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Special Issue "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".

Deadline for manuscript submissions: 20 May 2023 | Viewed by 4053

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Special Issue Editors

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

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

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 2300 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 ion
biomolecules
protein
enzyme
nucleic acid

Published Papers (5 papers)

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Research

Open AccessArticle

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

and

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

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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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Open AccessFeature PaperArticle

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

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

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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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Open AccessArticle

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

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

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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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Open AccessFeature PaperArticle

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

Nathalie Herlin-Boime

Colette Lebrun

and

Isabelle Michaud-Soret

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

Viewed by 801

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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Open AccessArticle

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

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

Cited by 1 | Viewed by 686

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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