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Special Issue "Application of Computational Methods and Biomolecular Structural Modeling to the Investigation of Metalloproteins"

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

Deadline for manuscript submissions: 15 March 2021.

Special Issue Editors

Prof. Dr. Antonio Rosato
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Guest Editor
Department of Chemistry and Center for Magnetic Resonance, University of Florence, Sesto Fiorentino, Italy
Interests: metalloproteins; NMR; metallomics; structural biology; metalloproteomics; bioinformatics
Prof. Dr. Francesco Musiani
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Guest Editor
Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
Interests: molecular dynamics; protein–ligand and protein–protein docking; bioinformatics; homology modeling; QM modeling
Prof. Claudia Andreini
Website
Guest Editor
Department of Chemistry and Center for Magnetic Resonance, University of Florence, Sesto Fiorentino, Italy
Interests: metalloproteins; bioinformatics; structural bioinformatics; metallomics; bioinorganic chemistry

Special Issue Information

Dear Colleagues,

The importance of metalloproteins for the proper functioning of the cells of all living organisms is well exemplified by their number: indeed, about 30%–40% of all proteins encoded by the genome need at least one metal ion to perform their biological function. The correct biosynthesis of metalloproteins requires living organisms to be able to cope with such issues as the limited bioavailability or the potential cytotoxicity of several essential metals. Thus, organisms have developed complex machineries that guarantee the proper intracellular concentration and distribution among compartments of each metal, i.e., metal homeostasis. To understand how the different metal-binding proteins and enzymes—together with the proteins responsible for metal homeostasis—carry out their function, it is necessary to investigate their three-dimensional (3D) structure and mobility at the atomic level. Simulations of molecular dynamics (MD) complement experimental information by showing how the 3D structure fluctuates over time and as a function of environmental conditions, with the possibility of exploring a wider range of timescales and conditions than usually amenable in experiments. Other computational techniques, such as comparative modeling and macromolecular docking, are also used routinely with similar aims. The structural bioinformatics of metalloproteins is important for providing links between 3D structure and biological function, with particular focus on the role of metal ions and how this role has evolved and become diversified among organisms. In this Special Issue, we wish to cover the most recent advances in all these aspects of computational methods for the study of metalloproteins by hosting a mix of original research articles and short critical reviews.

Prof. Francesco Musiani
Prof. Antonio Rosato
Prof. Claudia Andreini
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 papers will be 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 2000 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

  • molecular dynamics of metalloproteins
  • enhanced sampling techniques on metalloproteins
  • molecular modeling of metalloproteins
  • macromolecular docking between metalloproteins

Published Papers (2 papers)

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Research

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Open AccessArticle
Assessing the Direct Binding of Ark-Like E3 RING Ligases to Ubiquitin and Its Implication on Their Protein Interaction Network
Molecules 2020, 25(20), 4787; https://doi.org/10.3390/molecules25204787 - 19 Oct 2020
Abstract
The ubiquitin pathway required for most proteins’ targeted degradation involves three classes of enzymes: E1-activating enzyme, E2-conjugating enzyme, and E3-ligases. The human Ark2C is the single known E3 ligase that adopts an alternative, Ub-dependent mechanism for the activation of Ub transfer in the [...] Read more.
The ubiquitin pathway required for most proteins’ targeted degradation involves three classes of enzymes: E1-activating enzyme, E2-conjugating enzyme, and E3-ligases. The human Ark2C is the single known E3 ligase that adopts an alternative, Ub-dependent mechanism for the activation of Ub transfer in the pathway. Its RING domain binds both E2-Ub and free Ub with high affinity, resulting in a catalytic active UbR-RING-E2-UbD complex formation. We examined potential changes in the conformational plasticity of the Ark2C RING domain and its ligands in their complexed form within the ubiquitin pathway through molecular dynamics (MD). Three molecular mechanics force fields compared to previous NMR relaxation studies of RING domain of Arkadia were used for effective and accurate assessment of MDs. Our results suggest the Ark2C Ub-RING docking site has a substantial impact on maintaining the conformational rigidity of E2-E3 assembly, necessary for the E3’s catalytic activity. In the UbR-RING-E2-UbD catalytic complex, the UbR molecule was found to have greater mobility than the other Ub, bound to E2. Furthermore, network-based bioinformatics helped us identify E3 RING ligase candidates which potentially exhibit similar structural modules as Ark2C, along with predicted substrates targeted by the Ub-binding RING Ark2C. Our findings could trigger a further exploration of related unrevealed functions of various other E3 RING ligases. Full article
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Review

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Open AccessReview
Bioinformatics of Metalloproteins and Metalloproteomes
Molecules 2020, 25(15), 3366; https://doi.org/10.3390/molecules25153366 - 24 Jul 2020
Abstract
Trace metals are inorganic elements that are required for all organisms in very low quantities. They serve as cofactors and activators of metalloproteins involved in a variety of key cellular processes. While substantial effort has been made in experimental characterization of metalloproteins and [...] Read more.
Trace metals are inorganic elements that are required for all organisms in very low quantities. They serve as cofactors and activators of metalloproteins involved in a variety of key cellular processes. While substantial effort has been made in experimental characterization of metalloproteins and their functions, the application of bioinformatics in the research of metalloproteins and metalloproteomes is still limited. In the last few years, computational prediction and comparative genomics of metalloprotein genes have arisen, which provide significant insights into their distribution, function, and evolution in nature. This review aims to offer an overview of recent advances in bioinformatic analysis of metalloproteins, mainly focusing on metalloprotein prediction and the use of different metals across the tree of life. We describe current computational approaches for the identification of metalloprotein genes and metal-binding sites/patterns in proteins, and then introduce a set of related databases. Furthermore, we discuss the latest research progress in comparative genomics of several important metals in both prokaryotes and eukaryotes, which demonstrates divergent and dynamic evolutionary patterns of different metalloprotein families and metalloproteomes. Overall, bioinformatic studies of metalloproteins provide a foundation for systematic understanding of trace metal utilization in all three domains of life. Full article
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