Extended ensemble simulations of a SARS-CoV-2 nsp1–5’-UTR complex

  1. Shun Sakuraba
  2. Qilin Xie
  3. Kota Kasahara
  4. Junichi Iwakiri
  5. Hidetoshi Kono

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Abstract

Nonstructural protein 1 (nsp1) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a 180-residue protein that blocks translation of host mRNAs in SARS-CoV-2-infected cells. Although it is known that SARS-CoV-2’s own RNA evades nsp1’s host translation shutoff, the molecular mechanism underlying the evasion was poorly understood. We performed an extended ensemble molecular dynamics simulation to investigate the mechanism of the viral RNA evasion. Simulation results suggested that the stem loop structure of the SARS-CoV-2 RNA 5’-untranslated region (SL1) binds to both nsp1’s N-terminal globular region and intrinsically disordered region. The consistency of the results was assessed by modeling nsp1-40 S ribosome structure based on reported nsp1 experiments, including the X-ray crystallographic structure analysis, the cryo-EM electron density map, and cross-linking experiments. The SL1 binding region predicted from the simulation was open to the solvent, yet the ribosome could interact with SL1. Cluster analysis of the binding mode and detailed analysis of the binding poses suggest residues Arg124, Lys47, Arg43, and Asn126 may be involved in the SL1 recognition mechanism, consistent with the existing mutational analysis.

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  1. Version published to 10.1371/journal.pcbi.1009804
  2. Version published to 10.1101/2021.02.24.432807v2 on bioRxiv
  3. ScreenIT

    SciScore for 10.1101/2021.02.24.432807: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Modeling was performed by MODELLER.
    MODELLER
    suggested: (MODELLER, RRID:SCR_008395)
    Visualization was performed with VMD 42 and pymol.
    pymol
    suggested: (PyMOL, RRID:SCR_000305)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    Limitations of this study: Our simulation was performed based on several assumptions. Here, we list the limitations of the current study. First of all, our simulation was performed without the ribosome. This was mainly because the simulation started before the nsp1-ribosome complex structure was deposited. Furthermore, at the time of submitting this manuscript, the orientation of the nsp1 N-terminal domain attached to the 40S ribosome is still ambiguous in density maps. With the 40S ribosome, the environment around nsp1 may be altered, hence the interaction between the RNA and nsp1. Specifically, ribosome mostly consists of ribosomal RNAs and are thus strongly negatively charged, which may change the interaction environment significantly. We performed the simulation with restraints to G-C pairs in 5’-UTR to maintain the stability of the hairpin loop structure. The restraints may have hindered RNA forming other structures than the initial hairpin structure. However, in the secondary structure prediction using CentroidFold, 51 these base pairs were predicted to exist in more than 92 % of the ensemble. Furthermore, a recent study52 showed that, even with a rigorous extended ensemble simulation, the hairpin structure remained intact. From these results, the drawback of structural restraints to SL1 is expected to be minimal. Finally, as is always the case with the simulation study, the mismatch between the simulation force field and the real world leaves a non-negligible gap. In a...

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    About SciScore

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  4. Version published to 10.1101/2021.02.24.432807v1 on bioRxiv