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Biomolecule-Metal Ion Interaction

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A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Molecular Biophysics: Structure, Dynamics, and Function".

Deadline for manuscript submissions: closed (20 May 2023) | Viewed by 27261

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Prof. Dr. Hidetaka Torigoe

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Guest Editor

Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, Tokyo 162-8601, Japan
Interests: thermodynamics of biomolecules and biomolecular interaction; non-B DNA structure; nucleic acid-metal ion interaction; nucleic acid-protein interaction; artificial regulation of gene expression; telomere regulation mechanism

Prof. Dr. Li-June Ming

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Co-Guest Editor

Department of Chemistry, University of South Florida, Tampa, FL 33620, USA
Interests: bioinorganic; metallohydrolases; metalloantibiotics; metallodrugs; metallopolymers; paramagnetic NMR; kinetics; oxidation; oxidative stress; reactive oxygen species (ROS); metallo-beta-amyloid

Dr. Isabelle Michaud-Soret

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Co-Guest Editor

Centre National de la Recherche Scientifique (CNRS), LCBM-UMR 5249, 38000 Grenoble, France
Interests: iron; metalloprotein; transcription factor; metal homeostasis; silver nanoparticle; ferric uptake regulator; bioinorganic; antibacterial agent; biocide; antivirulence
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Special Issue Information

Dear Colleagues,

The presence of metal ions in biomolecules is essential. They play very important roles in many biological processes, such as molecular interactions, folding, self-organisation and assembly, signalling, energy and material transport, recognition, etc. Specifically, metal ions play several major roles in proteins, and especially in enzymes. They are an integral part of many enzymes and are indispensable in many catalytic reactions. In addition, metal ions also play an important role in nucleic acid structure formation, repressing electrostatic repulsion among negative charges of phosphate backbones. Metal ions are often necessary for the catalytic activity of nucleic acids, such as ribozymes. Moreover, our understanding of the interaction between the metal ions and biomolecules is expanding rapidly thanks to studies using a variety of experimental approaches and model systems.

Our Special Issue welcomes comprehensive reviews or original research articles related to the interaction between metal ions and biomolecules, as well as the new methods of exploring the interaction between them. We look forward to reading your contributions.

Prof. Dr. Hidetaka Torigoe
Prof. Dr. Li-June Ming
Dr. Isabelle Michaud-Soret
Guest Editors

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Keywords

metal ion
biomolecules
protein
enzyme
nucleic acid

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Published Papers (9 papers)

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Research

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15 pages, 3181 KiB

Open AccessArticle

Biochemical Characterization of the Copper Nitrite Reductase from Neisseria gonorrhoeae

by Daniela S. Barreiro, Ricardo N. S. Oliveira and Sofia R. Pauleta

Biomolecules 2023, 13(8), 1215; https://doi.org/10.3390/biom13081215 - 4 Aug 2023

Cited by 4 | Viewed by 2236

Abstract

The copper-containing nitrite reductase from Neisseria gonorrhoeae has been shown to play a critical role in the infection mechanism of this microorganism by producing NO and abolishing epithelial exfoliation. This enzyme is a trimer with a type 1 copper center per subunit and a type 2 copper center in the subunits interface, with the latter being the catalytic site. The two centers were characterized for the first time by EPR and CD spectroscopy, showing that the type 1 copper center has a high rhombicity due to its lower symmetry and more tetragonal structure, while the type 2 copper center has the usual properties, but with a smaller hyperfine coupling constant (A_// = 10.5 mT). The thermostability of the enzyme was analyzed by differential scanning calorimetry, which shows a single endothermic transition in the thermogram, with a maximum at 94 °C, while the CD spectra in the visible region indicate the presence of the type 1 copper center up to 80 °C. The reoxidation of the N. gonorrhoeae copper-containing nitrite reductase in the presence of nitrite were analyzed by visible spectroscopy and showed a pH dependence, being higher at pH 5.5–6.0. The high thermostability of this enzyme may be important to maintaining a high activity in the extracellular space and to making it less susceptible to denaturation and proteolysis, contributing to the proliferation of N. gonorrhoeae. Full article

(This article belongs to the Special Issue Biomolecule-Metal Ion Interaction)

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29 pages, 4603 KiB

Open AccessEditor’s ChoiceArticle

Structural and Biochemical Characterization of Mycobacterium tuberculosis Zinc SufU-SufS Complex

by Ingie Elchennawi, Philippe Carpentier, Christelle Caux, Marine Ponge and Sandrine Ollagnier de Choudens

Biomolecules 2023, 13(5), 732; https://doi.org/10.3390/biom13050732 - 24 Apr 2023

Cited by 10 | Viewed by 4573

Abstract

Iron-sulfur (Fe-S) clusters are inorganic prosthetic groups in proteins composed exclusively of iron and inorganic sulfide. These cofactors are required in a wide range of critical cellular pathways. Iron-sulfur clusters do not form spontaneously in vivo; several proteins are required to mobilize sulfur and iron, assemble and traffic-nascent clusters. Bacteria have developed several Fe-S assembly systems, such as the ISC, NIF, and SUF systems. Interestingly, in Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), the SUF machinery is the primary Fe-S biogenesis system. This operon is essential for the viability of Mtb under normal growth conditions, and the genes it contains are known to be vulnerable, revealing the Mtb SUF system as an interesting target in the fight against tuberculosis. In the present study, two proteins of the Mtb SUF system were characterized for the first time: Rv1464(sufS) and Rv1465(sufU). The results presented reveal how these two proteins work together and thus provide insights into Fe-S biogenesis/metabolism by this pathogen. Combining biochemistry and structural approaches, we showed that Rv1464 is a type II cysteine-desulfurase enzyme and that Rv1465 is a zinc-dependent protein interacting with Rv1464. Endowed with a sulfurtransferase activity, Rv1465 significantly enhances the cysteine-desulfurase activity of Rv1464 by transferring the sulfur atom from persulfide on Rv1464 to its conserved Cys40 residue. The zinc ion is important for the sulfur transfer reaction between SufS and SufU, and His354 in SufS plays an essential role in this reaction. Finally, we showed that Mtb SufS-SufU is more resistant to oxidative stress than E. coli SufS-SufE and that the presence of zinc in SufU is likely responsible for this improved resistance. This study on Rv1464 and Rv1465 will help guide the design of future anti-tuberculosis agents. Full article

(This article belongs to the Special Issue Biomolecule-Metal Ion Interaction)

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24 pages, 2034 KiB

Open AccessArticle

Inter-Site Cooperativity of Calmodulin N-Terminal Domain and Phosphorylation Synergistically Improve the Affinity and Selectivity for Uranyl

by Maria Rosa Beccia, Sandrine Sauge-Merle, Nicolas Brémond, David Lemaire, Pierre Henri, Christine Battesti, Philippe Guilbaud, Serge Crouzy and Catherine Berthomieu

Biomolecules 2022, 12(11), 1703; https://doi.org/10.3390/biom12111703 - 17 Nov 2022

Cited by 3 | Viewed by 2114

Abstract

Uranyl–protein interactions participate in uranyl trafficking or toxicity to cells. In addition to their qualitative identification, thermodynamic data are needed to predict predominant mechanisms that they mediate in vivo. We previously showed that uranyl can substitute calcium at the canonical EF-hand binding motif of calmodulin (CaM) site I. Here, we investigate thermodynamic properties of uranyl interaction with site II and with the whole CaM N-terminal domain by spectrofluorimetry and ITC. Site II has an affinity for uranyl about 10 times lower than site I. Uranyl binding at site I is exothermic with a large enthalpic contribution, while for site II, the enthalpic contribution to the Gibbs free energy of binding is about 10 times lower than the entropic term. For the N–terminal domain, macroscopic binding constants for uranyl are two to three orders of magnitude higher than for calcium. A positive cooperative process driven by entropy increases the second uranyl-binding event as compared with the first one, with ΔΔG = −2.0 ± 0.4 kJ mol⁻¹, vs. ΔΔG = −6.1 ± 0.1 kJ mol⁻¹ for calcium. Site I phosphorylation largely increases both site I and site II affinity for uranyl and uranyl-binding cooperativity. Combining site I phosphorylation and site II Thr7Trp mutation leads to picomolar dissociation constants Kd₁ = 1.7 ± 0.3 pM and Kd₂ = 196 ± 21 pM at pH 7. A structural model obtained by MD simulations suggests a structural role of site I phosphorylation in the affinity modulation. Full article

(This article belongs to the Special Issue Biomolecule-Metal Ion Interaction)

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11 pages, 1272 KiB

Open AccessFeature PaperArticle

Essential Role of Histidine for Rapid Copper(II)-Mediated Disassembly of Neurokinin B Amyloid

by Bhawantha M. Jayawardena, Lorraine Peacey, Roland Gamsjaeger and Christopher E. Jones

Biomolecules 2022, 12(11), 1585; https://doi.org/10.3390/biom12111585 - 28 Oct 2022

Cited by 2 | Viewed by 1785

Abstract

Neurokinin B is a tachykinin peptide involved in a diverse range of neuronal functions. It rapidly forms an amyloid, which is considered physiologically important for efficient packing into dense core secretory vesicles within hypothalamic neurons. Disassembly of the amyloid is thought to require the presence of copper ions, which interact with histidine at the third position in the peptide sequence. However, it is unclear how the histidine is involved in the amyloid structure and why copper coordination can trigger disassembly. In this work, we demonstrate that histidine contributes to the amyloid structure via π-stacking interactions with nearby phenylalanine residues. The ability of neurokinin B to form an amyloid is dependent on any aromatic residue at the third position in the sequence; however, only the presence of histidine leads to both amyloid formation and rapid copper-induced disassembly. Full article

(This article belongs to the Special Issue Biomolecule-Metal Ion Interaction)

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18 pages, 1783 KiB

Open AccessArticle

Use of an Acellular Assay to Study Interactions between Actinides and Biological or Synthetic Ligands

by Anne Van der Meeren, Catherine Berthomieu, Agnès Moureau, Martine Defrance and Nina M. Griffiths

Biomolecules 2022, 12(11), 1553; https://doi.org/10.3390/biom12111553 - 24 Oct 2022

Cited by 4 | Viewed by 1702

Abstract

Speciation of actinides, and more particularly bioligand-binding ability, influences in vivo behavior. Understanding these interactions is essential for estimation of radiological dose and improvement of decorporation strategies for accidentally contaminated victims. Because the handling of actinides imposes overwhelming difficulties, in vitro assays carried out in physiological conditions are lacking and data regarding such interactions are scarce. In this study, we used a bi-compartmental and dynamic assay, providing physiological conditions (presence of inorganic ions, pH, temperature) to explore interactions between the actinides plutonium (Pu) and americium (Am) and endogenous (proteins transferrin and ferritin) or exogenous ligands (the chelating agent diethylenetriaminpentaacetic acid, DTPA). In this assay, an agarose gel represents the retention compartment of actinides and a dynamic fluid phase, the transfer compartment. The proportion of actinides transferred from static to dynamic phase reflects interactions between Pu/Am and various ligands. The results show differences in the formation of actinide-protein or actinide-DTPA complexes in physiologically relevant media depending on which ligand is present and where. We observed differential behavior for Pu and Am similar to in vivo studies. Thus, our assay may be used to determine the ability of various actinides to interact with specific proteins or with drug candidates for decorporation in complex physiologically relevant environments. Full article

(This article belongs to the Special Issue Biomolecule-Metal Ion Interaction)

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18 pages, 2869 KiB

Open AccessFeature PaperArticle

Ligand-Promoted Surface Solubilization of TiO₂ Nanoparticles by the Enterobactin Siderophore in Biological Medium

by Jérôme Laisney, Mireille Chevallet, Caroline Fauquant, Camille Sageot, Yohann Moreau, Daniela Predoi, Nathalie Herlin-Boime, Colette Lebrun and Isabelle Michaud-Soret

Biomolecules 2022, 12(10), 1516; https://doi.org/10.3390/biom12101516 - 19 Oct 2022

Cited by 3 | Viewed by 2574

Abstract

Titanium dioxide nanoparticles (TiO₂-NPs) are increasingly used in consumer products for their particular properties. Even though TiO₂ is considered chemically stable and insoluble, studying their behavior in biological environments is of great importance to figure their potential dissolution and transformation. The interaction between TiO₂-NPs with different sizes and crystallographic forms (anatase and rutile) and the strong chelating enterobactin (ent) siderophore was investigated to look at a possible dissolution. For the first time, direct evidence of anatase TiO₂-NP surface dissolution or solubilization (i.e., the removal of Ti atoms located at the surface) in a biological medium by this siderophore was shown and the progressive formation of a hexacoordinated titanium–enterobactin (Ti–ent) complex observed. This complex was characterized by UV–visible and Fourier transform infrared (FTIR) spectroscopy (both supported by Density Functional Theory calculations) as well as electrospray ionization mass spectrometry (ESI-MS) and X-ray photoelectron spectroscopy (XPS). A maximum of ca. 6.3% of Ti surface atoms were found to be solubilized after 24 h of incubation, releasing Ti–ent complexes in the micromolar range that could then be taken up by bacteria in an iron-depleted medium. From a health and environmental point of view, the effects associated to the solubilization of the E171 TiO₂ food additive in the presence of enterobactin and the entrance of the Ti–enterobactin complex in bacteria were questioned. Full article

(This article belongs to the Special Issue Biomolecule-Metal Ion Interaction)

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17 pages, 2703 KiB

Open AccessArticle

Conformational Plasticity of Centrin 1 from Toxoplasma gondii in Binding to the Centrosomal Protein SFI1

by Luca Bombardi, Filippo Favretto, Marco Pedretti, Carolina Conter, Paola Dominici and Alessandra Astegno

Biomolecules 2022, 12(8), 1115; https://doi.org/10.3390/biom12081115 - 13 Aug 2022

Cited by 4 | Viewed by 1929

Abstract

Centrins are calcium (Ca²⁺)-binding proteins that are involved in many cellular functions including centrosome regulation. A known cellular target of centrins is SFI1, a large centrosomal protein containing multiple repeats that represent centrin-binding motifs. Recently, a protein homologous to yeast and mammalian SFI1, denominated TgSFI1, which shares SFI1-repeat organization, was shown to colocalize at centrosomes with centrin 1 from Toxoplasma gondii (TgCEN1). However, the molecular details of the interaction between TgCEN1 and TgSFI1 remain largely unknown. Herein, combining different biophysical methods, including isothermal titration calorimetry, nuclear magnetic resonance, circular dichroism, and fluorescence spectroscopy, we determined the binding properties of TgCEN1 and its individual N- and C-terminal domains to synthetic peptides derived from distinct repeats of TgSFI1. Overall, our data indicate that the repeats in TgSFI1 constitute binding sites for TgCEN1, but the binding modes of TgCEN1 to the repeats differ appreciably in terms of binding affinity, Ca²⁺ sensitivity, and lobe-specific interaction. These results suggest that TgCEN1 displays remarkable conformational plasticity, allowing for the distinct repeats in TgSFI1 to possess precise modes of TgCEN1 binding and regulation during Ca²⁺ sensing, which appears to be crucial for the dynamic association of TgCEN1 with TgSFI1 in the centrosome architecture. Full article

(This article belongs to the Special Issue Biomolecule-Metal Ion Interaction)

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Review

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31 pages, 3139 KiB

Open AccessReview

Recent Advances in Metalloproteomics

by James P. C. Coverdale, Sirilata Polepalli, Marco A. Z. Arruda, Ana B. Santos da Silva, Alan J. Stewart and Claudia A. Blindauer

Biomolecules 2024, 14(1), 104; https://doi.org/10.3390/biom14010104 - 13 Jan 2024

Cited by 6 | Viewed by 3999

Abstract

Interactions between proteins and metal ions and their complexes are important in many areas of the life sciences, including physiology, medicine, and toxicology. Despite the involvement of essential elements in all major processes necessary for sustaining life, metalloproteomes remain ill-defined. This is not only owing to the complexity of metalloproteomes, but also to the non-covalent character of the complexes that most essential metals form, which complicates analysis. Similar issues may also be encountered for some toxic metals. The review discusses recently developed approaches and current challenges for the study of interactions involving entire (sub-)proteomes with such labile metal ions. In the second part, transition metals from the fourth and fifth periods are examined, most of which are xenobiotic and also tend to form more stable and/or inert complexes. A large research area in this respect concerns metallodrug–protein interactions. Particular attention is paid to separation approaches, as these need to be adapted to the reactivity of the metal under consideration. Full article

(This article belongs to the Special Issue Biomolecule-Metal Ion Interaction)

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20 pages, 9308 KiB

Open AccessReview

Engineering Siderophore Biosynthesis and Regulation Pathways to Increase Diversity and Availability

by Hélène Puja, Gaëtan L. A. Mislin and Coraline Rigouin

Biomolecules 2023, 13(6), 959; https://doi.org/10.3390/biom13060959 - 7 Jun 2023

Cited by 21 | Viewed by 4464

Abstract

Siderophores are small metal chelators synthesized by numerous organisms to access iron. These secondary metabolites are ubiquitously present on Earth, and because their production represents the main strategy to assimilate iron, they play an important role in both positive and negative interactions between organisms. In addition, siderophores are used in biotechnology for diverse applications in medicine, agriculture and the environment. The generation of non-natural siderophore analogs provides a new opportunity to create new-to-nature chelating biomolecules that can offer new properties to expand applications. This review summarizes the main strategies of combinatorial biosynthesis that have been used to generate siderophore analogs. We first provide a brief overview of siderophore biosynthesis, followed by a description of the strategies, namely, precursor-directed biosynthesis, the design of synthetic or heterologous pathways and enzyme engineering, used in siderophore biosynthetic pathways to create diversity. In addition, this review highlights the engineering strategies that have been used to improve the production of siderophores by cells to facilitate their downstream utilization. Full article

(This article belongs to the Special Issue Biomolecule-Metal Ion Interaction)

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