Molecular Dynamics Reveals the Effects of Temperature on Critical SARS-CoV-2 Proteins

  1. Paul Morgan
  2. Chih-Wen Shu

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Abstract

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a newly identified RNA virus that causes the serious infection Coronavirus Disease 2019 (COVID-19). The incidence of COVID-19 is still increasing worldwide despite the summer heat and cool winter. However, little is known about seasonal stability of SARS-CoV-2. Herein, we employ Molecular Dynamics (MD) simulations to explore the effect of temperature on four critical SARS-CoV-2 proteins. Our work demonstrates that the spike Receptor Binding Domain (RBD), Main protease (Mpro), and nonstructural protein 3 (macro X) possesses extreme thermos-stability when subjected to temperature variations rendering them attractive drug targets. Furthermore, our findings suggest that these four proteins are well adapted to habitable temperatures on earth and are largely insensitive to cold and warm climates. Furthermore, we report that the critical residues in SARS-CoV-2 RBD were less responsive to temperature variations as compared to the critical residues in SARS-CoV. As such, extreme summer and winter climates, and the transition between the two seasons, are expected to have a negligible effect on the stability of SARS-CoV-2 which will marginally suppress transmission rates until effective therapeutics are available world-wide.

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    SciScore for 10.1101/2021.01.24.427990: (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
    Data analysis and correlation plots were generated using SPSS, Prism 5 and Python.
    SPSS
    suggested: (SPSS, RRID:SCR_002865)
    Python
    suggested: (IPython, RRID:SCR_001658)

    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:
    Nevertheless, there are practical limitations that must be considered as well. We have only computationally evaluated the thermo-stability of four critical SARS-CoV-2 proteins in response to temperature changes within an aqueous environment. However, this is not a comprehensive assessment of the plentiful proteins and conditions that exist as SARS-CoV-2 lingers within our communities. For instance, how is the stability of the RBD affected by surfaces such as cloth, wood and metal?13 Furthermore, it is not a trivial task to attempt simulating changes in humidity using MD simulations, despite its intimate relationship with temperature. Also, our MD simulations did not take into account the complex N-linked glycan at reside N-343 found on the core RBD.14 The shielding of receptor binding sites by glycans is a common feature of viral glycoproteins, which is consistent with that observed in SARS-CoV.14 Last, we have only considered the RBD, Mpro, macro X, and the nucleocapsid, which is but a small fraction of the entire pathogen. MD simulations are also currently incapable of simulating the homeostatic responses of the internal viral proteins and their complex interactions when subjected to extreme environmental parameters like changes in pH, pressure, and humidity along with temperature variations. Finally, the coronavirus machinery is intriguingly complex and may have other stabilizing mechanisms and protein-protein interactions to cope with environmental stresses that is brough...

    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.

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  2. Version published to 10.1101/2021.01.24.427990v2 on bioRxiv
  3. Version published to 10.1101/2021.01.24.427990v1 on bioRxiv