Allostery and inter-domain dynamics in NXF1: An insight into viral CTE-RNA binding

Nucleocytoplasmic export of mRNA is a fundamental process in eukaryotic cells, facilitating the transportation of mRNA transcripts from nucleus to cytoplasm. Central to this pathway is Nuclear Export Factor 1 (NXF1), a key RNA binding protein (RBP) mediating mRNA export through the Nuclear Pore Complex (NPC). The significance of NXF1 in the export pathway extends to viral infections and neurodegenerative diseases where aberrations in nucleocytoplasmic transport have been identified as critical factors in disease progression. This study focuses on the structural dynamics and binding interactions of NXF1 with Constitutive Transport Element (CTE) RNA. Through molecular dynamics simulation, we explore the conformational shift and stability of NXF1 upon RNA binding and assess the impact of point mutations on the binding affinity. Moreover, our study highlights allosteric communication between RNA Recognition Motif (RRM) and Leucine-Rich Repeat (LRR) domains of NXF1 upon RNA binding. Using network analysis, we identify potential allosteric sites and assess the impact of point mutations, showing their dual roles in RNA binding and allosteric regulation. This study advances the understanding of RNA recognition by NXF1 and lays the foundation for future therapeutic strategies targeting impaired NXF1-RNA interactions in diseases associated with nucleocytoplasmic transport defects.