The role of L1 stalk-tRNA interaction in the ribosome elongation cycle.
The ribosomal L1 stalk is a mobile structure implicated in directing tRNA movement during translocation through the ribosome. This article investigates three aspects of L1 stalk-tRNA interaction. First, by combining data from cryo electron microscopy, X-ray crystallography, and molecular dynamics simulations through the molecular dynamics flexible fitting method, we obtained atomic models of different tRNAs occupying the hybrid P/E state interacting with the L1 stalk. These models confirm the assignment of fluorescence resonance energy transfer states from previous single-molecule investigations of L1 stalk dynamics. Second, the models reconcile how initiator tRNA(fMet) interacts less strongly with the L1 stalk compared to elongator tRNA(Phe), as seen in previous single-molecule experiments. Third, results from a simulation of the entire ribosome in which the L1 stalk is moved from a half-closed conformation to its open conformation are found to support the hypothesis that L1 stalk opening is involved in tRNA release from the ribosome.
Trabuco
Leonardo G
LG
Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
Schreiner
Eduard
E
Eargle
John
J
Cornish
Peter
P
Ha
Taekjip
T
Luthey-Schulten
Zaida
Z
Schulten
Klaus
K
D020285:Cryoelectron Microscopy; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D010441:Peptide Chain Elongation, Translational; D014176:Protein Biosynthesis; D012343:RNA, Transfer / Q000737:chemistry / Q000378:metabolism*; D012358:RNA, Transfer, Met; D012360:RNA, Transfer, Phe; D012270:Ribosomes / Q000737:chemistry / Q000378:metabolism*
D012358:RNA, Transfer, Met; D012360:RNA, Transfer, Phe; D012343:RNA, Transfer