Functional implications of SNPs in spliceosomal network: a structural systems biology approach

Spliceosome is a dynamic macromolecular complex responsible for splicing precursor mRNA. Single Nucleotide Polymorphisms (SNPs) in spliceosomal proteins have been implicated in various diseases. Mutational studies and high-resolution structures have provided important functional insights, and these data can be used to evaluate the impact of SNPs on splicing. Here, we applied integrated sequence and structure-based approaches to investigate the functional consequences of SNPs in spliceosomal proteins. Changes in binding free energy (ΔΔG) for SNPs were compared with those of mutations with known functional implications. When human crystal structures were unavailable, homologous protein complexes from other organisms were used, and variants were mapped onto these structures via multiple-sequence alignment before ΔΔG estimation. Protein-protein interactions annotated with FoldX ΔΔG values were visualized as interaction networks, and molecular dynamics (MD) simulations were performed to assess SNP and mutation-induced structural perturbations. Target RNAs affected by functionally characterized SNPs and mutations were compiled. Stage-specific effects were evaluated by mapping variants onto yeast spliceosome complexes representing different stages of the spliceosome cycle. For the U2AF35-U2AF65 complex, ClusPro docking produced ΔΔG values comparable to experimental and AlphaFold-predicted complexes, whereas ZDOCK showed a distinct trend. Following MD simulations, ΔΔG values across models were comparable. However, predicted and docked complexes showed ∼10-15% interface variation relative to the crystal structure, highlighting the need for cautious interpretation, while our analysis was limited to protein subcomplexes due to the spliceosome's size and complexity. Overall, this study provides a structural systems biology framework for understanding how SNPs perturb spliceosome function and influence splicing.