Comparative analysis of ribosome atomic structures deduced computationally from EM images and X-ray structures

Ishida, Hisashi; Tsutsumi, Yu*; Matsumoto, Atsushi; Yura, Kei

We are developing an EM density-fitting refinement method to improve the modeled 3D structure of supramolecules. Our method first uses rigid body fitting to carry out initial fitting, and then uses a molecular dynamic simulation, in which a target function together with the standard all-atom energy function is used to constrain the atomic structure into the EM map. Here we report the application of this method to the Thermus thermophilus 70S ribosome. In this study we have fit the X-ray crystallographic structure of the ribosome into multiple EM images which show the ribosome in different stages of translation. The refined structures are compared and as a result differences in structures are observed. The differences are thought to indicate the functional movements of the ribosome.