Topic Editors

Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Russia
Department of Medical Biochemistry and Biophsyics, Umeå Univeristy, SE 90187 Umeå, Sweden

Metalloproteins and Metalloenzymes

Abstract submission deadline
30 September 2024
Manuscript submission deadline
31 December 2024
Viewed by
18204

Topic Information

Dear Colleagues,

The functioning of any biological system is impossible without metal ions. Any biological system contains proteins specifically interacting with metal ions. The ‘metals of life’ include sodium, potassium, magnesium, calcium, manganese, iron, cobalt, zinc, nickel, vanadium, molybdenum, and tungsten. Metal ions play several major roles in proteins: structural, regulatory, and enzymatic. Structural metal ions provide structural stability to proteins or protein domains. Some metal ions regulate various cell processes being first, second, or third messengers. Calcium ions are the most prominent examples of such intra- and extracellular messengers. Metal ions and especially transition metal ions are an essential part of many enzymes and are indispensable in many catalytic reactions. Despite the apparent good knowledge of the structure and properties of many metalloproteins and metalloenzymes, many aspects of their structure and, in particular, mechanisms of their functioning are still insufficiently studied. Studying their interactions with proteins of other classes, membranes, and nucleic acids allows us to reach a better understanding of their physiological functions. Modern methods of genetic engineering and knowledge of the three-dimensional structure of metalloproteins and metalloenzymes allow us to study their structure and functions on a new level. The obtained fundamental knowledge can already be used in medicine and biotechnology.

Dr. Eugene A. Permyakov
Prof. Dr. Ludmilla Morozova-Roche
Topic Editors

Keywords

  • metal ions
  • metalloproteins
  • metalloenzymes
  • structure
  • regulation
  • function

Participating Journals

Journal Name Impact Factor CiteScore Launched Year First Decision (median) APC
Biomolecules
biomolecules
5.5 8.3 2011 16.9 Days CHF 2700 Submit
Cells
cells
6.0 9.0 2012 16.6 Days CHF 2700 Submit
Current Issues in Molecular Biology
cimb
3.1 2.4 1999 13.5 Days CHF 2200 Submit
International Journal of Molecular Sciences
ijms
5.6 7.8 2000 16.3 Days CHF 2900 Submit
Journal of Molecular Pathology
jmp
- - 2020 24.9 Days CHF 1000 Submit
Molecules
molecules
4.6 6.7 1996 14.6 Days CHF 2700 Submit
Proteomes
proteomes
3.3 5.7 2013 28.3 Days CHF 1800 Submit

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Published Papers (9 papers)

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24 pages, 1139 KiB  
Review
“Alphabet” Selenoproteins: Their Characteristics and Physiological Roles
by Carmen Beatrice Dogaru, Corina Muscurel, Carmen Duță and Irina Stoian
Int. J. Mol. Sci. 2023, 24(21), 15992; https://doi.org/10.3390/ijms242115992 - 06 Nov 2023
Cited by 1 | Viewed by 1397
Abstract
Selenium (Se) is a metalloid that is recognized as one of the vital trace elements in our body and plays multiple biological roles, largely mediated by proteins containing selenium—selenoproteins. Selenoproteins mainly have oxidoreductase functions but are also involved in many different molecular signaling [...] Read more.
Selenium (Se) is a metalloid that is recognized as one of the vital trace elements in our body and plays multiple biological roles, largely mediated by proteins containing selenium—selenoproteins. Selenoproteins mainly have oxidoreductase functions but are also involved in many different molecular signaling pathways, physiological roles, and complex pathogenic processes (including, for example, teratogenesis, neurodegenerative, immuno-inflammatory, and obesity development). All of the selenoproteins contain one selenocysteine (Sec) residue, with only one notable exception, the selenoprotein P (SELENOP), which has 10 Sec residues. Although these mechanisms have been studied intensely and in detail, the characteristics and functions of many selenoproteins remain unknown. This review is dedicated to the recent data describing the identity and the functions of several selenoproteins that are less known than glutathione peroxidases (Gpxs), iodothyronine deiodinases (DIO), thioredoxin reductases (TRxRs), and methionine sulfoxide reductases (Msrs) and which are named after alphabetical letters (i.e., F, H, I, K, M, N, O, P, R, S, T, V, W). These “alphabet” selenoproteins are involved in a wide range of physiological and pathogenetic processes such as antioxidant defense, anti-inflammation, anti-apoptosis, regulation of immune response, regulation of oxidative stress, endoplasmic reticulum (ER) stress, immune and inflammatory response, and toxin antagonism. In selenium deficiency, the “alphabet” selenoproteins are affected hierarchically, both with respect to the particular selenoprotein and the tissue of expression, as the brain or endocrine glands are hardly affected by Se deficiency due to their equipment with LRP2 or LRP8. Full article
(This article belongs to the Topic Metalloproteins and Metalloenzymes)
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25 pages, 497 KiB  
Review
“Alphabet” Selenoproteins: Implications in Pathology
by Carmen Beatrice Dogaru, Carmen Duță, Corina Muscurel and Irina Stoian
Int. J. Mol. Sci. 2023, 24(20), 15344; https://doi.org/10.3390/ijms242015344 - 19 Oct 2023
Cited by 2 | Viewed by 1763
Abstract
Selenoproteins are a group of proteins containing selenium in the form of selenocysteine (Sec, U) as the 21st amino acid coded in the genetic code. Their synthesis depends on dietary selenium uptake and a common set of cofactors. Selenoproteins accomplish diverse roles in [...] Read more.
Selenoproteins are a group of proteins containing selenium in the form of selenocysteine (Sec, U) as the 21st amino acid coded in the genetic code. Their synthesis depends on dietary selenium uptake and a common set of cofactors. Selenoproteins accomplish diverse roles in the body and cell processes by acting, for example, as antioxidants, modulators of the immune function, and detoxification agents for heavy metals, other xenobiotics, and key compounds in thyroid hormone metabolism. Although the functions of all this protein family are still unknown, several disorders in their structure, activity, or expression have been described by researchers. They concluded that selenium or cofactors deficiency, on the one hand, or the polymorphism in selenoproteins genes and synthesis, on the other hand, are involved in a large variety of pathological conditions, including type 2 diabetes, cardiovascular, muscular, oncological, hepatic, endocrine, immuno-inflammatory, and neurodegenerative diseases. This review focuses on the specific roles of selenoproteins named after letters of the alphabet in medicine, which are less known than the rest, regarding their implications in the pathological processes of several prevalent diseases and disease prevention. Full article
(This article belongs to the Topic Metalloproteins and Metalloenzymes)
13 pages, 1347 KiB  
Review
The Role of ADAMTS Proteoglycanases in Thoracic Aortic Disease
by Marsioleda Kemberi, Yousuf Salmasi and Salvatore Santamaria
Int. J. Mol. Sci. 2023, 24(15), 12135; https://doi.org/10.3390/ijms241512135 - 28 Jul 2023
Cited by 2 | Viewed by 1269
Abstract
Thoracic aortic aneurysm and dissection (TAAD) are complex disease states with high morbidity and mortality that pose significant challenges to early diagnosis. Patients with an aneurysm are asymptomatic and typically present to the emergency department only after the development of a dissection. The [...] Read more.
Thoracic aortic aneurysm and dissection (TAAD) are complex disease states with high morbidity and mortality that pose significant challenges to early diagnosis. Patients with an aneurysm are asymptomatic and typically present to the emergency department only after the development of a dissection. The extracellular matrix (ECM) plays a crucial role in regulating the aortic structure and function. The histopathologic hallmark termed medial degeneration is characterised by smooth muscle cell (SMC) loss, the degradation of elastic and collagen fibres and proteoglycan (PG) accumulation. Covalently attached to the protein core of PGs are a number of glycosaminoglycan chains, negatively charged molecules that provide flexibility, compressibility, and viscoelasticity to the aorta. PG pooling in the media can produce discontinuities in the aortic wall leading to increased local stress. The accumulation of PGs is likely due to an imbalance between their synthesis by SMCs and decreased proteolysis by A Disintegrin-like and Metalloproteinase with Thrombospondin motifs (ADAMTS) proteoglycanases in the ECM. Mouse models of TAAD indicated that these proteases exert a crucial, albeit complex and not fully elucidated, role in this disease. This has led to a mounting interest in utilising ADAMTS proteoglycanases as biomarkers of TAAD. In this review, we discuss the role of ADAMTSs in thoracic aortic disease and their potential use in facilitating the clinical diagnosis of TAAD and disease progression. Full article
(This article belongs to the Topic Metalloproteins and Metalloenzymes)
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23 pages, 14523 KiB  
Article
A Molecular Analysis of the Aminopeptidase P-Related Domain of PID-5 from Caenorhabditis elegans
by Anna C. Lloyd, Kyle S. Gregory, R. Elwyn Isaac and K. Ravi Acharya
Biomolecules 2023, 13(7), 1132; https://doi.org/10.3390/biom13071132 - 14 Jul 2023
Cited by 1 | Viewed by 1273
Abstract
A novel protein, PID-5, has been shown to be a requirement for germline immortality and has recently been implicated in RNA-induced epigenetic silencing in the Caenorhabditis elegans embryo. Importantly, it has been shown to contain both an eTudor and aminopeptidase P-related domain. However, [...] Read more.
A novel protein, PID-5, has been shown to be a requirement for germline immortality and has recently been implicated in RNA-induced epigenetic silencing in the Caenorhabditis elegans embryo. Importantly, it has been shown to contain both an eTudor and aminopeptidase P-related domain. However, the silencing mechanism has not yet been fully characterised. In this study, bioinformatic tools were used to compare pre-existing aminopeptidase P molecular structures to the AlphaFold2-predicted aminopeptidase P-related domain of PID-5 (PID-5 APP-RD). Structural homology, metal composition, inhibitor-bonding interactions, and the potential for dimerisation were critically assessed through computational techniques, including structural superimposition and protein-ligand docking. Results from this research suggest that the metallopeptidase-like domain shares high structural homology with known aminopeptidase P enzymes and possesses the canonical ‘pita-bread fold’. However, the absence of conserved metal-coordinating residues indicates that only a single Zn2+ may be bound at the active site. The PID-5 APP-RD may form transient interactions with a known aminopeptidase P inhibitor and may therefore recognise substrates in a comparable way to the known structures. However, loss of key catalytic residues suggests the domain will be inactive. Further evidence suggests that heterodimerisation with C. elegans aminopeptidase P is feasible and therefore PID-5 is predicted to regulate proteolytic cleavage in the silencing pathway. PID-5 may interact with PID-2 to bring aminopeptidase P activity to the Z-granule, where it could influence WAGO-4 activity to ensure the balanced production of 22G-RNA signals for transgenerational silencing. Targeted experiments into APPs implicated in malaria and cancer are required in order to build upon the biological and therapeutic significance of this research. Full article
(This article belongs to the Topic Metalloproteins and Metalloenzymes)
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18 pages, 9986 KiB  
Review
Origin, Diversity, and Multiple Roles of Enzymes with Metallo-β-Lactamase Fold from Different Organisms
by Seydina M. Diene, Pierre Pontarotti, Saïd Azza, Nicholas Armstrong, Lucile Pinault, Eric Chabrière, Philippe Colson, Jean-Marc Rolain and Didier Raoult
Cells 2023, 12(13), 1752; https://doi.org/10.3390/cells12131752 - 30 Jun 2023
Cited by 4 | Viewed by 1584
Abstract
β-lactamase enzymes have generated significant interest due to their ability to confer resistance to the most commonly used family of antibiotics in human medicine. Among these enzymes, the class B β-lactamases are members of a superfamily of metallo-β-lactamase (MβL) fold proteins which are [...] Read more.
β-lactamase enzymes have generated significant interest due to their ability to confer resistance to the most commonly used family of antibiotics in human medicine. Among these enzymes, the class B β-lactamases are members of a superfamily of metallo-β-lactamase (MβL) fold proteins which are characterised by conserved motifs (i.e., HxHxDH) and are not only limited to bacteria. Indeed, as the result of several barriers, including low sequence similarity, default protein annotation, or untested enzymatic activity, MβL fold proteins have long been unexplored in other organisms. However, thanks to search approaches which are more sensitive compared to classical Blast analysis, such as the use of common ancestors to identify distant homologous sequences, we are now able to highlight their presence in different organisms including Bacteria, Archaea, Nanoarchaeota, Asgard, Humans, Giant viruses, and Candidate Phyla Radiation (CPR). These MβL fold proteins are multifunctional enzymes with diverse enzymatic or non-enzymatic activities of which, at least thirteen activities have been reported such as β-lactamase, ribonuclease, nuclease, glyoxalase, lactonase, phytase, ascorbic acid degradation, anti-cancer drug degradation, or membrane transport. In this review, we (i) discuss the existence of MβL fold enzymes in the different domains of life, (ii) present more suitable approaches to better investigating their homologous sequences in unsuspected sources, and (iii) report described MβL fold enzymes with demonstrated enzymatic or non-enzymatic activities. Full article
(This article belongs to the Topic Metalloproteins and Metalloenzymes)
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13 pages, 1287 KiB  
Article
Quick and Spontaneous Transformation between [3Fe–4S] and [4Fe–4S] Iron–Sulfur Clusters in the tRNA-Thiolation Enzyme TtuA
by Masato Ishizaka, Minghao Chen, Shun Narai, Yoshikazu Tanaka, Toyoyuki Ose, Masaki Horitani and Min Yao
Int. J. Mol. Sci. 2023, 24(1), 833; https://doi.org/10.3390/ijms24010833 - 03 Jan 2023
Viewed by 3329
Abstract
Iron–sulfur (Fe–S) clusters are essential cofactors for enzyme activity. These Fe–S clusters are present in structurally diverse forms, including [4Fe–4S] and [3Fe–4S]. Type-identification of the Fe–S cluster is indispensable in understanding the catalytic mechanism of enzymes. However, identifying [4Fe–4S] and [3Fe–4S] clusters in [...] Read more.
Iron–sulfur (Fe–S) clusters are essential cofactors for enzyme activity. These Fe–S clusters are present in structurally diverse forms, including [4Fe–4S] and [3Fe–4S]. Type-identification of the Fe–S cluster is indispensable in understanding the catalytic mechanism of enzymes. However, identifying [4Fe–4S] and [3Fe–4S] clusters in particular is challenging because of their rapid transformation in response to oxidation–reduction events. In this study, we focused on the relationship between the Fe–S cluster type and the catalytic activity of a tRNA-thiolation enzyme (TtuA). We reconstituted [4Fe–4S]-TtuA, prepared [3Fe–4S]-TtuA by oxidizing [4Fe–4S]-TtuA under strictly anaerobic conditions, and then observed changes in the Fe–S clusters in the samples and the enzymatic activity in the time-course experiments. Electron paramagnetic resonance analysis revealed that [3Fe–4S]-TtuA spontaneously transforms into [4Fe–4S]-TtuA in minutes to one hour without an additional free Fe source in the solution. Although the TtuA immediately after oxidation of [4Fe–4S]-TtuA was inactive [3Fe–4S]-TtuA, its activity recovered to a significant level compared to [4Fe–4S]-TtuA after one hour, corresponding to an increase of [4Fe–4S]-TtuA in the solution. Our findings reveal that [3Fe–4S]-TtuA is highly inactive and unstable. Moreover, time-course analysis of structural changes and activity under strictly anaerobic conditions further unraveled the Fe–S cluster type used by the tRNA-thiolation enzyme. Full article
(This article belongs to the Topic Metalloproteins and Metalloenzymes)
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17 pages, 2660 KiB  
Article
Non-Conserved Amino Acid Residues Modulate the Thermodynamics of Zn(II) Binding to Classical ββα Zinc Finger Domains
by Katarzyna Kluska, Aleksandra Chorążewska, Manuel David Peris-Díaz, Justyna Adamczyk and Artur Krężel
Int. J. Mol. Sci. 2022, 23(23), 14602; https://doi.org/10.3390/ijms232314602 - 23 Nov 2022
Cited by 5 | Viewed by 1497
Abstract
Classical zinc fingers domains (ZFs) bind Zn(II) ion by a pair of cysteine and histidine residues to adopt a characteristic and stable ββα fold containing a small hydrophobic core. As a component of transcription factors, they recognize specific DNA sequences to transcript particular [...] Read more.
Classical zinc fingers domains (ZFs) bind Zn(II) ion by a pair of cysteine and histidine residues to adopt a characteristic and stable ββα fold containing a small hydrophobic core. As a component of transcription factors, they recognize specific DNA sequences to transcript particular genes. The loss of Zn(II) disrupts the unique structure and function of the whole protein. It has been shown that the saturation of ZFs under cellular conditions is strictly related to their affinity for Zn(II). High affinity warrants their constant saturation, while medium affinity results in their transient structurization depending on cellular zinc availability. Therefore, there must be factors hidden in the sequence and structure of ZFs that impact Zn(II)-to-protein affinities to control their function. Using molecular dynamics simulations and experimental spectroscopic and calorimetric approaches, we showed that particular non-conserved residues derived from ZF sequences impact hydrogen bond formation. Our in silico and in vitro studies show that non-conserved residues can alter metal-coupled folding mechanisms and overall ZF stability. Furthermore, we show that Zn(II) binding to ZFs can also be entropically driven. This preference does not correlate either with Zn(II) binding site or with the extent of the secondary structure but is strictly related to a reservoir of interactions within the second coordination shell, which may loosen or tighten up the structure. Our findings shed new light on how the functionality of ZFs is modulated by non-coordinating residues diversity under cellular conditions. Moreover, they can be helpful for systematic backbone alteration of native ZF ββα scaffold to create artificial foldamers and proteins with improved stability. Full article
(This article belongs to the Topic Metalloproteins and Metalloenzymes)
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20 pages, 3304 KiB  
Article
Calcium-Bound S100P Protein Is a Promiscuous Binding Partner of the Four-Helical Cytokines
by Alexey S. Kazakov, Evgenia I. Deryusheva, Maria E. Permyakova, Andrey S. Sokolov, Victoria A. Rastrygina, Vladimir N. Uversky, Eugene A. Permyakov and Sergei E. Permyakov
Int. J. Mol. Sci. 2022, 23(19), 12000; https://doi.org/10.3390/ijms231912000 - 09 Oct 2022
Cited by 6 | Viewed by 1731
Abstract
S100 proteins are multifunctional calcium-binding proteins of vertebrates that act intracellularly, extracellularly, or both, and are engaged in the progression of many socially significant diseases. Their extracellular action is typically mediated by the recognition of specific receptor proteins. Recent studies indicate the ability [...] Read more.
S100 proteins are multifunctional calcium-binding proteins of vertebrates that act intracellularly, extracellularly, or both, and are engaged in the progression of many socially significant diseases. Their extracellular action is typically mediated by the recognition of specific receptor proteins. Recent studies indicate the ability of some S100 proteins to affect cytokine signaling through direct interaction with cytokines. S100P was shown to be the S100 protein most actively involved in interactions with some four-helical cytokines. To assess the selectivity of the S100P protein binding to four-helical cytokines, we have probed the interaction of Ca2+-bound recombinant human S100P with a panel of 32 four-helical human cytokines covering all structural families of this fold, using surface plasmon resonance spectroscopy. A total of 22 cytokines from all families of four-helical cytokines are S100P binders with the equilibrium dissociation constants, Kd, ranging from 1 nM to 3 µM (below the Kd value for the S100P complex with the V domain of its conventional receptor, receptor for advanced glycation end products, RAGE). Molecular docking and mutagenesis studies revealed the presence in the S100P molecule of a cytokine-binding site, which overlaps with the RAGE-binding site. Since S100 binding to four-helical cytokines inhibits their signaling in some cases, the revealed ability of the S100P protein to interact with ca. 71% of the four-helical cytokines indicates that S100P may serve as a poorly selective inhibitor of their action. Full article
(This article belongs to the Topic Metalloproteins and Metalloenzymes)
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19 pages, 3498 KiB  
Article
Controversial Role of Transferrin in the Transport of Ruthenium Anticancer Drugs
by Aviva Levina, Anthony R. M. Chetcuti and Peter A. Lay
Biomolecules 2022, 12(9), 1319; https://doi.org/10.3390/biom12091319 - 18 Sep 2022
Cited by 9 | Viewed by 1846
Abstract
Ruthenium complexes are at the forefront of developments in metal-based anticancer drugs, but many questions remain open regarding their reactivity in biological media, including the role of transferrin (Tf) in their transport and cellular uptake. A well-known anticancer drug, KP1019 ((IndH)[RuIIICl [...] Read more.
Ruthenium complexes are at the forefront of developments in metal-based anticancer drugs, but many questions remain open regarding their reactivity in biological media, including the role of transferrin (Tf) in their transport and cellular uptake. A well-known anticancer drug, KP1019 ((IndH)[RuIIICl4(Ind)2], where Ind = indazole) and a reference complex, [RuIII(nta)2]3− (nta = nitrilotriacetato(3−)) interacted differently with human apoTf, monoFeTf, or Fe2Tf. These reactions were studied by biolayer interferometry (BLI) measurements of Ru–Fe–Tf binding to recombinant human transferrin receptor 1 (TfR1) in conjunction with UV-vis spectroscopy and particle size analysis. Cellular Ru uptake in human hepatoma (HepG2) cells was measured under the conditions of the BLI assays. The mode of Tf binding and cellular Ru uptake were critically dependent on the nature of Ru complex, availability of Fe(III) binding sites of Tf, and the presence of proteins that competed for metal binding, particularly serum albumin. Cellular uptake of KP1019 was not Tf-mediated and occurred mostly by passive diffusion, which may also be suitable for treatments of inoperable cancers by intratumoral injections. High cellular Ru uptake from a combination of [RuIII(nta)2]3− and Fe2Tf in the absence of significant Ru–Tf binding was likely to be due to trapping of Ru(III) species into the endosome during TfR1-mediated endocytosis of Fe2Tf. Full article
(This article belongs to the Topic Metalloproteins and Metalloenzymes)
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