Journal
RNA
Volume 24, Issue 11, Pages 1457-1465Publisher
COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
DOI: 10.1261/rna.066464.118
Keywords
alanine scanning; protein-RNA complex; RNA-binding protein; ribonucleoprotein; secondary structure
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Funding
- AstraZeneca
- Bayer CropScience
- Bayer HealthCare
- Boehringer Ingelheim
- Merck KGaA
- Max-Planck-Society
- Deutsche Forschungsgemeinschaft (DFG) [GR3592/2-1]
- European Reasearch Council (ERC) [678623]
- European Research Council (ERC) [678623] Funding Source: European Research Council (ERC)
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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://prihotscore.labs.vu.nl).
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