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- W4210758411 abstract "Decoding is the key step during protein synthesis that enables information transfer from RNA to protein, a process critical for the survival of all organisms. We have used large-scale (2.64 x 10(6) atoms) all-atom simulations of the entire ribosome to understand a critical step of decoding. Although the decoding problem has been studied for more than four decades, the rate-limiting step of cognate tRNA selection has only recently been identified. This step, known as accommodation, involves the movement inside the ribosome of the aminoacyl-tRNA from the partially bound A/T state to the fully bound A/A state. Here, we show that a corridor of 20 universally conserved ribosomal RNA bases interacts with the tRNA during the accommodation movement. Surprisingly, the tRNA is impeded by the A-loop (23S helix 92), instead of enjoying a smooth transition to the A/A state. In particular, universally conserved 23S ribosomal RNA bases U2492, C2556, and C2573 act as a 3D gate, causing the acceptor stem to pause before allowing entrance into the peptidyl transferase center. Our simulations demonstrate that the flexibility of the acceptor stem of the tRNA, in addition to flexibility of the anticodon arm, is essential for tRNA selection. This study serves as a template for simulating conformational changes in large (>10(6) atoms) biological and artificial molecular machines. PMID: 16249344 Funding information This work was supported by: NIGMS NIH HHS, United States Grant ID: R01-GM072686 NIGMS NIH HHS, United States Grant ID: R01 GM072686" @default.
- W4210758411 created "2022-02-08" @default.
- W4210758411 creator A5073530333 @default.
- W4210758411 date "2005-12-01" @default.
- W4210758411 modified "2023-09-28" @default.
- W4210758411 title "Faculty Opinions recommendation of Simulating movement of tRNA into the ribosome during decoding." @default.
- W4210758411 doi "https://doi.org/10.3410/f.1029401.343725" @default.
- W4210758411 hasPublicationYear "2005" @default.
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