Cations and hydration in catalytic RNA: molecular dynamics of the hepatitis delta virus ribozyme.

ABSTRACT: The hepatitis delta virus (HDV) ribozyme is an RNA enzyme from the human pathogenic HDV. Cations play a crucial role in self-cleavage of the HDV ribozyme, by promoting both folding and chemistry. Experimental studies have revealed limited but intriguing details on the location and structural and catalytic functions of metal ions. Here, we analyze a total of approximately 200 ns of explicit-solvent molecular dynamics simulations to provide a complementary atomistic view of the binding of monovalent and divalent cations as well as water molecules to reaction precursor and product forms of the HDV ribozyme. Our simulations find that an Mg2+ cation binds stably, by both inner- and outer-sphere contacts, to the electronegative catalytic pocket of the reaction precursor, in a position to potenti

SUBMITTER: Krasovska MV 

PROVIDER: S-EPMC1483112 | biostudies-literature | 2006 Jul

REPOSITORIES: biostudies-literature