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Protein–RNA interactions: structural characteristics and hotspot amino acids

Structural information about protein–RNA complexes supports the understanding of crucial recognition processes in the cell, and it can allow the development of high affinity ligands to interfere with these processes. In this respect, the identification of amino acid hotspots is particularly importan...

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Detalles Bibliográficos
Autores principales: Krüger, Dennis M., Neubacher, Saskia, Grossmann, Tom N.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6191724/
https://www.ncbi.nlm.nih.gov/pubmed/30093489
http://dx.doi.org/10.1261/rna.066464.118
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author Krüger, Dennis M.
Neubacher, Saskia
Grossmann, Tom N.
author_facet Krüger, Dennis M.
Neubacher, Saskia
Grossmann, Tom N.
author_sort Krüger, Dennis M.
collection PubMed
description Structural information about protein–RNA complexes supports the understanding of crucial recognition processes in the cell, and it can allow the development of high affinity ligands to interfere with these processes. In this respect, the identification of amino acid hotspots is particularly important. In contrast to protein–protein interactions, in silico approaches for protein–RNA interactions lag behind in their development. Herein, we report an analysis of available protein–RNA structures. We assembled a data set of 322 crystal and NMR structures and analyzed them regarding interface properties. In addition, we describe a computational alanine-scanning approach which provides interaction scores for interface amino acids, allowing the identification of potential hotspots in protein–RNA interfaces. We have made the computational approach available as an online tool, which allows interaction scores to be calculated for any structure of a protein–RNA complex by uploading atomic coordinates to the PRI HotScore web server (https://pri-hotscore.labs.vu.nl).
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spelling pubmed-61917242018-11-02 Protein–RNA interactions: structural characteristics and hotspot amino acids Krüger, Dennis M. Neubacher, Saskia Grossmann, Tom N. RNA Bioinformatics Structural information about protein–RNA complexes supports the understanding of crucial recognition processes in the cell, and it can allow the development of high affinity ligands to interfere with these processes. In this respect, the identification of amino acid hotspots is particularly important. In contrast to protein–protein interactions, in silico approaches for protein–RNA interactions lag behind in their development. Herein, we report an analysis of available protein–RNA structures. We assembled a data set of 322 crystal and NMR structures and analyzed them regarding interface properties. In addition, we describe a computational alanine-scanning approach which provides interaction scores for interface amino acids, allowing the identification of potential hotspots in protein–RNA interfaces. We have made the computational approach available as an online tool, which allows interaction scores to be calculated for any structure of a protein–RNA complex by uploading atomic coordinates to the PRI HotScore web server (https://pri-hotscore.labs.vu.nl). Cold Spring Harbor Laboratory Press 2018-11 /pmc/articles/PMC6191724/ /pubmed/30093489 http://dx.doi.org/10.1261/rna.066464.118 Text en © 2018 Krüger et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society http://creativecommons.org/licenses/by/4.0/ This article, published in RNA, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
spellingShingle Bioinformatics
Krüger, Dennis M.
Neubacher, Saskia
Grossmann, Tom N.
Protein–RNA interactions: structural characteristics and hotspot amino acids
title Protein–RNA interactions: structural characteristics and hotspot amino acids
title_full Protein–RNA interactions: structural characteristics and hotspot amino acids
title_fullStr Protein–RNA interactions: structural characteristics and hotspot amino acids
title_full_unstemmed Protein–RNA interactions: structural characteristics and hotspot amino acids
title_short Protein–RNA interactions: structural characteristics and hotspot amino acids
title_sort protein–rna interactions: structural characteristics and hotspot amino acids
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6191724/
https://www.ncbi.nlm.nih.gov/pubmed/30093489
http://dx.doi.org/10.1261/rna.066464.118
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