Journal
JOURNAL OF MOLECULAR BIOLOGY
Volume 402, Issue 4, Pages 741-760Publisher
ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD
DOI: 10.1016/j.jmb.2010.07.056
Keywords
translocation; modified ribonucleosides; flexible fitting; MDFF; FRET
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Funding
- National Institutes of Health [P41-RR005969]
- National Science Foundation [PHY0822613, MCB0844670]
- Humboldt Foundation
- Div Of Molecular and Cellular Bioscience
- Direct For Biological Sciences [0844670] Funding Source: National Science Foundation
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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. (C) 2010 Elsevier Ltd. All rights reserved.
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