Deciphering the RNA recognition by Musashi-1 to design protein and RNA variants for in vitro and in vivo applications

TY - JOUR

T1 - Deciphering the RNA recognition by Musashi-1 to design protein and RNA variants for in vitro and in vivo applications

AU - Pérez-Ràfols, Anna

AU - Pérez-Ropero, Guillermo

AU - Cerofolini, Linda

AU - Sperotto, Luca

AU - Roca-Martínez, Joel

AU - Higuera-Rodríguez, R. Anahí

AU - Russomanno, Pasquale

AU - Kaiser, Wolfgang

AU - Vranken, Wim

AU - Danielson, U. Helena

AU - Provenzani, Alessandro

AU - Martelli, Tommaso

AU - Sattler, Michael

AU - Buijs, Jos

AU - Fragai, Marco

N1 - Publisher Copyright: © 2025 The Author(s). Published by Oxford University Press.

PY - 2025/8/28

Y1 - 2025/8/28

N2 - The Human Musashi-1 (MSI-1) is an RNA-binding protein that recognizes (G/A)U1-3AGU and UAG sequences in diverse RNAs through two RNA Recognition Motif (RRM) domains and regulates the fate of target RNA. Here, we have combined structural biology and computational approaches to analyse the binding of the RRM domains of human MSI-1 with single-stranded and structured RNA ligands. We have used our recently developed computational tool RRMScorer to design a set of substitutions in the MSI-1 protein and the investigated RNA strands to modulate the binding affinity and selectivity. The in silico predictions of the designed protein-RNA interactions are assessed by nuclear magnetic resonance and surface plasmon resonance. These experiments have also been used to study the competition of the two RRM domains of MSI-1 for the same binding site within linear and harpin RNA. Our experimental results shed light on MSI-RNA interactions, thus opening the way for the development of new biomolecules for in vitro and in vivo studies and downstream applications.

AB - The Human Musashi-1 (MSI-1) is an RNA-binding protein that recognizes (G/A)U1-3AGU and UAG sequences in diverse RNAs through two RNA Recognition Motif (RRM) domains and regulates the fate of target RNA. Here, we have combined structural biology and computational approaches to analyse the binding of the RRM domains of human MSI-1 with single-stranded and structured RNA ligands. We have used our recently developed computational tool RRMScorer to design a set of substitutions in the MSI-1 protein and the investigated RNA strands to modulate the binding affinity and selectivity. The in silico predictions of the designed protein-RNA interactions are assessed by nuclear magnetic resonance and surface plasmon resonance. These experiments have also been used to study the competition of the two RRM domains of MSI-1 for the same binding site within linear and harpin RNA. Our experimental results shed light on MSI-RNA interactions, thus opening the way for the development of new biomolecules for in vitro and in vivo studies and downstream applications.

UR - https://www.scopus.com/pages/publications/105013116448

U2 - 10.1093/nar/gkaf741

DO - 10.1093/nar/gkaf741

M3 - Article

C2 - 40795964

AN - SCOPUS:105013116448

SN - 0305-1048

VL - 53

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - 15

M1 - gkaf741

ER -