Modelling ion binding to AA platform motifs in RNA: a continuum solvent study including conformational adaptation.

ABSTRACT: Binding of monovalent and divalent cations to two adenine-adenine platform structures from the Tetrahymena group I intron ribozyme has been studied using continuum solvent models based on the generalised Born and the finite-difference Poisson-Boltzmann approaches. The adenine-adenine platform RNA motif forms an experimentally characterised monovalent ion binding site important for ribozyme folding and function. Qualitative agreement between calculated and experimental ion placements and binding selectivity was obtained. The inclusion of solvation effects turned out to be important to obtain low energy structures and ion binding placements in agreement with the experiment. The calculations indicate that differences in solvation of the isolated ions contribute to the calculated ion binding p

SUBMITTER: Burkhardt C 

PROVIDER: S-EPMC60250 | biostudies-literature | 2001 Oct

REPOSITORIES: biostudies-literature