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Roca-Martínez, J.* ; Kang, H.-S. ; Sattler, M. ; Vranken, W.F.*

Analysis of the inter-domain orientation of tandem RRM domains with diverse linkers: Connecting experimental with AlphaFold2 predicted models.

NAR Gen. Bioinfo. 6:lqae002 (2024)
Verlagsversion DOI PMC
Creative Commons Lizenzvertrag
The RNA recognition motif (RRM) is the most prevalent RNA binding domain in eukaryotes and is involved in most RNA metabolism processes. Single RRM domains have a limited RNA specificity and affinity and tend to be accompanied by other RNA binding domains, frequently additional RRMs that contribute to an avidity effect. Within multi-RRM proteins, the most common arrangement are tandem RRMs, with two domains connected by a variable linker. Despite their prevalence, little is known about the features that lead to specific arrangements, and especially the role of the connecting linker. In this work, we present a novel and robust way to investigate the relative domain orientation in multi-domain proteins using inter-domain vectors referenced to a stable secondary structure element. We apply this method to tandem RRM domains and cluster experimental tandem RRM structures according to their inter-domain and linker-domain contacts, and report how this correlates with their orientation. By extending our analysis to AlphaFold2 predicted structures, with particular attention to the inter-domain predicted aligned error, we identify new orientations not reported experimentally. Our analysis provides novel insights across a range of tandem RRM orientations that may help for the design of proteins with a specific RNA binding mode.
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Publikationstyp Artikel: Journalartikel
Dokumenttyp Wissenschaftlicher Artikel
Korrespondenzautor
ISSN (print) / ISBN 2631-9268
e-ISSN 2631-9268
Zeitschrift NAR: Genomics and Bioinformatics
Quellenangaben Band: 6, Heft: 1, Seiten: , Artikelnummer: lqae002 Supplement: ,
Verlag Oxford University Press
Nichtpatentliteratur Publikationen
Begutachtungsstatus Peer reviewed
Institut(e) Institute of Structural Biology (STB)