Molecular simulations of the pistol ribozyme: unifying the interpretation of experimental data and establishing functional links with the hammerhead ribozyme.

ABSTRACT: The pistol ribozyme (Psr) is among the most recently discovered RNA enzymes and has been the subject of experiments aimed at elucidating the mechanism. Recent biochemical studies have revealed exciting clues about catalytic interactions in the active site not apparent from available crystallographic data. The present work unifies the interpretation of the existing body of structural and functional data on Psr by providing a dynamical model for the catalytically active state in solution from molecular simulation. Our results suggest that a catalytic Mg²⁺ ion makes inner-sphere contact with G33:N7 and outer-sphere coordination to the pro-R_P of the scissile phosphate, promoting electrostatic stabilization of the dianionic transition state and neutralization of the

SUBMITTER: Kostenbader K 

PROVIDER: S-EPMC6795133 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature