title: The role of L1 stalk-tRNA interaction in the ribosome elongation cycle.
abstract: 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.
authors.affiliation: Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
authors.forename: Leonardo G
authors.initials: LG
authors.lastname: Trabuco
authors.forename: Eduard
authors.initials: E
authors.lastname: Schreiner
authors.forename: John
authors.initials: J
authors.lastname: Eargle
authors.forename: Peter
authors.initials: P
authors.lastname: Cornish
authors.forename: Taekjip
authors.initials: T
authors.lastname: Ha
authors.forename: Zaida
authors.initials: Z
authors.lastname: Luthey-Schulten
authors.forename: Klaus
authors.initials: K
authors.lastname: Schulten
mesh_terms: 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*
chemical_list: D012358:RNA, Transfer, Met; D012360:RNA, Transfer, Phe; D012343:RNA, Transfer