The conformational landscape of the ribosomal protein S15 and its influence on the protein interaction with 16S RNA.

ABSTRACT: The interaction between the ribosomal protein S15 and its binding sites in the 16S RNA was examined from two points of view. First, the isolated protein S15 was studied by comparing NMR conformer sets, available in the PDB and recalculated using the CNS-ARIA protocol. Molecular dynamics (MD) trajectories were then recorded starting from a conformer of each set. The recalculation of the S15 NMR structure, as well as the recording of MD trajectories, reveals that several orientations of the N-terminal alpha-helix alpha1 with respect to the structure core are populated. MD trajectories of the complex between the ribosomal protein S15 and RNA were also recorded in the presence and absence of Mg(2+) ions. The Mg(2+) ions are hexacoordinated by water and RNA oxygens. The coordination spheres mai

SUBMITTER: Crety T 

PROVIDER: S-EPMC1831693 | biostudies-literature | 2007 Apr

REPOSITORIES: biostudies-literature