Molecular dynamic simulations unveil conformational dynamics of SARS-CoV-2 RBD spike protein and ACE2 receptor
Researchers from the Federal University of Para, Brazil, presented a systematic analysis of the affinity and conformational dynamics between the spike protein (S) binding of the coronavirus receptor-binding domain 2 (SARS- CoV-2) of severe acute respiratory syndrome (RBD) and the host receptor for angiotensin-converting enzyme 2 (ACE2).
The researchers used accelerated molecular dynamics (aMD) simulations and free energy calculations to assess whether infectivity and transmission of SARS-CoV-2-related variants were related to receptor binding.
The study was published on the Research Square* preprint server and is currently under review at Scientific reports newspaper.
The SARS-CoV-2 glycoprotein S contains S1 and S2 subunits and is composed of a total of 1,273 residues. The interaction between the RBD located in the S1 domain with ACE2 guides viral entry into the cell. S1 RBD underwent conformational changes in specific residues that revealed receptor binding determinants.
Evidence from multiple studies has suggested that mutations involving K417N, S477N, T478K, E484A, and N501Y in SARS-CoV-2 Omicron and other variants conferred viral escape abilities or better binding affinity to the ACE2 receptor and therefore an increased risk of reinfection.
To further analyze this, the present study explored the effect of mutations in the S RBD of SARS-CoV-2 Alpha, Delta, and Omicron variants on binding affinity to the human ACE2 receptor.
In this study, the authors performed classical molecular dynamics (cMD) simulations to assess the mean dihedral and total energies of proteins as a benchmark for aMD simulations. They performed a 200 ns aMD simulation to explore conformations over time for the RBDWT-ACE2, RBDAlpha-ACE2, RBDDelta-ACE2 and RBDOmicron-ACE2 complex systems.
Root mean square fluctuation (RMSF) analysis revealed the flexibility of each residue in the protein-protein complex system. Principal component analysis (PCA) diagonalized the covariance matrix to obtain the principal components. PCA plots were constructed through combinations of PC1 vs PC2, PC2 vs PC3, and PC3 vs PC1 in which the clusters demonstrated two possible states for all systems in PC1 vs PC2.
The authors calculated the free energy binding for RBD-ACE2 compounds of different SARS-CoV-2 variants to estimate the SARS-CoV-2 affinity for the human ACE2 receptor and the potential risk of immune invasion by different SARS variants. -CoV-2. Decomposition energy assessed the energy contribution of amino acid with RBD and ACE2 bonding, while molecular mechanics, generalized Born model and solvent accessibility method (MMGBSA) implemented in AMBER calculated these free energies according to the greater stability of the trajectory aMD.
aMD simulations showed that RMSD of RBDWT-ACE2, RDBAlpha-ACE2 and RBDDelta-ACE2 complexes were in the fluctuation range of 1–3 Å. However, the RDBOmicron-The ACE2 complex represented different variations in the range of 1–4 Å. Curiously, all of the RBD-ACE2 complex systems had reached structural equilibrium.
RMSF analysis showed the greatest ACE2 fluctuation in the regions 123–178, 395–425, and 248–368 residues that shift to interact with the viral RBD. RDBalpha-ACE2 showed lower fluctuation compared to RBDWTDBRDelta, and RBDOmicron.
Essential dynamic analysis demonstrated clusters in PCA graphs showing two likely states for all systems in PC1 vs PC2. However, the Alpha variant showed a higher number of clusters in which each time interval was differentiated into small clusters.
The initial structure of the RBDOmicron system differed from the final structure leading to variations in aMD structures. RDBWT and the RDBOmicron strains elucidated substantial conformational fluctuations; however, the RBDAlpha variant had greater stability.
RDBOmicron showed the highest binding affinity to the human ACE2 receptor and similar conformational fluctuation compared to the other variants. RDBOmicron showed higher binding free energy (-75.4 kcal/mol) compared to RBDDelta (-66.1 kcal/mol), RBDAlpha (62.7836 kcal/mol), and the RBDWT (-59.7 kcal/mol).
The calculation of the decomposition energy showed that in RBDOmicronmutations N440K, T478K, Q493R and Q498R resulted in a favorable interaction between RBDOmicron and ACE2. Interestingly, all mutations in RBDOmicron included positively charged residues of Lys or Arg. The Omicron K478 mutation (decomposition energy, -85.8 kcal/mol) had a stabilizing effect while the T478 mutation in RBDWT (0.7 kcal/mol) has a destabilizing effect.
The T478K mutation was located in a solvent-oriented region and allowed ACE2 interaction due to the increased side chain. The Q493R substitution allowed a favorable interaction with the negatively charged residues Asp38 and Glu35 of ACE2 increasing protein S binding. The N440K mutation located in the solvent-focused region whereas the Q498R mutation enhanced the protein-protein interaction and this contribution was 24 times higher than RBDWT.
The N501Y mutation in RBDAlpha showed similar decay energy as RBDWT. Therefore, the conformational stability in RBDAlpha was responsible for its better binding to ACE2. In RBDDeltathe L352R and T478K mutations had a higher energy contribution of
-90.5 and -82.6 kcal/mol, respectively, showing increased enhancement of ACE2 receptor binding.
The results of this study demonstrated that SARS-CoV-2 RBDOmicron– ACE2 complex elucidated identical fluctuations compared to protein S of wild-type, Alpha and Delta strains.
Overall, RBD mutationsOmicron increased protein S binding affinity for ACE2 and other mutations from uncharged residues to positively charged Lys and arg residues in a key position with RBD. This explains the high transmissibility of the SARS-CoV-2 Omicron variant compared to other variants.
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