New Approach of 3D Protein Structure Superimposition: Case Study of “SARS-COV-2” and “SARS-COV”

COVID-19 is a disease caused by SARS-CoV-2. The entry of a virus into human cells is a critical phase in its infection. The binding of the spike protein of SARS-CoV-2 to Angiotensin converting enzyme 2 ACE2, an enzyme found on the surface of human cells, initiates the infection. Online software tools that overlay the three-dimensional structures of viruses, including SARS-CoV-2, address the problem of structure superposition by overlaying the ACE2 and spike complexes of the first protein on those of the second protein. In this work, overlaying the three-dimensional structures of viruses was addressed by superimposing ACE2 and then applying the resulting transformation from this superposition to the spike. Finally, the root mean square deviation RMSD was calculated. We used the discrete to continuous DTC algorithm to align the 3D structures; the results from the DTC were compared to the results from TopMatch and SuperPose, which are online tools for aligning 3D structures. The obtained results prove that aligning each structure then combining them is the most suitable approach for properly studying the structural evolution of SARS-CoV-2.