chains) present equivalent and relevant functions as protectors against oxidative damage and against the accumulation of double-strand breaks in the DNA. We present evidence demonstrating that these effects are exclusively observed with oxidative agents that operate through the Fenton reaction, such as H2O2. Here, we also discuss the ferritin requirement for N-glycosylation to exert these functions. We believe that our approach might contribute to extending the knowledge around ferritin function and its consequent relevance to human health. Full article
(This article belongs to the Special Issue Recent Insights into Metal Binding Proteins)
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15 pages, 4077 KiB  
Article
Investigating MerR’s Selectivity: The Crosstalk Between Cadmium and Copper Under Elevated Stress Conditions
by Anne Soisig Steunou, Anne Durand, Sylviane Liotenberg, Marie-Line Bourbon and Soufian Ouchane
Biomolecules 2024, 14(11), 1429; https://doi.org/10.3390/biom14111429 - 9 Nov 2024
Cited by 1 | Viewed by 1047
Abstract
Bacteria respond to metal pollution through sensors that control the uptake and the detoxification machineries. Specificity in metal recognition is therefore a prerequisite for triggering the appropriate response, particularly when facing a mixture of metals. In response to Cu+, the purple [...] Read more.
Bacteria respond to metal pollution through sensors that control the uptake and the detoxification machineries. Specificity in metal recognition is therefore a prerequisite for triggering the appropriate response, particularly when facing a mixture of metals. In response to Cu+, the purple bacterium Rubrivivax gelatinosus induces the efflux Cu+-ATPase CopA by the Cu+ regulator CopR. However, genetic analyses have suggested the presence of additional regulators. Here, we show that CadR, the Cd2+ sensor, is involved in Cd2+ and Cu+ tolerance and demonstrate that CopR and CadR share common target genes. Interestingly, expression of the Cu+ detoxification and efflux (CopI/CopA) system was induced by Cd2+ and downregulated in the double mutant copRcadR−. This double mutant was more sensitive to low Cu+ concentration than the single copR− mutant, and accumulation of coproporphyrin III pointed to a significantly decreased expression of CopA. Furthermore, analyses of Cd2+ toxicity in the cadR− mutant suggested that although CopR is Cu+ selective, CopR is involved in Cd2+ response since the addition of Cu+ alleviates Cd2+ toxicity. Based on our current knowledge of metal transport across the inner membrane, Cd2+ and Cu+ do not share common efflux routes nor do they share common regulators. Nevertheless, the crosstalk between Cd2+ and Cu+ tolerance systems is demonstrated in the present study. The modulation of Cu+ detoxification by a Cd2+ regulator in vivo places emphasis on the relaxed selectivity, under elevated metal concentration, in MerR regulators. Full article
(This article belongs to the Special Issue Recent Insights into Metal Binding Proteins)
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13 pages, 3609 KiB  
Article
Crystallization of Ethylene Plant Hormone Receptor—Screening for Structure
by Buket Rüffer, Yvonne Thielmann, Moritz Lemke, Alexander Minges and Georg Groth
Biomolecules 2024, 14(3), 375; https://doi.org/10.3390/biom14030375 - 20 Mar 2024
Viewed by 2326
Abstract
The plant hormone ethylene is a key regulator of plant growth, development, and stress adaptation. Many ethylene-related responses, such as abscission, seed germination, or ripening, are of great importance to global agriculture. Ethylene perception and response are mediated by a family of integral [...] Read more.
The plant hormone ethylene is a key regulator of plant growth, development, and stress adaptation. Many ethylene-related responses, such as abscission, seed germination, or ripening, are of great importance to global agriculture. Ethylene perception and response are mediated by a family of integral membrane receptors (ETRs), which form dimers and higher-order oligomers in their functional state as determined by the binding of Cu(I), a cofactor to their transmembrane helices in the ER-Golgi endomembrane system. The molecular structure and signaling mechanism of the membrane-integral sensor domain are still unknown. In this article, we report on the crystallization of transmembrane (TM) and membrane-adjacent domains of plant ethylene receptors by Lipidic Cubic Phase (LCP) technology using vapor diffusion in meso crystallization. The TM domain of ethylene receptors ETR1 and ETR2, which is expressed in E. coli in high quantities and purity, was successfully crystallized using the LCP approach with different lipids, lipid mixtures, and additives. From our extensive screening of 9216 conditions, crystals were obtained from identical crystallization conditions for ETR1 (aa 1-316) and ETR2 (aa 1-186), diffracting at a medium–high resolution of 2–4 Å. However, data quality was poor and not sufficient for data processing or further structure determination due to rotational blur and high mosaicity. Metal ion loading and inhibitory peptides were explored to improve crystallization. The addition of Zn(II) increased the number of well-formed crystals, while the addition of ripening inhibitory peptide NIP improved crystal morphology. However, despite these improvements, further optimization of crystallization conditions is needed to obtain well-diffracting, highly-ordered crystals for high-resolution structural determination. Overcoming these challenges will represent a major breakthrough in structurally determining plant ethylene receptors and promote an understanding of the molecular mechanisms of ethylene signaling. Full article
(This article belongs to the Special Issue Recent Insights into Metal Binding Proteins)
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Review

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24 pages, 8307 KiB  
Review
Encapsulated Ferritin-like Proteins: A Structural Perspective
by Elif Eren, Norman R. Watts, Felipe Montecinos and Paul T. Wingfield
Biomolecules 2024, 14(6), 624; https://doi.org/10.3390/biom14060624 - 25 May 2024
Cited by 1 | Viewed by 2407
Abstract
Encapsulins are self-assembling nano-compartments that naturally occur in bacteria and archaea. These nano-compartments encapsulate cargo proteins that bind to the shell’s interior through specific recognition sequences and perform various metabolic processes. Encapsulation enables organisms to perform chemical reactions without exposing the rest of [...] Read more.
Encapsulins are self-assembling nano-compartments that naturally occur in bacteria and archaea. These nano-compartments encapsulate cargo proteins that bind to the shell’s interior through specific recognition sequences and perform various metabolic processes. Encapsulation enables organisms to perform chemical reactions without exposing the rest of the cell to potentially harmful substances while shielding cargo molecules from degradation and other adverse effects of the surrounding environment. One particular type of cargo protein, the ferritin-like protein (FLP), is the focus of this review. Encapsulated FLPs are members of the ferritin-like protein superfamily, and they play a crucial role in converting ferrous iron (Fe+2) to ferric iron (Fe+3), which is then stored inside the encapsulin in mineralized form. As such, FLPs regulate iron homeostasis and protect organisms against oxidative stress. Recent studies have demonstrated that FLPs have tremendous potential as biosensors and bioreactors because of their ability to catalyze the oxidation of ferrous iron with high specificity and efficiency. Moreover, they have been investigated as potential targets for therapeutic intervention in cancer drug development and bacterial pathogenesis. Further research will likely lead to new insights and applications for these remarkable proteins in biomedicine and biotechnology. Full article
(This article belongs to the Special Issue Recent Insights into Metal Binding Proteins)
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