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- Title
Energy barriers and driving forces in tRNA translocation through the ribosome.
- Authors
Bock, Lars V; Blau, Christian; Schröder, Gunnar F; Davydov, Iakov I; Fischer, Niels; Stark, Holger; Rodnina, Marina V; Vaiana, Andrea C; Grubmüller, Helmut
- 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.
- Subjects
CHROMOSOMAL translocation; TRANSFER RNA; RIBOSOMES; PROTEIN synthesis; BACTERIAL genetics; ESCHERICHIA coli
- Publication
Nature Structural & Molecular Biology, 2013, Vol 20, Issue 12, p1390
- ISSN
1545-9993
- Publication type
Article
- DOI
10.1038/nsmb.2690