Molecular Dynamics Simulations Elucidate the Molecular Basis of Pre-mRNA Translocation by the Prp2 Spliceosomal Helicase

J Chem Inf Model. 2023 Jul 10;63(13):4180-4189. doi: 10.1021/acs.jcim.3c00585. Epub 2023 Jun 28.

Abstract

The spliceosome machinery catalyzes precursor-messenger RNA (pre-mRNA) splicing by undergoing at each splicing cycle assembly, activation, catalysis, and disassembly processes, thanks to the concerted action of specific RNA-dependent ATPases/helicases. Prp2, a member of the DExH-box ATPase/helicase family, harnesses the energy of ATP hydrolysis to translocate a single pre-mRNA strand in the 5' to 3' direction, thus promoting spliceosome remodeling to its catalytic-competent state. Here, we established the functional coupling between ATPase and helicase activities of Prp2. Namely, extensive multi-μs molecular dynamics simulations allowed us to unlock how, after pre-mRNA selection, ATP binding, hydrolysis, and dissociation induce a functional typewriter-like rotation of the Prp2 C-terminal domain. This movement, endorsed by an iterative swing of interactions established between specific Prp2 residues with the nucleobases at 5'- and 3'-ends of pre-mRNA, promotes pre-mRNA translocation. Notably, some of these Prp2 residues are conserved in the DExH-box family, suggesting that the translocation mechanism elucidated here may be applicable to all DExH-box helicases.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Triphosphatases
  • Adenosine Triphosphate / metabolism
  • DEAD-box RNA Helicases / genetics
  • Molecular Dynamics Simulation
  • RNA Precursors / analysis
  • RNA Precursors / genetics
  • RNA Precursors / metabolism
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae Proteins* / chemistry
  • Spliceosomes* / chemistry
  • Spliceosomes* / genetics
  • Spliceosomes* / metabolism

Substances

  • RNA Precursors
  • Saccharomyces cerevisiae Proteins
  • DEAD-box RNA Helicases
  • Adenosine Triphosphatases
  • Adenosine Triphosphate