Binding interactions between the core central domain of 16S rRNA and the ribosomal protein S15 determined by molecular dynamics simulations.

ABSTRACT: The goal of the current study is to utilize molecular dynamic (MD) simulations to investigate the dynamic behavior of 16S rRNA in the presence and absence of S15 and to identify the binding interactions between these two molecules. The simulations show that: (i) 16S rRNA remains in a highly folded structure when it is bound to S15; (ii) in the absence of S15, 16S rRNA significantly alters its conformation and transiently forms conformations that are similar to the bound structure that make it available for binding with S15; (iii) the unbound rRNA spends the majority of its time in extended conformations. The formation of the extended conformations is a result of the molecule reaching a lower electrostatic energy and the formation of the highly folded, crystal-like conformation is a result

SUBMITTER: Li W 

PROVIDER: S-EPMC140513 | biostudies-literature | 2003 Jan

REPOSITORIES: biostudies-literature