Effect on the conformations of spike protein of SARS-CoV-2 due to mutation

• Published in: bioRxiv 2022-05
• Main Authors: Aayatti Mallick Gupta, Chakrabarti, Jaydeb
• Format: Article
• Language: English
• Subjects: Binding sites; Biophysics; Immunogenicity; Mutants; Mutation; Protein structure; Proteins; Severe acute respiratory syndrome coronavirus 2; Spike protein
• ISSN: 2692-8205
• DOI: 10.1101/2022.05.11.491583

The spike protein of SARS CoV-2 mediates receptor binding and cell entry and is the key immunogenic target for virus neutralization and the present attention of many vaccine layouts. It exhibits significant conformational flexibility. We study the structural fluctuations of spike protein among the most common mutations appeared in variant of concerns (VOC). We report the thermodynamics of conformational changes in mutant spike protein with respect to the wildtype from the distributions of the dihedral angles obtained from the equilibrium configurations generated via all-atom molecular dynamics simulations. We find that the mutation causes the increase in distance between N-terminal domain and receptor binding domain leading to an obtuse angle cosine distribution in the trimeric structure in spike protein. Thus, increase in open-state is conferred to the more infectious variants of SARS-CoV-2. The thermodynamically destabilized and disordered residues of receptor binding motif among the mutant variants of spike protein are proposed to serve as better binding sites for host factor. We identify a short stretch of region connecting the N-terminal domain and receptor binding domain forming linker loop where many residues undergo stabilization in the open state compared to the closed one. Competing Interest Statement The authors have declared no competing interest.