Transfer RNA in the hybrid P/E state: correlating molecular dynamics simulations with cryo-EM data.
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.
Li
Wen
W
Wadsworth Center, Empire State Plaza, Albany, NY 12201-0509, USA.
Frank
Joachim
J
D020285:Cryoelectron Microscopy; D009690:Nucleic Acid Conformation; D012333:RNA, Messenger / Q000737:chemistry; D012338:RNA, Ribosomal, 23S / Q000737:chemistry; D012343:RNA, Transfer / Q000737:chemistry*; D012270:Ribosomes / Q000737:chemistry*
D012333:RNA, Messenger; D012338:RNA, Ribosomal, 23S; D012343:RNA, Transfer