Open AccessTransfer RNA in the hybrid P/E state: Correlating molecular dynamics simulations with cryo-EM data
Author(s) -
Wen Li,
Joachim Frank
Publication year - 2007
Publication title -
proceedings of the national academy of sciences of the united states of america
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.011
H-Index - 771
eISSN - 1091-6490
pISSN - 0027-8424
DOI - 10.1073/pnas.0708094104
Subject(s) - transfer rna , ribosome , molecular dynamics , rna , ribosomal rna , t arm , 23s ribosomal rna , helix (gastropod) , translation (biology) , ef tu , biology , biophysics , physics , chemistry , messenger rna , biochemistry , gene , computational chemistry , ecology , snail
Transfer RNA (tRNA) transiently occupies the hybrid P/E state (P/E-tRNA) when mRNA–tRNA are translocated in the ribosome. In this study, we characterize the structure of P/E-tRNA and its interactions with the ribosome by correlating the results from molecular dynamics simulations on free tRNA with the cryo-EM map of P/E-tRNA. In our approach, we show that the cryo-EM map may be interpreted as a conformational average. Along the molecular dynamics trajectories (44 ns, 18 ns, and 18 ns), some of the snapshots prove to be quite close to the observed density. In a representative structure, the CCA (3′) arm is uniquely twisted, and the anticodon stem loop is kinked at the junctions to both the anticodon loop and the D stem. In addition, the map shows that the P/E-tRNA is no longer bound to helix H69 of 23S rRNA and is flexible, and the conformations of helices H68 and h44 of 16S rRNA differ from those in the x-ray structure. Thus, our study presents structural and dynamic information on the P/E-tRNA and characterizes its interactions with the translocating ribosome.