title: Energy barriers and driving forces in tRNA translocation through the ribosome.
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.
authors.affiliation: 1] Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany. [2].
authors.forename: Lars V
authors.initials: LV
authors.lastname: Bock
authors.forename: Christian
authors.initials: C
authors.lastname: Blau
authors.forename: Gunnar F
authors.initials: GF
authors.lastname: Schröder
authors.forename: Iakov I
authors.initials: II
authors.lastname: Davydov
authors.forename: Niels
authors.initials: N
authors.lastname: Fischer
authors.forename: Holger
authors.initials: H
authors.lastname: Stark
authors.forename: Marina V
authors.initials: MV
authors.lastname: Rodnina
authors.forename: Andrea C
authors.initials: AC
authors.lastname: Vaiana
authors.forename: Helmut
authors.initials: H
authors.lastname: Grubmüller
mesh_terms: D001692:Biological Transport; D020285:Cryoelectron Microscopy; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000235:genetics; D007700:Kinetics; D009690:Nucleic Acid Conformation; D014176:Protein Biosynthesis; D012343:RNA, Transfer / Q000737:chemistry / Q000378:metabolism* / Q000502:physiology; D012270:Ribosomes / Q000378:metabolism* / Q000502:physiology
chemical_list: D012343:RNA, Transfer