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Multifaceted Role of Metalloproteins
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Multifaceted Role of Metalloproteins

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Inorganic Chemistry".

Deadline for manuscript submissions: closed (30 April 2023) | Viewed by 4665

Special Issue Editors

Dr. Gianantonio Battistuzzi

E-Mail Website
Guest Editor
Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Modena, Italy
Interests: redox chemistry of immobilized metalloproteins; redox thermodynamics in metalloproteins; conformational equilibria in metalloproteins; biosensing; protein electrochemistry; UV-Vis spectroelectrochemistry; MCD spectroscopy; electrode immobilization; cytochromes c; heme peroxidases; blue copper proteins; neuroglobin
Special Issues, Collections and Topics in MDPI journals
Dr. Carlo Augusto Bortolotti

E-Mail Website
Guest Editor
Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
Interests: biophysical chemistry; organic bioelectronics; electron transfer
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Metalloproteins contain one or more permanently bound metal ions, which can be coordinated to the sidechain of specific aminoacids, can be incorporated into metal cofactors (such as heme, other tetrapyrrolic rings, and molybdopterin), or can form inorganic clusters (such as FeS clusters and FeMo cofactor of nitrogenase).

Metalloproteins play crucial roles in all living organisms, being involved in catalysis and regulation of a wide array of different reactions, in electron transfer chains associated with respiration and photosynthesis, in signaling events, in O2 transport, in metal ion trafficking, and in replication of the genetic information. Therefore, comprehension of the molecular details of the relationship between their structure and function is mandatory to fully understand their physiological roles. This would greatly contribute to expanding our knowledge of life processes, understanding the molecular basis of diseases, designing metalloprotein-based nanosensors, and devising new environmentally friendly processes for industrial production or detoxification of polluted sites.

The present Special Issue of Molecules entitled “Multifaced Roles of Metalloproteins” welcomes contributions in all areas of basic and application-oriented research associated with metalloproteins from the aspects of coordination chemistry, biophysics, biochemistry, and molecular biology.

Dr. Gianantonio Battistuzzi
Dr. Carlo Augusto Bortolotti
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. Molecules is an international peer-reviewed open access semimonthly 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

  • alkaline-earth metals
  • artificial metalloproteins
  • binding motif
  • buffering action
  • Ca-binding proteins
  • cell signaling
  • coordination chemistry
  • Cu proteins
  • enzyme catalysis
  • Fe proteins
  • heavy metal stress
  • metal cofactors
  • metal ion trafficking
  • Mg-binding proteins
  • Mo and W proteins
  • protein engineering
  • protein–protein interaction
  • sensor proteins
  • trace elements
  • transcription factors
  • transition metals
  • Zn enzymes

Published Papers (4 papers)

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Research

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14 pages, 2050 KiB  
Article
Biochemical, Biophysical, and Structural Analysis of an Unusual DyP from the Extremophile Deinococcus radiodurans
by Kelly Frade, Célia M. Silveira, Bruno A. Salgueiro, Sónia Mendes, Lígia O. Martins, Carlos Frazão, Smilja Todorovic and Elin Moe
Molecules 2024, 29(2), 358; https://doi.org/10.3390/molecules29020358 - 11 Jan 2024
Viewed by 719
Abstract
Dye-decolorizing peroxidases (DyPs) are heme proteins with distinct structural properties and substrate specificities compared to classical peroxidases. Here, we demonstrate that DyP from the extremely radiation-resistant bacterium Deinococcus radiodurans is, like some other homologues, inactive at physiological pH. Resonance Raman (RR) spectroscopy confirms [...] Read more.
Dye-decolorizing peroxidases (DyPs) are heme proteins with distinct structural properties and substrate specificities compared to classical peroxidases. Here, we demonstrate that DyP from the extremely radiation-resistant bacterium Deinococcus radiodurans is, like some other homologues, inactive at physiological pH. Resonance Raman (RR) spectroscopy confirms that the heme is in a six-coordinated-low-spin (6cLS) state at pH 7.5 and is thus unable to bind hydrogen peroxide. At pH 4.0, the RR spectra of the enzyme reveal the co-existence of high-spin and low-spin heme states, which corroborates catalytic activity towards H2O2 detected at lower pH. A sequence alignment with other DyPs reveals that DrDyP possesses a Methionine residue in position five in the highly conserved GXXDG motif. To analyze whether the presence of the Methionine is responsible for the lack of activity at high pH, this residue is substituted with a Glycine. UV-vis and RR spectroscopies reveal that the resulting DrDyPM190G is also in a 6cLS spin state at pH 7.5, and thus the Methionine does not affect the activity of the protein. The crystal structures of DrDyP and DrDyPM190G, determined to 2.20 and 1.53 Å resolution, respectively, nevertheless reveal interesting insights. The high-resolution structure of DrDyPM190G, obtained at pH 8.5, shows that one hydroxyl group and one water molecule are within hydrogen bonding distance to the heme and the catalytic Asparagine and Arginine. This strong ligand most likely prevents the binding of the H2O2 substrate, reinforcing questions about physiological substrates of this and other DyPs, and about the possible events that can trigger the removal of the hydroxyl group conferring catalytic activity to DrDyP. Full article
(This article belongs to the Special Issue Multifaceted Role of Metalloproteins)
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14 pages, 3492 KiB  
Article
Hydrolytic Mechanism of a Metalloenzyme Is Modified by the Nature of the Coordinated Metal Ion
by Zeyad H. Nafaee, Bálint Hajdu, Éva Hunyadi-Gulyás and Béla Gyurcsik
Molecules 2023, 28(14), 5511; https://doi.org/10.3390/molecules28145511 - 19 Jul 2023
Viewed by 763
Abstract
The nuclease domain of colicin E7 cleaves double-strand DNA non-specifically. Zn2+ ion was shown to be coordinated by the purified NColE7 as its native metal ion. Here, we study the structural and catalytic aspects of the interaction with Ni2+, Cu [...] Read more.
The nuclease domain of colicin E7 cleaves double-strand DNA non-specifically. Zn2+ ion was shown to be coordinated by the purified NColE7 as its native metal ion. Here, we study the structural and catalytic aspects of the interaction with Ni2+, Cu2+ and Cd2+ non-endogenous metal ions and the consequences of their competition with Zn2+ ions, using circular dichroism spectroscopy and intact protein mass spectrometry. An R447G mutant exerting decreased activity allowed for the detection of nuclease action against pUC119 plasmid DNA via agarose gel electrophoresis in the presence of comparable metal ion concentrations. It was shown that all of the added metal ions could bind to the apoprotein, resulting in a minor secondary structure change, but drastically shifting the charge distribution of the protein. Zn2+ ions could not be replaced by Ni2+, Cu2+ and Cd2+. The nuclease activity of the Ni2+-bound enzyme was extremely high in comparison with the other metal-bound forms, and could not be inhibited by the excess of Ni2+ ions. At the same time, this activity was significantly decreased in the presence of equivalent Zn2+, independent of the order of addition of each component of the mixture. We concluded that the Ni2+ ions promoted the DNA cleavage of the enzyme through a more efficient mechanism than the native Zn2+ ions, as they directly generate the nucleophilic OH− ion. Full article
(This article belongs to the Special Issue Multifaceted Role of Metalloproteins)
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Review

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13 pages, 3094 KiB  
Review
Protein Metalation by Medicinal Gold Compounds: Identification of the Main Features of the Metalation Process through ESI MS Experiments
by Andrea Geri, Lara Massai and Luigi Messori
Molecules 2023, 28(13), 5196; https://doi.org/10.3390/molecules28135196 - 04 Jul 2023
Cited by 4 | Viewed by 1292
Abstract
Gold compounds form a new class of promising anticancer agents with innovative modes of action. It is generally believed that anticancer gold compounds, at variance with clinically established platinum drugs, preferentially target proteins rather than nucleic acids. The reactions of several gold compounds [...] Read more.
Gold compounds form a new class of promising anticancer agents with innovative modes of action. It is generally believed that anticancer gold compounds, at variance with clinically established platinum drugs, preferentially target proteins rather than nucleic acids. The reactions of several gold compounds with a few model proteins have been systematically explored in recent years through ESI MS measurements to reveal adduct formation and identify the main features of those reactions. Here, we focus our attention on a group of five gold compounds of remarkable medicinal interest, i.e., Auranofin, Au(NHC)Cl, [Au(NHC)2]PF6, Aubipyc, and Auoxo6, and on their reactions with four different biomolecular targets, i.e., the proteins HEWL, hCA I, HSA and the C-terminal dodecapeptide of the enzyme thioredoxin reductase. Complete ESI MS data are available for those reactions due to previous experimental work conducted in our laboratory. From the comparative analysis of the ESI MS reaction profiles, some characteristic trends in the metallodrug-protein reactivity may be identified as detailed below. The main features are described and analyzed in this review. Overall, all these observations are broadly consistent with the concept that cytotoxic gold drugs preferentially target cancer cell proteins, with a remarkable selectivity for the cysteine and selenocysteine proteome. These interactions typically result in severe damage to cancer cell metabolism and profound alterations in the redox state, leading to eventual cancer cell death. Full article
(This article belongs to the Special Issue Multifaceted Role of Metalloproteins)
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34 pages, 5250 KiB  
Review
Heme–Protein Interactions and Functional Relevant Heme Deformations: The Cytochrome c Case
by Reinhard Schweitzer-Stenner
Molecules 2022, 27(24), 8751; https://doi.org/10.3390/molecules27248751 - 09 Dec 2022
Cited by 1 | Viewed by 1312
Abstract
Heme proteins are known to perform a plethora of biologically important functions. This article reviews work that has been conducted on various class I cytochrome c proteins over a period of nearly 50 years. The article focuses on the relevance of symmetry-lowering heme–protein [...] Read more.
Heme proteins are known to perform a plethora of biologically important functions. This article reviews work that has been conducted on various class I cytochrome c proteins over a period of nearly 50 years. The article focuses on the relevance of symmetry-lowering heme–protein interactions that affect the function of the electron transfer protein cytochrome c. The article provides an overview of various, mostly spectroscopic studies that explored the electronic structure of the heme group in these proteins and how it is affected by symmetry-lowering deformations. In addition to discussing a large variety of spectroscopic studies, the article provides a theoretical framework that should enable a comprehensive understanding of the physical chemistry that underlies the function not only of cytochrome c but of all heme proteins. Full article
(This article belongs to the Special Issue Multifaceted Role of Metalloproteins)
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