Kant, S.; Maity, A.; Masipeddi, S.; Bhagat, M. R.; Bahadur, R. P.

A crucial step in early spliceosome assembly is the interaction between splicing factor 3A1 (SF3A1) of U2 snRNP and stem-loop 4 (SL4) of U1 snRNA. This interaction facilitates the spatial alignment of the 5' and the 3' splice sites, leading to the formation of the pre-spliceosomal A complex. In this study, we investigate the structural and dynamic basis of non-canonical recognition between ubiquitin-like domain (ULD) of SF3A1 and SL4 of U1 snRNA. Extensive all-atom molecular dynamics simulations reveal a dual recognition mechanism involving sequence-specific interactions mediated by the C-terminal RGGR motif and structural recognition governed by the UUCG tetraloop of SL4 snRNA. The RGGR motif primarily engages the duplex region of the snRNA, whereas the stem-loop nucleotides interact with the globular region of the ULD. Mutations of key residues R788 and R791 result in a significant loss of protein-RNA interactions, as reflected in the reduced binding affinities and altered conformational stability. Nucleotides C6 to C9 in the duplex region, stabilized by strong base-pairing and backbone-mediated interactions with SF3A1, exhibit constrained torsional distributions and minimal sensitivity to mutation. In contrast, nucleotides G10 to C15 in the tetraloop exhibit broader torsional distributions with moderate occupancy, consistent with weaker base-pairing but stronger protein-RNA interactions. Mutations significantly alter torsional distribution, enabling the nucleotides to adopt alternate conformations that preserve interactions with the globular domain of SF3A1. These findings provide a mechanistic insight into non-canonical RNA recognition and highlight the role of coupled sequence and structural determinants in stabilizing early spliceosomal assembly.