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Life
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Significance of RNA-Protein Interactions: From Origins of Life to Modern...
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Significance of RNA-Protein Interactions: From Origins of Life to Modern Biology

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Evolutionary Biology".

Deadline for manuscript submissions: closed (15 November 2021) | Viewed by 2603

Special Issue Editors

Dr. Ranajay Saha

E-Mail Website
Guest Editor
Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
Interests: origin of life; RNA world; minimal synthetic cells; molecular biology; protein and RNA biophysics; macromolecular crowding and confinement; UV damage; fluorescence spectroscopy
Special Issues, Collections and Topics in MDPI journals
Dr. Tanumoy Mondol

E-Mail Website
Guest Editor
Institute of Physical Chemistry, Albert-Ludwigs-University Freiburg, Germany
Interests: protein–nucleic acid interaction; chaperone biology; protein folding; DNA replication; single molecule fluorescence microscopy; protein biophysics; structural biology
Dr. Celia Blanco

E-Mail Website
Guest Editor
Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA, 90095, USA
Interests: molecular evolution; biological homochirality; fitness landscapes; directed evolution; origin of life; mathematical modeling; sequence analysis; numerical simulation; bioinformatics; RNA world

Special Issue Information

Dear Colleagues,

The interaction between RNA and proteins plays an essential role in biology. Life on Earth is believed to have originated through the mutual chaperoning and coevolution of RNA and proteins. Understanding how RNA and proteins interact is critical in order to interpret the complex cellular evolution in biology. This knowledge enables us not only to infer the biophysical properties of the earliest functional proteins, but also to potentially decipher the characteristics of plausible prebiotic scenarios.

In modern organisms, complex RNA–protein regulatory networks control diverse cellular processes including RNA metabolism and gene expression. While the complex regulatory networks of RNA and protein are key to cellular homeostasis, dysregulation of these networks can lead to several life-threatening diseases, including neurologic disorders and cancers. Remarkably, the Human SARS Coronavirus nucleoprotein (an RNA-binding protein) is highly immunogenic, and is being considered as a potential pharmaceutical target for SARS-CoV-2 infection. The implementation of new methods to probe RNA–protein physical interactions and understand their mutual regulation through diverse in vitro and in vivo studies will accelerate progress in this expanding area of biology.

The objective of this Special Issue is to cover current developments related to RNA–protein interactions. We welcome research papers, review articles, and case reports of experimental, theoretical, or computational nature.

Dr. Ranajay Saha
Dr. Tanumoy Mondol
Dr. Celia Blanco
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 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. Life is an international peer-reviewed open access monthly 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 2600 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

  • RNA–protein interactions
  • RNA metabolism
  • gene expression
  • RNA binding protein
  • RNA–protein binding prediction
  • protein–RNA recognition
  • electrostatic interaction
  • biophysics
  • origins of life
  • evolutionary biology
  • RNA–protein chaperoning

Published Papers (1 paper)

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Research

13 pages, 725 KiB  
Article
A Max-Margin Model for Predicting Residue—Base Contacts in Protein–RNA Interactions
by Shunya Kashiwagi, Kengo Sato and Yasubumi Sakakibara
Life 2021, 11(11), 1135; https://doi.org/10.3390/life11111135 - 25 Oct 2021
Cited by 2 | Viewed by 1726
Abstract
Protein–RNA interactions (PRIs) are essential for many biological processes, so understanding aspects of the sequences and structures involved in PRIs is important for unraveling such processes. Because of the expensive and time-consuming techniques required for experimental determination of complex protein–RNA structures, various computational [...] Read more.
Protein–RNA interactions (PRIs) are essential for many biological processes, so understanding aspects of the sequences and structures involved in PRIs is important for unraveling such processes. Because of the expensive and time-consuming techniques required for experimental determination of complex protein–RNA structures, various computational methods have been developed to predict PRIs. However, most of these methods focus on predicting only RNA-binding regions in proteins or only protein-binding motifs in RNA. Methods for predicting entire residue–base contacts in PRIs have not yet achieved sufficient accuracy. Furthermore, some of these methods require the identification of 3D structures or homologous sequences, which are not available for all protein and RNA sequences. Here, we propose a prediction method for predicting residue–base contacts between proteins and RNAs using only sequence information and structural information predicted from sequences. The method can be applied to any protein–RNA pair, even when rich information such as its 3D structure, is not available. In this method, residue–base contact prediction is formalized as an integer programming problem. We predict a residue–base contact map that maximizes a scoring function based on sequence-based features such as k-mers of sequences and the predicted secondary structure. The scoring function is trained using a max-margin framework from known PRIs with 3D structures. To verify our method, we conducted several computational experiments. The results suggest that our method, which is based on only sequence information, is comparable with RNA-binding residue prediction methods based on known binding data. Full article
(This article belongs to the Special Issue Significance of RNA-Protein Interactions: From Origins of Life to Modern Biology)
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