Investigation of the Effect of Temperature on the Structure of SARS-CoV-2 Spike Protein by Molecular Dynamics Simulations

Frontiers in Molecular Biosciences
Soumya Lipsa Rath, Kishant Kumar

Abstract

Statistical and epidemiological data imply temperature sensitivity of the SARS-CoV-2 coronavirus. However, the molecular level understanding of the virus structure at different temperature is still not clear. Spike protein is the outermost structural protein of the SARS-CoV-2 virus which interacts with the Angiotensin Converting Enzyme 2 (ACE2), a human receptor, and enters the respiratory system. In this study, we performed an all atom molecular dynamics simulation to study the effect of temperature on the structure of the Spike protein. After 200 ns of simulation at different temperatures, we came across some interesting phenomena exhibited by the protein. We found that the solvent exposed domain of Spike protein, namely S1, is more mobile than the transmembrane domain, S2. Structural studies implied the presence of several charged residues on the surface of N-terminal Domain of S1 which are optimally oriented at 10-30°C. Bioinformatics analyses indicated that it is capable of binding to other human receptors and should not be disregarded. Additionally, we found that receptor binding motif (RBM), present on the receptor binding domain (RBD) of S1, begins to close around temperature of 40°C and attains a completely closed conf...Continue Reading

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Mar 2, 2021·Journal of Biomolecular Structure & Dynamics·Grijesh JaiswalVeerendra Kumar
May 18, 2021·Matter·Marcelo D T TorresCesar de la Fuente-Nunez
Jul 9, 2021·Renewable & Sustainable Energy Reviews·Gagan Deep SharmaMrinalini Srivastava
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Aug 28, 2021·International Journal of Molecular Sciences·Kwang-Eun ChoiNam Sook Kang

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Datasets Mentioned

BETA
QHD43416.1

Software Mentioned

Blast
CHARMM
GROMACS
VMD
Protein Blast
Pymol
Spike
Blast Tree
PyMOL Molecular Graphics System

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