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Special Issue "Frontiers in RNA Structure"

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

Deadline for manuscript submissions: 15 February 2020.

Special Issue Editor

Dr. Quentin Vicens
E-Mail Website
Guest Editor
Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA
Interests: biochemistry; cryo-electron microscopy; molecular biology; ribosome; RNA structure and folding; structure prediction; X-ray crystallography

Special Issue Information

Dear Colleagues,

Ribonucleic acids (RNA) can code for information, act as enzymes or change shape upon binding to an effector. Significantly, the dynamic nature of RNA means that RNA is able to adopt transient structures with diverse functions. In addition, the fraction of noncoding RNA in our genomes is much larger than that of messenger RNA. Hence, RNA has now emerged as one of the key molecules in the regulation of gene expression. However, our understanding of the functions and structures of these myriad RNAs pales in comparison to what we know about proteins.

The focus of this Special Issue is on the frontier of RNA structure discovery and the structure–function relationship. We welcome submissions about any type of RNA or ribonucleoprotein complex, and any structural biology methodology, including but not limited to: X-ray/electron crystallography, NMR, cryo-electron microscopy, small-angle X-ray scattering, FRET, structure mapping, and computational modeling.

Articles reporting original research as well as reviews will be considered for publication.

Authors are strongly encouraged to submit a brief abstract (200 words) to the guest editor by October 15, 2019. Abstracts will be reviewed in consultation with the editors at Molecules. Full manuscripts submitted by February 15, 2020 will be guaranteed full consideration.

Dr. Quentin Vicens
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 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

  • coding and noncoding RNA
  • regulatory RNA
  • RNA dynamics
  • RNA–protein complex
  • structured RNA element
  • three-dimensional structure

Published Papers (1 paper)

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Research

Open AccessArticle
Structural Bases for the Fitness Cost of the Antibiotic-Resistance and Lethal Mutations at Position 1408 of 16S rRNA
Molecules 2020, 25(1), 159; https://doi.org/10.3390/molecules25010159 - 31 Dec 2019
Abstract
To understand a structural basis for the fitness cost of the A1408G antibiotic-resistance mutation in the ribosomal A-site RNA, we have determined crystal structures of its A1408C and A1408U lethal mutants, and made comparison with previously solved structures of the wild type and [...] Read more.
To understand a structural basis for the fitness cost of the A1408G antibiotic-resistance mutation in the ribosomal A-site RNA, we have determined crystal structures of its A1408C and A1408U lethal mutants, and made comparison with previously solved structures of the wild type and the antibiotic-resistant mutant. The A-site RNA containing an asymmetric internal loop functions as a molecular switch to discriminate a single cognate tRNA from several near-cognate tRNAs by its conformational ON/OFF switching. Overall structures of the “off” states of the A1408C/U lethal mutants are very similar to those of the wild type and the A1408G antibiotic-resistant mutant. However, significant differences are found in local base stacking interactions including the functionally important A1492 and A1493 residues. In the wild type and the A1408G antibiotic-resistant mutant “off” states, both adenines are exposed to the solvent region. On the other hand, one of the corresponding adenines of the lethal A1408C/U mutants stay deeply inside their A-site helices by forming a purine-pyrimidine AoC or A-U base pair and is sandwiched between the upper and lower bases. Therefore, the ON/OFF switching might unfavorably occur in the lethal mutants compared to the wild type and the A1408G antibiotic-resistant mutant. It is probable that bacteria manage to acquire antibiotic resistance without losing the function of the A-site molecular switch by mutating the position 1408 only from A to G, but not to pyrimidine base C or U. Full article
(This article belongs to the Special Issue Frontiers in RNA Structure)
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: The multiple scales of ribosome heterogeneity: recent advances and computational challenges in cryoEM
Authors: Frederic Poitevin 1 and Khanh Dao Duc 2
Affiliations: 1 Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA;2 Departments of Mathematics, Computer Science, and Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
Email: [email protected]
Abstract: The extent of ribosomal heterogeneity has caught increasing interest over the past few years, as recent studies have highlighted the presence of structural variations of the ribosome, yielding specialized gene expression at the cellular and sub-cellular scale. As a matter of fact, the heterogeneity of the ribosome extends well beyond these scales, including the dynamical aspects of ribosomal motion at the single particle level, or evolutionary differences across species. Investigating these other forms of ribosome heterogeneity has been enabled by the renement and wide use of cryo-electron microscopy (cryo-EM), giving access to the ribosome atomic structure at high resolution. In this review article, we present some recent advances in quantifying ribosome heterogeneity, with a specic focus on conformational and evolutionary variations of the ribosome, with their functional implications. Interestingly, these recent eorts also highlight the need for new computational methods and comparative tools, to comprehensively model the continuous conformational transition pathways of the ribosome, as well as its evolution. While developing these methods presents some important challenges, it also provides an opportunity to extend our interpretation and usage of cryo-EM data which, more generally, would benet to studying in detail the molecular dynamics and evolution of proteins and other complexes.

 

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