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Molecular Dynamics Simulations of Metal-Binding Proteins and Nucleic Acids
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Molecular Dynamics Simulations of Metal-Binding Proteins and Nucleic Acids

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: closed (30 April 2023) | Viewed by 5197

Special Issue Editor

Prof. Dr. Antonio Rosato

E-Mail Website
Guest Editor
Department of Chemistry and Center for Magnetic Resonance, University of Florence, 50019 Sesto Fiorentino, Italy
Interests: metalloproteins; NMR; metallomics; structural biology; metalloproteomics; bioinformatics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

More than one-third of all known proteins encoded need at least one metal ion to perform their biological function. In line with their importance, and with the potential cytotoxicity of some essential metals, the concentration and distribution of metal ions in the cell are tightly controlled. This control depends upon the combined action of sensing, transport, delivery, storage, detoxification, and efflux machineries. In addition, various metal-containing cofactors require dedicated biosynthetic enzymes for their assembly. Metal ions are also crucial to tune and stabilize the three-dimensional (3D) structure of nucleic acids, and to promote intermolecular interactions.

To understand how the aforementioned processes work, it is necessary to investigate the 3D structure and mobility of the involved macromolecules at the atomic level. Molecular dynamics (MD) simulations complement experimental information and generate new hypotheses on the molecular and cellular functions of metal ions. Among the specific challenges posed by the MD of metal-binding macromolecular systems, a particularly relevant one is the parametrization of the metal site. This is obviously crucial to achieve an accurate interpretation of the data.

In this Special Issue, we wish to cover recent technical advances in MD simulations of metal-binding to proteins and nucleic acids, as well as novel applications to all kinds of metal-dependent systems, by hosting a mix of original research articles and short critical reviews.

Prof. Dr. Antonio Rosato
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.

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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 ions
  • metal-containing cofactors
  • metal binding
  • affinity constants
  • enzymatic catalysis
  • toxicity
  • regulation

Published Papers (3 papers)

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Research

12 pages, 3269 KiB  
Article
A Comparison of Bonded and Nonbonded Zinc(II) Force Fields with NMR Data
by Milana Bazayeva, Andrea Giachetti, Marco Pagliai and Antonio Rosato
Int. J. Mol. Sci. 2023, 24(6), 5440; https://doi.org/10.3390/ijms24065440 - 13 Mar 2023
Viewed by 1490
Abstract
Classical molecular dynamics (MD) simulations are widely used to inspect the behavior of zinc(II)-proteins at the atomic level, hence the need to properly model the zinc(II) ion and the interaction with its ligands. Different approaches have been developed to represent zinc(II) sites, with [...] Read more.
Classical molecular dynamics (MD) simulations are widely used to inspect the behavior of zinc(II)-proteins at the atomic level, hence the need to properly model the zinc(II) ion and the interaction with its ligands. Different approaches have been developed to represent zinc(II) sites, with the bonded and nonbonded models being the most used. In the present work, we tested the well-known zinc AMBER force field (ZAFF) and a recently developed nonbonded force field (NBFF) to assess how accurately they reproduce the dynamic behavior of zinc(II)-proteins. For this, we selected as benchmark six zinc-fingers. This superfamily is extremely heterogenous in terms of architecture, binding mode, function, and reactivity. From repeated MD simulations, we computed the order parameter (S2) of all backbone N-H bond vectors in each system. These data were superimposed to heteronuclear Overhauser effect measurements taken by NMR spectroscopy. This provides a quantitative estimate of the accuracy of the FFs in reproducing protein dynamics, leveraging the information about the protein backbone mobility contained in the NMR data. The correlation between the MD-computed S2 and the experimental data indicated that both tested FFs reproduce well the dynamic behavior of zinc(II)-proteins, with comparable accuracy. Thus, along with ZAFF, NBFF represents a useful tool to simulate metalloproteins with the advantage of being extensible to diverse systems such as those bearing dinuclear metal sites. Full article
(This article belongs to the Special Issue Molecular Dynamics Simulations of Metal-Binding Proteins and Nucleic Acids)
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13 pages, 2625 KiB  
Article
Effects of Active-Center Reduction of Plant-Type Ferredoxin on Its Structure and Dynamics: Computational Analysis Using Molecular Dynamics Simulations
by Tomoki Nakayoshi, Yusuke Ohnishi, Hideaki Tanaka, Genji Kurisu, Hiroko X. Kondo and Yu Takano
Int. J. Mol. Sci. 2022, 23(24), 15913; https://doi.org/10.3390/ijms232415913 - 14 Dec 2022
Cited by 1 | Viewed by 1774
Abstract
“Plant-type” ferredoxins (Fds) in the thylakoid membranes of plants, algae, and cyanobacteria possess a single [2Fe-2S] cluster in active sites and mediate light-induced electron transfer from Photosystem I reaction centers to various Fd-dependent enzymes. Structural knowledge of plant-type Fds is relatively limited to [...] Read more.
“Plant-type” ferredoxins (Fds) in the thylakoid membranes of plants, algae, and cyanobacteria possess a single [2Fe-2S] cluster in active sites and mediate light-induced electron transfer from Photosystem I reaction centers to various Fd-dependent enzymes. Structural knowledge of plant-type Fds is relatively limited to static structures, and the detailed behavior of oxidized and reduced Fds has not been fully elucidated. It is important that the investigations of the effects of active-center reduction on the structures and dynamics for elucidating electron-transfer mechanisms. In this study, model systems of oxidized and reduced Fds were constructed from the high-resolution crystal structure of Chlamydomonas reinhardtii Fd1, and three 200 ns molecular dynamics simulations were performed for each system. The force field parameters of the oxidized and reduced active centers were independently obtained using quantum chemical calculations. There were no substantial differences in the global conformations of the oxidized and reduced forms. In contrast, active-center reduction affected the hydrogen-bond network and compactness of the surrounding residues, leading to the increased flexibility of the side chain of Phe61, which is essential for the interaction between Fd and the target protein. These computational results will provide insight into the electron-transfer mechanisms in the Fds. Full article
(This article belongs to the Special Issue Molecular Dynamics Simulations of Metal-Binding Proteins and Nucleic Acids)
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16 pages, 10987 KiB  
Article
Computational Study of Helicase from SARS-CoV-2 in RNA-Free and Engaged Form
by Francesca Di Matteo, Giorgia Frumenzio, Balasubramanian Chandramouli, Alessandro Grottesi, Andrew Emerson and Francesco Musiani
Int. J. Mol. Sci. 2022, 23(23), 14721; https://doi.org/10.3390/ijms232314721 - 25 Nov 2022
Cited by 2 | Viewed by 1352
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the pandemic that broke out in 2020 and continues to be the cause of massive global upheaval. Coronaviruses are positive-strand RNA viruses with a genome of ~30 kb. The genome is [...] Read more.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the pandemic that broke out in 2020 and continues to be the cause of massive global upheaval. Coronaviruses are positive-strand RNA viruses with a genome of ~30 kb. The genome is replicated and transcribed by RNA-dependent RNA polymerase together with accessory factors. One of the latter is the protein helicase (NSP13), which is essential for viral replication. The recently solved helicase structure revealed a tertiary structure composed of five domains. Here, we investigated NSP13 from a structural point of view, comparing its RNA-free form with the RNA-engaged form by using atomistic molecular dynamics (MD) simulations at the microsecond timescale. Structural analyses revealed conformational changes that provide insights into the contribution of the different domains, identifying the residues responsible for domain–domain interactions in both observed forms. The RNA-free system appears to be more flexible than the RNA-engaged form. This result underlies the stabilizing role of the nucleic acid and the functional core role of these domains. Full article
(This article belongs to the Special Issue Molecular Dynamics Simulations of Metal-Binding Proteins and Nucleic Acids)
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