Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy

Proceedings of the National Academy of Sciences of the United States of America - Tập 100 Số 16 - Trang 9319-9323 - 2003
Florence Tama1, Mikel Valle1, Joachim Frank2,1, Charles L. Brooks1
1Department of Molecular Biology (TPC6), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037; Howard Hughes Medical Institute, Health Research, Inc., Wadsworth Center, Albany, NY 12201-2002; and Department of Biomedical Sciences, State University of New York, Empire State Plaza, Albany, NY 12201-0509
2Department of Biomedical Sciences, State University of New York, Empire State Plaza, Albany, NY 12201-0509

Tóm tắt

Combining structural data for the ribosome from x-ray crystallography and cryo-electron microscopy with dynamic models based on elastic network normal mode analysis, an atomically detailed picture of functionally important structural rearrangements that occur during translocation is elucidated. The dynamic model provides a near-atomic description of the ratchet-like rearrangement of the 70S ribosome seen in cryo-electron microscopy, and permits the identification of bridging interactions that either facilitate the conformational switching or maintain structural integrity of the 50S/30S interface. Motions of the tRNAs residing in the A and P sites also suggest the early stages of tRNA translocation as a result of this ratchet-like movement. Displacement of the L1 stalk, alternately closing and opening the intersubunit space near the E site, is observed in the dynamic model, in line with growing experimental evidence for the role of this structural component in facilitating the exiting of tRNA. Finally, a hinge-like transition in the 30S ribosomal subunit, similar to that observed in crystal structures of this complex, is also manifest as a dynamic mode of the ribosome. The coincidence of these dynamic transitions with the individual normal modes of the ribosome and the good correspondence between these motions and those observed in experiment suggest an underlying principle of nature to exploit the shape of molecular assemblies such as the ribosome to provide robustness to functionally important motions.

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Proceedings of the National Academy of Sciences of the United States of America

Tập 100 Số 16

9319-9323

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