Investigation of the SARS-CoV-2 spike protein using EnviroESCA

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Langmuir, Issue July 5, 2022

The impact of the global pandemic due to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has engaged the researchers and clinicians to find the key features triggering the viral infection to lung cells. By utilizing such crucial information, researchers and scientists try to combat the spread of the virus.

In this cooperation between Indian and German researchers an in silico analysis of the protein-protein interactions between the receptor-binding domain (RBD) of the viral spike protein and the human angiotensin-converting enzyme 2 (hACE2) receptor was performed to highlight the key alteration that happened from SARS-CoV to SARS-CoV-2.

They analyzed and compared the molecular differences between spike proteins of the two viruses using various computational approaches such as binding affinity calculations, computational alanine, and molecular dynamics simulations. The binding affinity calculations showed that SARS-CoV-2 binds a little more firmly to the hACE2 receptor than SARS-CoV. The major finding obtained from molecular dynamics simulations was that the RBD-ACE2 interface is populated with water molecules and interacts strongly with both RBD and ACE2 interfacial residues during the simulation periods. The water-mediated hydrogen bond by the bridge water molecules is crucial for stabilizing the RBD and ACE2 domains.

Near-ambient pressure X-ray photoelectron spectroscopy (NAP-XPS) using an EnviroESCA confirmed the presence of vapor and molecular water phases in the protein–protein interfacial domain, further validating the computationally predicted interfacial water molecules. In addition, the role of interfacial water molecules in virus uptake by lung cell A549 by binding and maintaining the RBD/hACE2 complex at varying temperatures was examined using nanourchins coated with spike proteins as pseudoviruses and fluorescence-activated cell sorting (FACS) as a quantitative approach. The structural and dynamical features presented in this work may serve as a guide for developing new drug molecules, vaccines, or antibodies to combat the COVID-19 pandemic.

Click here for the full article: Langmuir, Issue July 5, 2022

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