Tracing Allostery in the Spliceosome Ski2-like RNA Helicase Brr2

• Published in: The journal of physical chemistry letters 2024-04, Vol.15 (13), p.3502-3508
• Main Authors: Guidarelli Mattioli, Francesco, Saltalamacchia, Andrea, Magistrato, Alessandra
• Format: Article
• Language: English
• Subjects: Adenosine Triphosphatases - metabolism; Humans; Physical Insights into Chemistry, Catalysis, and Interfaces; Ribonucleoprotein, U4-U6 Small Nuclear - chemistry; Ribonucleoprotein, U4-U6 Small Nuclear - genetics; Ribonucleoprotein, U4-U6 Small Nuclear - metabolism; Ribonucleoproteins, Small Nuclear - metabolism; RNA - metabolism; RNA Helicases - chemistry; RNA Helicases - genetics; RNA Helicases - metabolism; Spliceosomes - genetics; Spliceosomes - metabolism
• ISSN: 1948-7185; 1948-7185
• DOI: 10.1021/acs.jpclett.3c03538

RNA ATPases/helicases remodel substrate RNA–protein complexes in distinct ways. The different RNA ATPases/helicases, taking part in the spliceosome complex, reshape the RNA/RNA-protein contacts to enable premature-mRNA splicing. Among them, the bad response to refrigeration 2 (Brr2) helicase promotes U4/U6 small nuclear (sn)­RNA unwinding via ATP-driven translocation of the U4 snRNA strand, thus playing a pivotal role during the activation, catalytic, and disassembly phases of splicing. The plastic Brr2 architecture consists of an enzymatically active N-terminal cassette (N-cassette) and a structurally similar but inactive C-terminal cassette (C-cassette). The C-cassette, along with other allosteric effectors and regulators, tightly and timely controls Brr2’s function via an elusive mechanism. Here, microsecond-long molecular dynamics simulations, dynamical network theory, and community network analysis are combined to elucidate how allosteric effectors/regulators modulate the Brr2 function. We unexpectedly reveal that U4 snRNA itself acts as an allosteric regulator, amplifying the cross-talk of distal Brr2 domains and triggering a conformational reorganization of the protein. Our findings offer fundamental understanding into Brr2’s mechanism of action and broaden our knowledge on the sophisticated regulatory mechanisms by which spliceosome ATPases/helicases control gene expression. This includes their allosteric regulation exerted by client RNA strands, a mechanism that may be broadly applicable to other RNA-dependent ATPases/helicases.