Unraveling the Molecular Mechanism of Pre-mRNA Splicing From Multi-Scale Simulations

Pre-mRNA splicing is a vital step of gene expression and regulation executed by self-cleaving ribozymes in simpler organisms, and by a majestic and sophisticated molecular machine-the spliceosome-in eukaryotes. Along the catalytic cycle, the spliceosome undergoes a continuous remodeling that interconverts this extraordinary protein-directed ribozyme into eight distinct functional states, exhibiting a pivotal compositional and conformational variability. Irrespectively of the complexity of the organism and of its genome, splicing occurs via two transesterification reactions mediated by the presence of two Mg2+ ions. The recent advances in structural biology enabled rationalizing decades of biochemical and functional studies on splicing, opening new avenues to tackle its mechanistic basis by means of atomic-level simulations. Nevertheless, the complexity of the spliceosome and its convoluted mechanism call for an integrated use of state-of-the-art techniques ranging from classical all-atom simulations to quantum-classical approaches in order to dissect its many functional intricacies. In this opinion, we report recent advances in this direction and we discuss how strengths and limits of current molecular simulations may address the unsolved questions in forthcoming years, with a focus on drug discovery and gene targeting studies.