Receptor Binding Domain (RBD) Structural Susceptibility in the SARS-CoV-2 Virus Spike Protein Exposed to a Pulsed Electric Field
Open Access
- 10 February 2021
- journal article
- Published by Chitkara University Publications in Journal of Nuclear Physics, Material Sciences, Radiation and Applications
- Vol. 8 (2), 177-182
- https://doi.org/10.15415/jnp.2021.82023
Abstract
SARS-CoV-2 is responsible for causing the Coronavirus disease 2019 (COVID-19) pandemic, which has so far infected more than thirty million people and caused almost a million deaths. For this reason, it has been a priority to stop the transmission of the outbreak through preventive measures, such as surface disinfection, and to establish bases for the design of an effective disinfection technique without chemical components. In this study, we performed in silico analysis to identify the conformational alterations of the SARS-CoV-2 Spike Receptor Binding Domain (RBD) caused by the effect of a pulsed electric field at two different intensities. We found that both stimuli, especially the one with the highest angular frequency and amplitude, modified the electrical charge distribution in the RBD surface and the number of hydrogen bonds. Moreover, the secondary structure was significantly affected, with a decrease of the structured regions, particularly the regions with residues involved in recognizing and interacting with the receptor ACE2. Since many regions suffered conformational changes, we calculated RMSF and ΔRMSF to identify the regions and residues with larger fluctuations and higher flexibility. We found that regions conformed by 353-372, 453-464, and 470-490 amino acid residues fluctuate the most, where the first is considered a therapeutic target, and the last has alreadybeen characterized for its flexibility. Our results indicate that a pulsed electric field can cause loss of stability in the Spike-RBD, and we were able to identify the vulnerable sites to be used as a starting point for the development of viral inhibition or inactivation mechanisms.Keywords
This publication has 16 references indexed in Scilit:
- Receptor Recognition by the Novel Coronavirus from Wuhan: an Analysis Based on Decade-Long Structural Studies of SARS CoronavirusJournal of Virology, 2020
- Electric-field-stimulated protein mechanicsNature, 2016
- Environmental Applications, Food and Biomass Processing by Pulsed Electric FieldsPublished by Springer Science and Business Media LLC ,2016
- Inactivation Effects of PEF on Horseradish Peroxidase (HRP) and Pectinesterase (PE)IEEE Transactions on Plasma Science, 2006
- WritingTheory, Culture & Society, 2006
- Photoemission from Liquid Aqueous SolutionsChemical Reviews, 2006
- Pulsed electric fields effects on the molecular structure and gelation of β-lactoglobulin concentrate and egg whiteFood Research International, 2004
- Inactivation of Pectin Methyl Esterase in Orange Juice by Pulsed Electric FieldsJournal of Food Science, 2002
- Effects of high voltage electric pulses on protein-based food constituents and structuresTrends in Food Science & Technology, 2001
- Quantum Dynamics and Vibrational RelaxationThe Journal of Physical Chemistry A, 1999