Mg²⁺ Binding Promotes SLV as a Scaffold in Varkud Satellite Ribozyme SLI-SLV Kissing Loop Junction.

ABSTRACT: Though the structure of the substrate stem loop I (SLI)-stem loop V (SLV) kissing loop junction of the Varkud Satellite ribozyme has been experimentally characterized, the dynamics of this Mg²⁺-dependent loop-loop interaction have been elusive. Specifically, each hairpin loop contains a U-turn motif, but only SLV shows a conformational shift triggered by Mg²⁺ ion association. Here, we use molecular dynamics simulations to analyze the binding and dynamics of this kissing loop junction. We show that SLV acts as a scaffold, providing stability to the junction. Mg²⁺ ions associate with SLV when it is part of the junction in a manner similar to when it is unbound, but there is no specificity in Mg²⁺ binding for the SLI loop. This suggests that the ent

SUBMITTER: Bergonzo C 

PROVIDER: S-EPMC5529310 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature