ABSTRACT
Remarkable infectivity of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV2) is due to the rapid emergence of various strains, thus enable the virus to rule the world. Over the course of SARS-CoV2 pandemic, the scientific communities worldwide are responding to newly emerging genetic variants. However, the mechanism behind the persistent infection of these variants is still not known due to the paucity of study of these variants at molecular level. In this scenario, computational methods have immense utility in understanding the molecular and functional properties of different variants. Therefore, in this study various mutants (MTs) of SpikeS1 receptor binding domain (RBD) of highly infectious SARS-CoV2 strains were carried and elucidated the protein structure and dynamics using molecular dynamics (MD) approach. MD simulation study showed that all MTs exhibited stable structures with altered functional properties. Furthermore, the binding strength of different MTs along with WT (wildtype) was revealed through protein-protein docking and observed that MTs showed high binding affinities than WT. Hence, this study shed light on the molecular basis of infection caused by different variants of SARS-CoV2, which might play an important role in to cease the transmission and pathogenesis of virus and also implicate in rational designing of a specific drug.
Competing Interest Statement
The authors have declared no competing interest.
List of abbreviations
- ACE2
- Angiotensin converting enzyme2
- COVID-19
- Coronavirus disease-2019
- DSSP
- Dictionary of secondary structure of protein
- ED
- Essential dynamics
- GROMACS
- Groningen machine for chemical simulation
- HADDOCK
- High ambiguity driven docking
- MDS
- Molecular dynamics simulation
- MT
- Mutant
- PCA
- Principle component analysis
- PDB
- Protein data bank
- ProSA
- Protein structure analysis
- QMEAN
- Qualitative model energy analysis
- RBD
- Receptor binding domain
- Rg
- Radius of gyration
- RIN
- Residues interaction network
- RMSD
- Root mean square deviation
- RMSF
- Root mean square fluctuation
- SARS-CoV2
- Severe acute respiratory syndrome-coronavirus 2
- SASA
- Solvent accessible surface area
- SAVES
- Structure analysis and verification server
- WT
- Wildtype