The SARS-CoV-2 spike protein structure: a symmetry tale on distortion trail

Abstract

Only after the RBD has migrated and changed the protein's symmetry can the SARS-CoV-2 spike protein bind to the human receptor. The distortion level of the initial state can predict the spike's transmissibility.

Complementary Pocket and Network-Based Approach to Search for Spike Protein Allosteric Pocket Sites

“…Meanwhile, higher B -factors were observed for the Omicron BA.1 spike protein in chains A and C of the receptor-binding domain (Figure a,e) and the HR1 in chain B (Figure d). Asymmetry is observed in the change in B -factor across chains in the spike protein variants, in line with an existing study that shows increasing distortion in the symmetry of the spike protein at the receptor-binding domains, especially in the Omicron variant …”

“…Asymmetry is observed in the change in B-factor across chains in the spike protein variants, in line with an existing study that shows increasing distortion in the symmetry of the spike protein at the receptor-binding domains, especially in the Omicron variant. 72 The visualization of the relative B-factor using a threedimensional (3D) B-factor worm plot allows for the comparison of conformational flexibility among different spike protein variants. The ratio between the B-factor of a spike protein variant and that of the wild type is plotted along the structure of the wild-type spike protein, revealing the more flexible regions in the variants compared to the wild type.…”

CSM Software: Continuous Symmetry and Chirality Measures for Quantitative Structural Analysis

“…3 In the following years, the method was applied to study the role of approximate symmetry in numerous molecular systems, including symmetry of crystals, 4,5 distortion paths of inorganic complexes, 6 reactive processes, 7−10 host−guest interactions, 11 molecular dynamics 12 and symmetry of biomolecules. 13,14 Application of this approach beyond chemistry were also documented, e.g., in archeology. 15,16 The main challenge in calculating symmetry measures is to find the reference structure with the desired symmetry.…”

“…Following this paper, the method was extended to measure chirality and shape . In the following years, the method was applied to study the role of approximate symmetry in numerous molecular systems, including symmetry of crystals, , distortion paths of inorganic complexes, reactive processes, − host–guest interactions, molecular dynamics and symmetry of biomolecules. , Application of this approach beyond chemistry were also documented, e.g., in archeology. , …”