Accepted for/Published in: JMIR Bioinformatics and Biotechnology
Date Submitted: Feb 18, 2022
Date Accepted: May 16, 2022
Comparative analysis of spike protein of SARS CoV-2 variants functional, structural and evolutionary properties: An in silico method
ABSTRACT
Background:
A recent global outbreak of COVID-19 caused by the severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) created a pandemic situation and emerged a potential threat to humanity. Analysis of virus genetic composition has revealed that the spike protein, one of the major structural proteins, facilitates the entry of virus to host cells.
Objective:
The spike protein has become the main target for prophylactics and therapeutics studies. Here, we compare spike proteins of variants using bioinformatics tools.
Methods:
All the spike protein sequences were retrieved from the NCBI database. The ClustalX program was used to sequence multiple alignment and mutational analysis. Several online bioinformatics tools were used to predict physiological, immunological and structural features of spike proteins of SARS CoV-2 variants. The phylogenetic tree was constructed using CLC software.
Results:
Multiple sequences analysis revealed P681R mutation in delta variant, where change of amino acid from H (histidine) to R (arginine) made protein more alkaline, due to its high pKa value (12.5) compared to amino acid H (6.0). Physicochemical properties revealed relatively higher pI (7.34) and aliphatic index (84.65) of variant delta compared to others. Generation of 2D gel map showed separation of delta spike protein with other group of variants. The phylogenetic tree of spike proteins showed that the delta variant was close and a mix of Rousettus bat coronavirus and MERS-CoV.
Conclusions:
Comparative analysis of SARS CoV-2 variants revealed that delta variant is more aliphatic in nature which provide more stability to it and subsequently influencing the virus behavior. Clinical Trial: NIL
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