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Steric interactions lead to collective tilting motion in the ribosome during mRNA–tRNA translocation

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  • Kien Nguyen

    (Northeastern University, Dana Research Center 111)

  • Paul C. Whitford

    (Northeastern University, Dana Research Center 111)

Abstract

Translocation of mRNA and tRNA through the ribosome is associated with large-scale rearrangements of the head domain in the 30S ribosomal subunit. To elucidate the relationship between 30S head dynamics and mRNA–tRNA displacement, we apply molecular dynamics simulations using an all-atom structure-based model. Here we provide a statistical analysis of 250 spontaneous transitions between the A/P–P/E and P/P–E/E ensembles. Consistent with structural studies, the ribosome samples a chimeric ap/P–pe/E intermediate, where the 30S head is rotated ∼18°. It then transiently populates a previously unreported intermediate ensemble, which is characterized by a ∼10° tilt of the head. To identify the origins of head tilting, we analyse 781 additional simulations in which specific steric features are perturbed. These calculations show that head tilting may be attributed to specific steric interactions between tRNA and the 30S subunit (PE loop and protein S13). Taken together, this study demonstrates how molecular structure can give rise to large-scale collective rearrangements.

Suggested Citation

  • Kien Nguyen & Paul C. Whitford, 2016. "Steric interactions lead to collective tilting motion in the ribosome during mRNA–tRNA translocation," Nature Communications, Nature, vol. 7(1), pages 1-9, April.
    • Handle: RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms10586
    DOI: 10.1038/ncomms10586
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    Cited by:

    1. Ju Zhou & Anhui Wang & Yinlong Song & Nan Liu & Jia Wang & Yan Li & Xin Liang & Guohui Li & Huiying Chu & Hong-Wei Wang, 2023. "Structural insights into the mechanism of GTP initiation of microtubule assembly," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    2. Vivek Singh & Yuzuru Itoh & Samuel Del’Olio & Asem Hassan & Andreas Naschberger & Rasmus Kock Flygaard & Yuko Nobe & Keiichi Izumikawa & Shintaro Aibara & Juni Andréll & Paul C. Whitford & Antoni Barr, 2024. "Mitoribosome structure with cofactors and modifications reveals mechanism of ligand binding and interactions with L1 stalk," Nature Communications, Nature, vol. 15(1), pages 1-22, December.

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