Unveiling mutation effects on the structural dynamics of the main protease from SARS-CoV-2 with hybrid simulation methods

  1. P. Gasparini
  2. E.A. Philot
  3. S.Q. Pantaleão
  4. N.E.S.M. Torres-Bonfim
  5. A. Kliousoff
  6. R.C.N. Quiroz
  7. D. Perahia
  8. R.P. Simões
  9. A.J. Magro
  10. A.L. Scott

Reviewed by

Read the full article

Listed in

Log in to save this article

Abstract

No abstract available

Article activity feed

  1. Version published to 10.1016/j.jmgm.2023.108443
  2. Version published to 10.1101/2021.07.17.452787v2 on bioRxiv
  3. ScreenIT

    SciScore for 10.1101/2021.07.17.452787: (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
    The characterization of the protein structural dynamics was done with the following analyses: a) flexibility with the Root Mean Square Fluctuation (RMSF); b) analysis of collective modes of wild-type and mutants (correspondence/correlation calculation); c) conformational sampling using hybrid methods; d) distance analysis between the two residues of the catalytic dyad; e) SASA analysis for different regions; f) analysis of the frequency of occurrence of mutants in the patient data deposited in the GISAID database. 2.1.
    GISAID
    suggested: (GISAID, RRID:SCR_018279)
    Wild-type and apo crystal SARS-CoV-2 Mpro structures with 1.91 Å resolution (PDB ID: 7C2Y [DOI: 10.2210/pdb7C2Y/pdb]) were used to generate 48 mutants with single point mutations [17]using PyMOL software [The PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC].
    PyMOL
    suggested: (PyMOL, RRID:SCR_000305)
    The normal modes were calculated using the DIMB (Iterative Mixed-Basis Diagonalization) module [24] implemented in CHARMM software [25, 26] considering all the atoms of the protein and a force field corresponding to the CHARMM36m [27].
    CHARMM
    suggested: (CHARMM, RRID:SCR_014892)
    The Heatmap, Violin and Boxplot representations were generated in Python using the Pandas [34, 35], NumPy [36], Matplotlib [37] and Seaborn [38] libraries.
    Python
    suggested: (IPython, RRID:SCR_001658)
    NumPy
    suggested: (NumPy, RRID:SCR_008633)
    Matplotlib
    suggested: (MatPlotLib, RRID:SCR_008624)
    Using the PISA web server, we calculate the solvation free energy gain upon formation of the interface, interface area and number of potential hydrogen bonds and salt bridge [39].
    PISA
    suggested: (PISA, RRID:SCR_015749)

    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.
    • No funding statement was detected.
    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.

    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 10.1101/2021.07.17.452787v1 on bioRxiv