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  Energy barriers and driving forces in tRNA translocation through the ribosome.

Bock, L. V., Blau, C., Schröder, G. F., Davydov, I. I., Fischer, N., Stark, H., et al. (2013). Energy barriers and driving forces in tRNA translocation through the ribosome. Nature Structural and Molecular Biology, 20(12), 1390-1396. doi:10.1038/nsmb.2690.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-A575-8 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0027-CDB0-0
Genre: Journal Article

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 Creators:
Bock, L. V.1, Author              
Blau, C.1, Author              
Schröder, G. F., Author
Davydov, I. I., Author
Fischer, N.2, Author              
Stark, H.2, Author              
Rodnina, M. V.3, Author              
Vaiana, A. C.1, Author              
Grubmüller, H.1, Author              
Affiliations:
1Department of Theoretical and Computational Biophysics, MPI for biophysical chemistry, Max Planck Society, ou_578631              
2Research Group of 3D Electron Cryo-Microscopy, MPI for biophysical chemistry, Max Planck Society, ou_578577              
3Department of Physical Biochemistry, MPI for biophysical chemistry, Max Planck Society, ou_578598              

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 Abstract: During protein synthesis, tRNAs move from the ribosome's aminoacyl to peptidyl to exit sites. Here we investigate conformational motions during spontaneous translocation, using molecular dynamics simulations of 13 intermediate-translocation-state models obtained by combining Escherichia coli ribosome crystal structures with cryo-EM data. Resolving fast transitions between states, we find that tRNA motions govern the transition rates within the pre- and post-translocation states. Intersubunit rotations and L1-stalk motion exhibit fast intrinsic submicrosecond dynamics. The L1 stalk drives the tRNA from the peptidyl site and links intersubunit rotation to translocation. Displacement of tRNAs is controlled by 'sliding' and 'stepping' mechanisms involving conserved L16, L5 and L1 residues, thus ensuring binding to the ribosome despite large-scale tRNA movement. Our results complement structural data with a time axis, intrinsic transition rates and molecular forces, revealing correlated functional motions inaccessible by other means.

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Language(s): eng - English
 Dates: 2013-11-032013-12
 Publication Status: Published in print
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 Rev. Method: Peer
 Identifiers: DOI: 10.1038/nsmb.2690
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Title: Nature Structural and Molecular Biology
Source Genre: Journal
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Pages: - Volume / Issue: 20 (12) Sequence Number: - Start / End Page: 1390 - 1396 Identifier: -