Flexibility and mobility of SARS-CoV-2-related protein structures

Rudolf Römer (1, 2) , Navodya Römer (3) , A. Katrine Wallis (4)

1 University of Warwick [Coventry]
2 LPTM - UMR 8089 - Laboratoire de Physique Théorique et Modélisation
3 School of Life Sciences
4 School of Life Sciences [Warwick]

Abstract The worldwide CoVid-19 pandemic has led to an unprecedented push across the whole of the scientific community to develop a potent antiviral drug and vaccine as soon as possible. Existing academic, governmental and industrial institutions and companies have engaged in large-scale screening of existing drugs, in vitro, in vivo and in silico. Here, we are using in silico modelling of possible SARS-CoV-2 drug targets, as deposited on the Protein Databank (PDB), and ascertain their dynamics, flexibility and rigidity. For example, for the SARS-CoV-2 spike protein—using its complete homo-trimer configuration with 2905 residues—our method identifies a large-scale opening and closing of the S1 subunit through movement of the S $${}^\text{B}$$ B domain. We compute the full structural information of this process, allowing for docking studies with possible drug structures. In a dedicated database, we present similarly detailed results for the further, nearly 300, thus far resolved SARS-CoV-2-related protein structures in the PDB.

Domaines: Virologie

Rudolf Römer, Navodya Römer, A. Katrine Wallis. Flexibility and mobility of SARS-CoV-2-related protein structures. Scientific Reports, 2021, 11 (1), pp.4257. ⟨10.1038/s41598-021-82849-2⟩. ⟨hal-03636461⟩