Structural implications of SARS-CoV-2 Surface Glycoprotein N501Y mutation within receptor-binding domain [499-505] – computational analysis of the most frequent Asn501 polar uncharged amino acid mutations

Abstract

The aim of this study was to evaluate the impact of the most frequent Asn501 polar uncharged amino acid mutations upon important structural properties of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) Surface Glycoprotein RBD – hACE2 (human angiotensin-converting enzyme 2) heterodimer. Mutations N501Y, N501T and N501S were considered and their impact upon complex solubility, secondary motifs formation and intermolecular hydrogen bonding interface was analyzed. Results and findings are reported based on 50 ns run in Gromacs molecular dynamics simulation software. Special attention is paid on the biomechanical shifts in the receptor-binding domain (RBD) [499-505]: ProThrAsn(Tyr)GlyValGlyTyr, having substituted Asparagine to Tyrosine at position 501. The main findings indicate that the N501S mutation increases SARS-CoV-2 S-protein RBD – hACE2 solubility over N501T, N501 (wild type): ${\mathrm{SASA}}_{\mathrm{N}501\mathrm{S}}=364.66\pm 3.2842\mathrm{ }{\mathrm{nm}}^2$, ${\mathrm{SASA}}_{\mathrm{N}501\mathrm{T}}=360\pm 3.4156\mathrm{ }{\mathrm{nm}}^2,\mathrm{ }{\mathrm{SASA}}_{\mathrm{N}501}=359.56\pm 3.6473\mathrm{ }{\mathrm{nm}}^2$. The N501Y mutation shifts $\alpha$-helix S-protein RBD [366-370]: SerValLeuTyrAsn into π-helix for t > 38.5 ns. An S-protein RBD [503-505]: ValGlyTyr shift from $3_{10}$-helix into a turn is observed due to the N501Y mutation in t > 33 ns. An empirical proof for the presence of a Y501-binding pocket, based on RBD [499-505]: PTYGVGY ${\mathrm{C}}_{\mathrm{\alpha }}$’s RMSF peak formation is presented. There is enhanced electrostatic interaction between Tyr505 (RBD) phenolic -OH group and Glu37 (hACE2) side chain oxygen atoms due to the N501Y mutation. The N501Y mutation shifts the ${\mathrm{Gly}502}_{\mathrm{S}\text{-}\mathrm{Protein}}\mathrm{N}\text{-}\mathrm{H}\dots \mathrm{O}=\mathrm{C}{\mathrm{Lys}353}_{\mathrm{hACE}2}$ hydrogen bond into permanent polar contact; ${{\mathrm{E}(\mathrm{Gly}502}_{\mathrm{S}\text{-}\mathrm{Protein}}\mathrm{N}\text{-}\mathrm{H}\dots \mathrm{O}=\mathrm{C}{\mathrm{Lys}353}_{\mathrm{hACE}2})}_{\mathrm{N}501\mathrm{Y}}=4.816210332\mathrm{kcal}/\mathrm{mol}$; ${{\mathrm{E}(\mathrm{Gly}502}_{\mathrm{S}\text{-}\mathrm{Protein}}\mathrm{N}\text{-}\mathrm{H}\dots \mathrm{O}=\mathrm{C}{\mathrm{Lys}353}_{\mathrm{hACE}2})}_{\mathrm{N}501}=3.909532232\mathrm{kcal}/\mathrm{mol}$.

Keywords:

• SARS-CoV-2
• N501Y
• mutation
• COVID-19
• surface glycoprotein
• hydrogen bonds

Author contributions

Done Stojanov: conceptualization, methodology, simulation, validation, investigation, writing—original draft preparation and revision, visualization.

Data availability

The data that support the findings reported in this paper are available in the Appendix files: RMSD_analysis.xlsx; RMSF_analysis.xlsx; SASA_analysis.xlsx; H_bonds_analysis.xlsx; Gly502_Lys353_H-bond_Energy.xlsx

Disclosure statement

The author declares that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Additional information

Funding

The author(s) reported there is no funding associated with the work featured in this article.