The Mechanism of SARS-CoV-2 Nucleocapsid Protein Recognition by the Human 14-3-3 Proteins

  1. Kristina V. Tugaeva
  2. Dorothy E.D.P. Hawkins
  3. Jake L.R. Smith
  4. Oliver W. Bayfield
  5. De-Sheng Ker
  6. Andrey A. Sysoev
  7. Oleg I. Klychnikov
  8. Alfred A. Antson
  9. Nikolai N. Sluchanko

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Abstract

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  1. Version published to 10.1016/j.jmb.2021.166875
  2. Version published to 10.1101/2020.12.26.424450v2 on bioRxiv
  3. ScreenIT

    SciScore for 10.1101/2020.12.26.424450: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Protein expression and purification: The tagless SARS-CoV-2 N gene coding for Uniprot ID P0DTC9 protein sequence was commercially synthesized (GeneWiz) and cloned into pET-SUMO bacterial expression vectors using NdeI and HindIII restriction endonuclease sites.
    GeneWiz
    suggested: (GENEWIZ, RRID:SCR_003177)
    Protein concentration was determined by spectrophotometry at 280 nm on a N80 Nanophotometer (Implen, Munich, Germany) using sequence-specific extinction coefficients calculated using the ProtParam tool in ExPASy (see Supplementary table 5).
    ProtParam
    suggested: (ProtParam Tool, RRID:SCR_018087)
    ExPASy
    suggested: None
    Graphing and fitting were performed in Origin 9.0 (OriginLab Corporation, Northampton, MA, USA)
    OriginLab Corporation
    suggested: (Origin, RRID:SCR_014212)
    All processing was performed in ASTRA 8.0 software (Wyatt Technologies) taking dn/dc equal to 0.185 and using extinction coefficients listed in Supplementary table 5.
    ASTRA
    suggested: (ASTRA, RRID:SCR_016255)

    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: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    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

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  4. Version published to 10.1101/2020.12.26.424450v1 on bioRxiv