Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation.

ABSTRACT: Molecular dynamics simulations have been performed to investigate the role of Mg2+ in the full-length hammerhead ribozyme cleavage reaction. In particular, the aim of this work is to characterize the binding mode and conformational events that give rise to catalytically active conformations and stabilization of the transition state. Toward this end, a series of eight 12 ns molecular dynamics simulations have been performed with different divalent metal binding occupations for the reactant, early and late transition state using recently developed force field parameters for metal ions and reactive intermediates in RNA catalysis. In addition, hybrid QM/MM calculations of the early and late transition state were performed to study the proton-transfer step in general acid catalysis that is faci

SUBMITTER: Lee TS 

PROVIDER: S-EPMC2535817 | biostudies-literature | 2008 Mar

REPOSITORIES: biostudies-literature