Evaluating SARS-CoV-2 RBD helices stability throughout the lens of molecular dynamics simulation

This study aims to evaluate the stability of SARS-CoV-2 RBD helix domains, given the 6m0j.pdb record of the crystal structure of S protein receptor-binding domain bound to ACE2 receptor as a target molecule. We have performed stability evaluation based on motifs’ occupancy during 50 ns molecular dynamics simulation in GROMACS molecular dynamics simulation software.
At first, we placed the molecule into a cubic solute box and dissolved it under the SPC/E water model. The system was well-prepared that guarantees energetically optimized solute to the solvent and vice versa. We used a simulation output trajectory file for time series analysis and a DSSP (dictionary of protein secondary structure) program for RBD secondary structure assignment. The DSSP program assigned RBD motifs to known secondary structures, such as helix, strand, or coil. DSSP program uses a pure electrostatic model on hydrogen bond computation and assigns protein secondary structure based on known bonding patterns in common secondary structures.
A total of 5 (five) helices, with variable stability rates, were identified: RBD340–343=GEVF, RBD366–369=SVLY, RBD384–389=PTKLND, RBD417–421=KIADY and RBD439–442=NNLD. The most stable helices are: RBD417–421=KIADY (occupancy=98.12%), followed by: RBD340–343=GEVF (occupancy=94.6%) and RBD366–369=SVLY (occupancy=93.04%). The third motif, RBD384–389=PTKLND shifts into a permanent turn in t>30 ns, and rather than stable helix formation, alternating helix-to-turn transitions can be uniquely attributed to RBD439–442=NNLD.
This study reports on the most stable SARS-CoV-2 RBD helix RBD417–421=KIADY, given the presence of K (Lysine) at position 417. Substitutions at RBD position 417, have usually been associated with immune evasion, which might be induced by RBD417–421=KIADY destabilization to some extent. Although P384 can act as an alpha helix breaker in RBD384–389=PTKLND and K386, and L387 have helix-forming propensities, the presence of N388 and D389 do not allow stable helix formation, unfolding the helix into turn in t>30 ns.
RBD417–421 helix destabilization might be one of the factors contributing to SARS-CoV-2 immune evasion.