RNA–protein interaction
Most functional RNA acts together with proteins, and the specificity of that recognition is decided by structure on both sides: the RNA has to present its binding motif in an accessible conformation, and the RNA-binding domains of the protein have to fit it. The computational work here combines sequence and structure analysis of the RNA with molecular dynamics and docking of the complex.
Musashi-1 runs through several of these posts, from a comparative study of its binding elements in Zika and related flavivirus 3′UTRs, through molecular dynamics of its two RNA-binding domains, to a refinement protocol for RNA–protein complexes that combines AI-based modelling with flexible docking. Two posts on archaeal Sm-like proteins and the translation factor aIF5A complete the set. The glossary entry Musashi gives the background.
From structure to function in Musashi-RNA complexes
This review article surveys how computational modeling, molecular dynamics, and AI-derived structures help explain Musashi-RNA recognition in both cellular regulation and viral pathogenesis.
A conserved G-quadruplex in the Zika virus 3' terminal region
This study examines evidence for a conserved G-quadruplex in the Zika virus 3' terminal region and discusses what the observed DDX17 interaction does, and does not, imply.
RNA-protein complex refinement using AI modeling and docking
This article explains a workflow for refining protein-RNA complexes by combining AI-based structural models with flexible docking and enhanced sampling.
How Musashi-1 recognizes RNA: molecular dynamics of RBD1 and RBD2 binding
Molecular dynamics and binding-energy calculations are used here to compare how Musashi-1 recognizes different RNA motifs and to identify determinants of binding specificity.
Musashi binding elements in Zika virus 3'UTR
A comparative analysis of Musashi binding element accessibility in Zika virus and related flavivirus 3' UTRs using thermodynamic RNA structure modeling.