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Thermodynamic modeling reveals widespread multivalent binding by RNA-binding proteins

View ORCID ProfileSalma Sohrabi-Jahromi, View ORCID ProfileJohannes Söding
doi: https://doi.org/10.1101/2021.01.30.428941
Salma Sohrabi-Jahromi
1Quantitative and Computational Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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Johannes Söding
1Quantitative and Computational Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
2Campus-Institut Data Science (CIDAS), Göttingen, Germany
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Abstract

Motivation Understanding how proteins recognize their RNA targets is essential to elucidate regulatory processes in the cell. Many RNA-binding proteins (RBPs) form complexes or have multiple domains that allow them to bind to RNA in a multivalent, cooperative manner. They can thereby achieve higher specificity and affinity than proteins with a single RNA-binding domain. However, current approaches to de-novo discovery of RNA binding motifs do not take multivalent binding into account.

Results We present Bipartite Motif Finder (BMF), which is based on a thermodynamic model of RBPs with two cooperatively binding RNA-binding domains. We show that bivalent binding is a common strategy among RBPs, yielding higher affinity and sequence specificity. We furthermore illustrate that the spatial geometry between the binding sites can be learned from bound RNA sequences. These discovered bipartite motifs are consistent with previously known motifs and binding behaviors. Our results demonstrate the importance of multivalent binding for RNA-binding proteins and highlight the value of bipartite motif models in representing the multivalency of protein-RNA interactions.

Availability BMF source code is available at https://github.com/soedinglab/bipartite_motif_finder under a GPL license. The BMF web server is accessible at https://bmf.soedinglab.org.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted February 01, 2021.
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Thermodynamic modeling reveals widespread multivalent binding by RNA-binding proteins
Salma Sohrabi-Jahromi, Johannes Söding
bioRxiv 2021.01.30.428941; doi: https://doi.org/10.1101/2021.01.30.428941
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Thermodynamic modeling reveals widespread multivalent binding by RNA-binding proteins
Salma Sohrabi-Jahromi, Johannes Söding
bioRxiv 2021.01.30.428941; doi: https://doi.org/10.1101/2021.01.30.428941

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