Study of surface potential and hydrophobicity of amino acids in mutated spike proteins of variants of SARS-CoV-2 and its impact on attachment and internalization of virus with human host cells

Abstract

The Spike protein as a whole and Receptor Binding Region in particular are the main molecules which participate in the process of attachment and internalization of SARS-CoV-2 into human cells. Detailed study of physical and chemical changes in spike protein of SARS-CoV-2 from Wuhan to Omicron strains is needed for the public health and therapeutic utility. Amino acid sequences of all strains of novel coronavirus (Wuhan, alpha, beta, delta, gamma and omicron) were studied and analysed using software, Clustal Omega. Present paper reports analysis of all mutations in the Spike protein of different strains focusing on the chemical and physical interaction of the amino acids of RBD of Spike Protein with amino acids of ACE-2 receptor, to explain basis of transmissibility and clinical severity of viral strains. We report how potential based affinity of Spike protein and host ACE-2 receptor has affected the virus-host attachment and that how hydrophobicity of amino acids in the RBD region will affect the internalization of virus molecule into host cells.