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Structure and Function of Metalloenzymes

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

Deadline for manuscript submissions: closed (30 September 2020) | Viewed by 13954

Special Issue Editor

Special Issue Information

Dear Colleagues,

Metal ion cofactors play a fundamental role in many biologically enzymes contributing to the diversification of their associated chemistry, the strengthening of their catalytic role, and the modulation of their activity. In fact, metalloenzymes are very often among the most proficient catalysts in nature. For many of these systems, the presence of the metal atoms is directly involved in the catalytic activity displayed, while in others, the metal plays a structural role. Features like the identity of the metal atom and its oxidation and spin state often have a dramatic impact on the structure and activity of many metalloenzymes. However, some enzymes can accommodate without penalty different metal atoms.

The sheer impact that one single atom—metal—can have on the structure and activity of a biomolecule composed of several thousand non-metal atoms continues to impress scientists to this day, particularly as researchers worldwide continue to clarify, to the atomic level, the catalytic mechanisms of many metalloenzymes, using a variety of experimental and computational methodologies.

This Special Issue aims to gather original research papers, reviews, and communications focusing on the relation between metals, enzymes, and their structure and activity.

Dr. Sergio F. Sousa
Guest Editor

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.

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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

  • biocatalysts
  • metals
  • coordination-sphere
  • active-site
  • transition state
  • metal stabilization
  • metal role

Published Papers (3 papers)

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Research

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10 pages, 4112 KiB  
Article
The Generation of the Oxidant Agent of a Mononuclear Nonheme Fe(II) Biomimetic Complex by Oxidative Decarboxylation. A DFT Investigation
by Angela Parise, Maria Costanza Muraca, Nino Russo, Marirosa Toscano and Tiziana Marino
Molecules 2020, 25(2), 328; https://doi.org/10.3390/molecules25020328 - 14 Jan 2020
Cited by 3 | Viewed by 2245
Abstract
The oxidative decarboxylation of the iron(II) α-hydroxy acid (mandelic acid) complex model, biomimetic of Rieske dioxygenase, has been investigated at the density functional level. The explored mechanism sheds light on the role of the α-hydroxyl group on the dioxygen activation. The potential energy [...] Read more.
The oxidative decarboxylation of the iron(II) α-hydroxy acid (mandelic acid) complex model, biomimetic of Rieske dioxygenase, has been investigated at the density functional level. The explored mechanism sheds light on the role of the α-hydroxyl group on the dioxygen activation. The potential energy surfaces have been explored in different electronic spin states. The rate-determining step of the process is the proton transfer. The oxidative decarboxylation preferentially takes place on the quintet state. Full article
(This article belongs to the Special Issue Structure and Function of Metalloenzymes)
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18 pages, 3579 KiB  
Article
A Single-Turnover Kinetic Study of DNA Demethylation Catalyzed by Fe(II)/α-Ketoglutarate-Dependent Dioxygenase AlkB
by Lyubov Yu. Kanazhevskaya, Irina V. Alekseeva and Olga S. Fedorova
Molecules 2019, 24(24), 4576; https://doi.org/10.3390/molecules24244576 - 13 Dec 2019
Cited by 7 | Viewed by 3152
Abstract
AlkB is a Fe(II)/α-ketoglutarate-dependent dioxygenase that repairs some alkylated bases of DNA and RNA in Escherichia coli. In the course of catalysis, oxidation of a co-substrate (α-ketoglutarate, αKG) leads to the formation of a highly reactive ‘oxyferryl’ enzyme-bound intermediate, Fe(IV) = O, [...] Read more.
AlkB is a Fe(II)/α-ketoglutarate-dependent dioxygenase that repairs some alkylated bases of DNA and RNA in Escherichia coli. In the course of catalysis, oxidation of a co-substrate (α-ketoglutarate, αKG) leads to the formation of a highly reactive ‘oxyferryl’ enzyme-bound intermediate, Fe(IV) = O, ensuring hydroxylation of the alkyl nucleobase adducts. Previous studies have revealed that AlkB is a flexible protein and can adopt different conformations during interactions with cofactors and DNA. To assess the conformational dynamics of the enzyme in complex with single- or double-stranded DNA in real-time mode, we employed the stopped-flow fluorescence method. N1-Methyladenine (m1A) introduced into a sequence of 15-mer oligonucleotides was chosen as the specific damage. Single-turnover kinetics were monitored by means of intrinsic fluorescence of the protein’s Trp residues, fluorescent base analogue 2-aminopurine (2aPu), and a dye–quencher pair (FAM/BHQ1). For all the fluorescent labels, the fluorescent traces showed several phases of consistent conformational changes, which were assigned to specific steps of the enzymatic process. These data offer an overall picture of the structural dynamics of AlkB and DNA during their interaction. Full article
(This article belongs to the Special Issue Structure and Function of Metalloenzymes)
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Review

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33 pages, 7438 KiB  
Review
Molecular Imaging Probes Based on Matrix Metalloproteinase Inhibitors (MMPIs)
by Loganathan Rangasamy, Bruno Di Geronimo, Irene Ortín, Claire Coderch, José María Zapico, Ana Ramos and Beatriz de Pascual-Teresa
Molecules 2019, 24(16), 2982; https://doi.org/10.3390/molecules24162982 - 16 Aug 2019
Cited by 37 | Viewed by 6824
Abstract
Matrix metalloproteinases (MMPs) are a family of zinc- and calcium-dependent endopeptidases which are secreted or anchored in the cell membrane and are capable of degrading the multiple components of the extracellular matrix (ECM). MMPs are frequently overexpressed or highly activated in numerous human [...] Read more.
Matrix metalloproteinases (MMPs) are a family of zinc- and calcium-dependent endopeptidases which are secreted or anchored in the cell membrane and are capable of degrading the multiple components of the extracellular matrix (ECM). MMPs are frequently overexpressed or highly activated in numerous human diseases. Owing to the important role of MMPs in human diseases, many MMP inhibitors (MMPIs) have been developed as novel therapeutics, and some of them have entered clinical trials. However, so far, only one MMPI (doxycycline) has been approved by the FDA. Therefore, the evaluation of the activity of a specific subset of MMPs in human diseases using clinically relevant imaging techniques would be a powerful tool for the early diagnosis and assessment of the efficacy of therapy. In recent years, numerous MMPIs labeled imaging agents have emerged. This article begins by providing an overview of the MMP subfamily and its structure and function. The latest advances in the design of subtype selective MMPIs and their biological evaluation are then summarized. Subsequently, the potential use of MMPI-labeled diagnostic agents in clinical imaging techniques are discussed, including positron emission tomography (PET), single-photon emission computed tomography (SPECT) and optical imaging (OI). Finally, this article concludes with future perspectives and clinical utility. Full article
(This article belongs to the Special Issue Structure and Function of Metalloenzymes)
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