Distant residues modulate conformational opening in SARS-CoV-2 spike protein

Abstract

Infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) involves the attachment of the receptor-binding domain (RBD) of its spike proteins to the ACE2 receptors on the peripheral membrane of host cells. Binding is initiated by a down-to-up conformational change in the spike protein, the change that presents the RBD to the receptor. To date, computational and experimental studies that search for therapeutics have concentrated, for good reason, on the RBD. However, the RBD region is highly prone to mutations, and is therefore a hotspot for drug resistance. In contrast, we here focus on the correlations between the RBD and residues distant to it in the spike protein. This allows for a deeper understanding of the underlying molecular recognition events and prediction of the highest-effect key mutations in distant, allosteric sites, with implications for therapeutics. Also, these sites can appear in emerging mutants with possibly higher transmissibility and virulence, and preidentifying them can give clues for designing pan-coronavirus vaccines against future outbreaks. Our model, based on time-lagged independent component analysis (tICA) and protein graph connectivity network, is able to identify multiple residues that exhibit long-distance coupling with the RBD opening. Residues involved in the most ubiquitous D614G mutation and the A570D mutation of the highly contagious UK SARS-CoV-2 variant are predicted ab initio from our model. Conversely, broad-spectrum therapeutics like drugs and monoclonal antibodies can target these key distant-but-conserved regions of the spike protein.

Keywords: COVID-19; molecular biophysics; molecular dynamics; statistical mechanics; virus structure.

Fig. 1.

The RBD opening transition in the SARS-CoV-2 spike protein: The RBD of the chain shown in green is undergoing the down-to-up transition leading to the binding of the human ACE2 receptor.

Fig. 2.

(A) Structure of spike protein with the residues in RBD shown in green color. Non-RBD residues strongly correlated with the RBD opening motion are represented by spheres (color code: chain A, yellow; chain B, blue; chain C, red). The RBD of chain A is performing down-to-up conformational change. (B) The projection of all unbiased trajectories along the two slowest degrees of freedom (tICs) obtained from tICA analysis. (C) Average number of hydrogen bonds for the highest correlated residues/residue pairs (Table 1) in the closed and the partially open states. (D) Normalized distribution of representative backbone dihedral angles strongly correlated with tIC 1 and tIC 2 (Table 1). The distributions are calculated from closed and partially open state trajectories. The corresponding values of the dihedral angles in the PDB structures are marked in the plot for reference.

Fig. 3.

Representative snapshots of the hydrogen bonding pattern of some of the groups of residues from Table 1 and Fig. 1C. Upper corresponds to the closed state, and Lower shows the partially open state.

Fig. 4.

(A−D) Cross-correlation matrices for four states (A, closed; B, slightly open; C, partially open; D, fully open) computed using LMI. (E−G) Difference in correlation matrix elements for the (E) slightly, (F) partially, and (G) fully open states with respect to the closed state. RBD regions form highly correlated blocks (D and G), indicating that these residues are largely decoupled from the rest of the protein. Still, signatures of long-distance correlated motion are detectable.

Fig. 5.

Residues with large changes in normalized BC due to RBD opening. (Upper) Largest positive changes; (Lower) negative changes; chain index (A, B, or C) mentioned before the residue number. The location of the residue (NTD, RBD, linker, or S2) is also mentioned next to the residue number.

Fig. 6.

(A) Structures of the slightly open, partially open, and fully open states of the spike protein, with residues colored according to the difference of BC with respect to the closed conformation. Red indicates most negative and blue indicates most positive values of BC difference. The RBD of chain A that undergoes opening motion is colored in green. The NTD and S2 domains are also indicated. (B) The values of the difference in centrality with respect to closed state plotted as a function of residue indices. Residues with a BC difference of $>0.2$ are marked with a circle.