Book of Abstracts: Albany 2003

category image Albany 2003
Conversation 13
Abstract Book
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.

Haixiao Gao1*
Jayati Sengupta2
Mikel Valle1
Andrei Korostelev3
Narayanan Eswar4
Scott M. Stagg5
Patrick Van Roey2
Rajendra K. Agrawal2,6
Stephen C. Harvey5
Andrej Sali4
Michael S. Chapman3
Joachim Frank1,2,6

1Howard Hughes Medical Institute
Health Research, Inc.
Empire State Plaza
Albany, NY 12201-0509
Phone: (518) 402 5726
Fax: (518) 486 2191
2Wadsworth Center
New York State Department of Health
Empire State Plaza
Albany, NY 12201-0509
3Kasha Laboratory
Institute of Molecular Biophysics
Department of Chemistry and Biochemistry
Florida State University
Tallahassee, FL 32306-4380
4Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry
California Institute for Quantitative Biomedical Research
University of California, San Francisco
San Francisco, CA 94143-2240
5School of Biology
Georgia Institute of Technology
Atlanta, GA 30332
6Department of Biomedical Sciences
State University of New York at Albany
Albany, NY 12222

References and Footnotes
  1. Frank, J. and Agrawal, R.K. Nature 406, 318-322 (2000).
  2. Chapman, M. S. Acta Cryst. A51, 69-80 (1995).