期刊
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
卷 102, 期 44, 页码 15854-15859出版社
NATL ACAD SCIENCES
DOI: 10.1073/pnas.0503456102
关键词
proofreading; protein synthesis; molecular dynamics simulations; RNA; high-performance computing
资金
- NIGMS NIH HHS [R01-GM072686, R01 GM072686] Funding Source: Medline
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/A 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 (235 helix 92), instead of enjoying a smooth transition to the A/A state. In particular, universally conserved 235 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.
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