Analysis of Structural Dynamics in the Ribosome by TLS Crystallographic Refinement

A major goal in the study of ribosome structure and function is to obtain a complete description of the conformational dynamics of the ribosome during the many steps of protein synthesis. Here, we report a new approach to the study of ribosome dynamics using translation-libration-screw (TLS) refinement against experimental X-ray diffraction data. TLS analysis of complexes of the 70 S ribosome suggests that many of its structural features have an inherent tendency for anisotropic movement. Analysis of displacements of the 30 S and 50 S ribosomal subunits reveals an intrinsic bias for “ratchet-like” intersubunit rotation. The libration axes for both subunits pass through the peptidyl transferase center (PTC), indicating a tendency for structural rotations to occur around the site of peptide bond formation. The modes of anisotropic movement of ribosomal RNA components, including the head of the 30 S subunit, the L1 and L11 stalks and the two main arms of the tRNAs were found to correlate with their respective modes of movement previously inferred from comparisons of ribosomes trapped in different functional states. In the small subunit, the mobilities of features interacting with the Shine–Dalgarno helix are decreased in the presence of the Shine–Dalgarno helix, supporting the proposal that that formation of the Shine–Dalgarno helix during initiation may contribute to stabilization of the small subunit for optimal interaction with initiator tRNAfMet. The similarity of TLS parameters for two independently solved structures of similar ribosome complexes suggests that TLS analysis can provide useful information about the dynamics of very large macromolecular objects and at resolutions lower than those at which TLS refinement has commonly been applied.