Disclosing the Impact of Carcinogenic SF3b Mutations on Pre-mRNA Recognition Via All-Atom Simulations

Abstract

The spliceosome accurately promotes precursor messenger-RNA splicing by recognizing specific noncoding intronic tracts including the branch point sequence (BPS) and the 3’-splice-site (3’SS). Mutations of Hsh155 (yeast)/SF3B1 (human), which is a protein of the SF3b factor involved in BPS recognition and induces altered BPS binding and 3’SS selection, lead to mis-spliced mRNA transcripts. Although these mutations recur in hematologic malignancies, the mechanism by which they change gene expression remains unclear. In this study, multi-microsecond-long molecular-dynamics simulations of eighth distinct ∼700,000 atom models of the spliceosome Bact complex, and gene sequencing of SF3B1, disclose that these carcinogenic isoforms destabilize intron binding and/or affect the functional dynamics of Hsh155/SF3B1 only when binding non-consensus BPSs, as opposed to the non-pathogenic variants newly annotated here. This pinpoints a cross-talk between the distal Hsh155 mutation and BPS recognition sites. Our outcomes unprecedentedly contribute to elucidating the principles of pre-mRNA recognition, which provides critical insights on the mechanism underlying constitutive/alternative/aberrant splicing.

Investigating the Molecular Mechanism of H3B-8800: A Splicing Modulator Inducing Preferential Lethality in Spliceosome-Mutant Cancers

“…The C-terminal domain of SF3B1, the main component of the SF3b complex, is composed of a sequence of 20 HEAT repeats domains [25]. This gives SF3B1 a highly flexible nature, which becomes very sensitive to perturbation induced by mutations and the binding of different SMs as revealed by previous MD simulations [19,20]. Hence, in this study, we have performed a principal component analysis (PCA, Figure S3) to investigate how the binding of H3B affects the large-scale collective motions of WT SF3b and K700E SF3b.…”

“…The most recurrent K700E SF3B1 mutation often occurs in patients affected by myelodysplastic syndromes, such as myelodysplasia with ring sideroblasts [13]. In this scenario, the SPL is emerging as an appealing target for cancer treatment via small molecules, also due to the increased understanding of its mechanism provided by recent structural [14][15][16], functional [17,18], and computational studies [19,20]. SF3b was the first SF for which structural information in complex with small-molecules splicing modulators (SMs) were solved [14][15][16].…”

MD simulations reveal the basis for dynamic assembly of Hfq–RNA complexes

“…In this study, we used atomistic molecular dynamics (MD) simulations to explore the conformational variation of the Hfq-RNA binary complex and the higher order quaternary complexes formed with Crc. Our MD simulations utilize a set of carefully calibrated molecular mechanics models (21,22) that have been applied in many studies of protein-RNA complexes with predictive power (21,(23)(24)(25)(26)(27)(28). MD allows the study of atomic movements at spatiotemporal resolutions inaccessible to any currently available experimental method and can help rationalize experimental observations (21).…”

Is the Rigidity of SARS-CoV-2 Spike Receptor-Binding Motif the Hallmark for Its Enhanced Infectivity and Pathogenesis?

“…The normalized covariance matrix by using the Pearson's coefficient gives the cross-correlation matrix (CCM) where each element ij corresponds to the Pearson's correlation coefficient (CCij), between residue i and j. CCij ranges from a value of -1, indicative of a totally anti-correlated motion between the two residues, to a value of +1, representative of a correlated motion. 19 Figure S1. Root mean square deviation (RMSD, Å) vs simulation time (ns) calculated on the SARS-CoV/ACE2 and of SARS-CoV-2/ACE2 complex (top), the receptor-binding domain (RDB) of SARS-CoV and SARS-CoV-2 (middle) and the ACE2 receptor (bottom).…”