The N-glycosylation sites and Glycan-binding ability of S-protein in SARS-CoV-2 Coronavirus

  1. Wentian Chen
  2. Ziye Hui
  3. Xiameng Ren
  4. Yijie Luo
  5. Jian Shu
  6. Hanjie Yu
  7. Zheng Li

Reviewed by

Read the full article

Listed in

Log in to save this article

Abstract

The emerging acute respiratory disease, COVID-19, caused by SARS-CoV-2 Coronavirus (SARS2 CoV) has spread fastly all over the word. As a member of RNA viruses, the glycosylation of envelope glycoprotein plays the crucial role in protein folding, evasing host immune system, invading host cell membrane, even affecting host preference. Therefore, detail glyco-related researches have been adopted in the Spike protein (S-protein) of SARS2 CoV from the bioinformatic perspective. Phylogenic analysis of S-protein sequences revealed the evolutionary relationship of N-glycosylation sites in different CoVs. Structural comparation of S-proteins indicated their similarity and distributions of N-glycosylation sites. Further potential sialic acid or galactose affinity domains have been described in the S-protein by docking analysis. Molecular dynamic simulation for the glycosylated complexus of S-protein-ACE2 implied that the complicate viral binding of receptor-binding domain may be influenced by peripheric N-glycans from own and adjacent monoers. These works will contribute to investigate the N-glycosylation in S-protein and explain the highly contagious of COVID-19.

Article activity feed

  1. ScreenIT

    SciScore for 10.1101/2020.12.01.406025: (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
    An alignment of whole sequences was performed by ClustalW 2.0 in MEGA 7.0 (File S1)[16].
    ClustalW
    suggested: (ClustalW, RRID:SCR_017277)
    MEGA
    suggested: (Mega BLAST, RRID:SCR_011920)
    Minimization and equilibration were performed using the NAMD 2.8 program with the CHARMM22 all-atom force field for the protein as previous describing[22].
    NAMD
    suggested: (NAMD, RRID:SCR_014894)
    The automated docking analysis between S-protein and glyco-ligands was performed using the AutoDock Vina program.
    AutoDock Vina
    suggested: (AutoDock Vina, RRID:SCR_011958)

    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: Please consider improving the rainbow (“jet”) colormap(s) used on pages 17, 19 and 20. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

    Results from rtransparent:
    • No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
    • 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.

  2. Version published to 10.1101/2020.12.01.406025v1 on bioRxiv