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Binding of SARS-CoV-2 non-structured protein 1 to 40S ribosome inhibits mRNA translation

View ORCID ProfileHung Nguyen, View ORCID ProfileHoang Linh Nguyen, Mai Suan Li
doi: https://doi.org/10.1101/2023.02.24.529933
Hung Nguyen
1Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668, Warsaw, Poland
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  • ORCID record for Hung Nguyen
Hoang Linh Nguyen
3Institute of Fundamental and Applied Sciences, Duy Tan University, Ho Chi Minh City 700000, Vietnam
4Faculty of Natural Sciences, Duy Tan University, Danang City 550000, Vietnam
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Mai Suan Li
1Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668, Warsaw, Poland
2Life Science Lab, Institute for Computational Science and Technology, QuangTrung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 729110, Vietnam
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  • For correspondence: masli@ifpan.edu.pl
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Abstract

Experiments have shown that non-structural protein 1 (NSP1) of SARS-CoV-2 is a factor that restricts cellular gene expression and prevents mRNA translation in the ribosome 40S subunit. However, the molecular mechanism of this phenomenon remains unclear. To clarify this issue, all-atom steered molecular dynamics and coarse-grained alchemical simulations were used to compare the binding affinity of mRNA to 40S ribosome in the absence and presence of NSP1. We found that NSP1 binding to the 40S ribosome dramatically increases the binding affinity of mRNA, which, in agreement with experiment, suggests that NSP1 can stall mRNA translation. The mRNA translation has been found to be driven by electrostatic mRNA-40S ribosome interactions. Water molecules have been demonstrated to play an important role in stabilizing the mRNA-40S ribosome complex. The NSP1 residues that are critical in triggering a translation arrest have been identified.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted February 27, 2023.
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Binding of SARS-CoV-2 non-structured protein 1 to 40S ribosome inhibits mRNA translation
Hung Nguyen, Hoang Linh Nguyen, Mai Suan Li
bioRxiv 2023.02.24.529933; doi: https://doi.org/10.1101/2023.02.24.529933
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Binding of SARS-CoV-2 non-structured protein 1 to 40S ribosome inhibits mRNA translation
Hung Nguyen, Hoang Linh Nguyen, Mai Suan Li
bioRxiv 2023.02.24.529933; doi: https://doi.org/10.1101/2023.02.24.529933

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