Binding behavior of spike protein and receptor binding domain of the SARS-CoV-2 virus at different environmental conditions

Abstract

A novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified as the cause of the COVID-19 pandemic that originated in China in December 2019. Although extensive research has been performed on SARS-CoV-2, the binding behavior of spike (S) protein and receptor binding domain (RBD) of SARS-CoV-2 at different environmental conditions have yet to be studied. The objective of this study is to investigate the effect of temperature, fatty acids, ions, and protein concentration on the binding behavior and rates of association and dissociation between the S protein and RBD of SARS-CoV-2 and the hydrophobic aminopropylsilane (APS) biosensors using biolayer interferometry (BLI) validated with molecular dynamics simulation. Our results suggest three conditions—high ionic concentration, presence of hydrophobic fatty acids, and low temperature—favor the attachment of S protein and RBD to hydrophobic surfaces. Increasing the temperature within an hour from 0 to 25 °C results in S protein detachment, suggesting that freezing can cause structural changes in the S protein, affecting its binding kinetics at higher temperature. At all the conditions, RBD exhibits lower dissociation capabilities than the full-length S trimer protein, indicating that the separated RBD formed stronger attachment to hydrophobic surfaces compared to when it was included in the S protein.

Environmental Effects on Viable Virus Transport and Resuspension in Ventilation Airflow

“…This binding interaction occurs in a hydrophobic region. The BLI results will show how the S protein would bind to human cell receptors after coming into contact with these 3 surfaces in a hospital [ 29 , 30 ]. Each biosensor was hydrated in Phosphate Buffer Saline (PBS) buffer (pH 7.4) for 10 min before use.…”

“…Polymers composed of exclusively hydrocarbon constituents (PP) are most hydrophobic, while PU may interact at higher humidity with the phosphate ions in the PBS buffer, resulting in the detachment of the virus particles from the surface. In a recent study with bovine coronavirus, the authors found increased attachment to hydrophobic surfaces [ 29 ].…”

Temporal Variation of SARS-CoV-2 Levels in Wastewater from a Meat Processing Plant

“…This is the first known study to show the dynamic changes in virus concentrations in meat processing plants, which often contain a unique environment—low temperature, high RH, high fat and protein content in the air—that was shown by a previous study of the authors to favor the attachment and preservation of SARS-CoV-2 viruses [ 19 ]. A three-month campaign was launched in early 2022 to monitor the wastewater samples collected from a meat processing plant in Canada by detecting and quantifying the SARS-CoV-2 viruses using RT-qPCR to understand the temporal variation of the virus levels over the project period and to find any correlation between the virus levels in wastewater and clinically confirmed cases in the surrounding city area.…”

Design of novel disturbing peptides against ACE2 SARS-CoV-2 spike-binding region by computational approaches

“…Computational techniques and molecular dynamics simulations have been widely applied in COVID-19-related studies in different areas such as interactions between the virus and human its human receptors (Spinello et al, 2020;Wang et al, 2020), mutations of SARS-CoV-2 (Shah et al, 2020;Kullappan et al, 2021;Luan et al, 2021;Spinello et al, 2021), characteristics of SARS-CoV-2 proteins (Kordzadeh and Saadatabadi, 2021;Zhang et al, 2022;Bignon et al, 2022;Borisõek et al, 2021), and drug discovery (Aallaei et al, 2021;Bayati and Ebrahimi, 2021;Mora et al, 2022). In our previous study, we designed peptide inhibitors with the last strategy inspired by the RBD domain of the SARS-CoV-2 spike (Pourmand et al, 2022).…”