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. 2022 Dec;48(4):399-414.
doi: 10.1007/s10867-022-09615-x. Epub 2022 Nov 23.

Computational and comparative investigation of hydrophobic profile of spike protein of SARS-CoV-2 and SARS-CoV

Uma Shekhawat  1   2 , Anindita Roy Chowdhury Chakravarty  3
Affiliations

Computational and comparative investigation of hydrophobic profile of spike protein of SARS-CoV-2 and SARS-CoV

Uma Shekhawat et al. J Biol Phys. 2022 Dec.

Abstract

The hydrophobic force is one of the most dominant factors in protein folding. A protein becomes functional only when it achieves its three-dimensional structure and stability upon folding. For a better understanding of the hydrophobic effects and their function in protein folding, quantitative measurement of the hydrophobicity of amino acid side chains is crucial. Spike protein is the primary structural protein in SARS-CoV-2 and SARS-CoV. This study explores how protein sequences in SARS-CoV-2 and SARS-CoV spike proteins encode hydrophobic interactions. Computational tools/techniques have been utilized to investigate the protein sequences of the spike proteins of SARS-CoV-2 and SARS-CoV. Investigations provided an estimate of hydrophobic distribution and its relative strength, indicating a hydrophobic pattern. Analysis of the spike protein's hydrophobic profile may help identify and treat the virus-caused disease; additionally, it can give an insight into the transmissibility and pathogenicity of the virus.

Keywords: Aliphatic; Aromatic; Hydrophobicity; SARS-CoV; SARS-CoV-2; Spike protein.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Contribution of hydrophobic aromatic residues in the spike protein of SARS-CoV-2 (UniProt ID: P0DTC2) and SARS-CoV (UniProt ID: P59594)
Fig. 2
Fig. 2
Contribution of hydrophobic aliphatic residues in the spike protein of SARS-CoV-2 (UniProt ID: P0DTC2) and SARS-CoV (UniProt ID: P59594)
Fig. 3
Fig. 3
Contribution of hydrophobic aromatic residues of the maximum aligned sequences of spike proteins of SARS-CoV-2 (UniProt ID: P0DTC2) and SARS-CoV (UniProt ID: P59594)
Fig. 4
Fig. 4
Contribution of hydrophobic aliphatic residues of the maximum aligned sequences of spike proteins of SARS-CoV-2 (UniProt ID: P0DTC2) and SARS-CoV (UniProt ID: P59594)
Fig. 5
Fig. 5
Presence of highest aromatic and aliphatic contributor in PDB ID: 5I08_A
Fig. 6
Fig. 6
Presence of highest aromatic and aliphatic contributor in PDB ID: 7KIP_A
See this image and copyright information in PMC

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