All-Atom Simulations Decrypt the Molecular Terms of RNA Catalysis in the Exon-Ligation Step of the Spliceosome

The spliceosome, a protein-directed metalloribozyme, catalyzes premature mRNA splicing via two transesterification reactions. The atomic-level details of the splicing mechanism and the role of the entwined protein-RNA environment during catalysis remain unresolved. Here, quantum-classical molecular dynamics simulations along with thermodynamic integration unveil that the second catalytic (exon-ligation) step occurs via an associative two-Mg2+-ion mechanism, exclusively catalyzed by RNA, with the scissile phosphate mediating a proton transfer from the nucleophile to the leaving group. Our outcomes provide fundamental advances in understanding the splicing mechanism in eukaryotes disclosing how the catalytic core of spliceosome's ancestors self-splicing ribozymes remained conserved during evolution.