Book of Abstracts: Albany 2003
June 17-21 2003
The Dynamics of the E. coli 70S Ribosome: An Application of Real-Space Refinement
During the elongation cycle of protein synthesis, following the binding of the elongation factor G (EF-G), the small and large subunits of 70S ribosome undergo a relative ratchet-like movement (1). In order to link the large conformational changes to the local molecular rearrangements, a real-space refinement algorithm (2) was utilized for modeling the E. coli 70S ribosome in the initiation-like state and the EF-G·GTP-bound state, which are related by a ratchet-like reorganization of the ribosome. The building of the models exploited multi-resolution structural data of ribosome from x-ray crystallography, homology modeling, and cryo-EM work. In the real-space refinement, atomic structures of RNA and protein obtained from x-ray crystallography and homology modeling were treated as rigid pieces of presumed stability, e.g. helices and domains, and docked into 11-12 Å cryo-EM density maps, while observing stereo-chemical constraints. On the basis of the two atomic models that represent the two states of the ratchet-like movement, our analysis shows that the 70S ribosome undergoes a complicated local reorganization during the inter-subunits ratchet movement, especially in the region of the subunit interfaces. The most extensive molecular rearrangements are seen in the ribosomal proteins, particularly in the functional regions including mRNA entrance and exit channels, polypeptide exit tunnel, and inter-subuit bridges, suggesting an important role of ribosome proteins in facilitating the dynamics of translation.
1Howard Hughes Medical Institute