TY - JOUR
T1 - The Role of L1 Stalk-tRNA Interaction in the Ribosome Elongation Cycle
AU - Trabuco, Leonardo G.
AU - Schreiner, Eduard
AU - Eargle, John
AU - Cornish, Peter
AU - Ha, Taekjip
AU - Luthey-Schulten, Zaida
AU - Schulten, K.
PY - 2010/10
Y1 - 2010/10
N2 - 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 tRNAfMet interacts less strongly with the L1 stalk compared to elongator tRNAPhe, 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.
AB - 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 tRNAfMet interacts less strongly with the L1 stalk compared to elongator tRNAPhe, 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.
KW - FRET
KW - Flexible fitting
KW - MDFF
KW - Modified ribonucleosides
KW - Translocation
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U2 - 10.1016/j.jmb.2010.07.056
DO - 10.1016/j.jmb.2010.07.056
M3 - Article
C2 - 20691699
AN - SCOPUS:77956935085
SN - 0022-2836
VL - 402
SP - 741
EP - 760
JO - Journal of molecular biology
JF - Journal of molecular biology
IS - 4
ER -