The inherent flexibility of receptor binding domains in SARS-CoV-2 spike protein
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Japan
- Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Japan
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Japan
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Japan
Figures
Figure 1 with 10 supplements
Comparisons of spike (S) protein structures in molecular dynamics (MD) simulations with cryo-electron microscopy (cryo-EM) structures.
(a) Twenty-seven coarse-grained beads representations of four representative cryo-EM structures: Down (PDB ID: 6ZGE), 1Up (6XKL), 2Up (7K8U), and 3Up (6XCN). Chains A, B, and C in S-protein are …
Figure 1—figure supplement 1
Structural model of the spike protein used in this study.
(a) Left: cartoon representation of the receptor binding domain (RBD) in the original cryo-electron microscopy (cryo-EM) structure (PDB:6VXX). The terminal residues before and after the missing …
Figure 1—figure supplement 2
Glycans in our spike protein models.
Schematic representations of the glycan structures and types used in gREST_Down and gREST_Up simulations including the location of the glycosylation sites.
Figure 1—figure supplement 3
Performance of the gREST_SSCR simulations.
(a) Top view the S1 subunit, where the positively and negatively charged residues used for solute region in gREST are shown as blue and red sticks, respectively. (b, c, d) Time courses of the …
Figure 1—figure supplement 4
Characterization of the receptor binding domain (RBD) conformational change in the three gREST_SSCR simulations.
(a, c, e) Time courses of the root mean square deviation (RMSD) of the Cα atoms with respect to Down structure upon fitting the Cα atoms of the S2 subunit in the selected replicas from the …
Figure 1—figure supplement 5
Analysis of the intra-domain stability of receptor binding domain (RBD) and N-terminal domain (NTD) in the gREST_SSCR simulations.
(a, b) Probability distribution of the Cα root mean square deviation (RMSD) of the RBDs (a) and NTDs (b) at 310 K of the gREST_Down, gREST_Up, and gREST_Down w/o glycan simulations as well as our …
Figure 1—figure supplement 6
Scheme of the protomer rotation and analysis of the rotated trajectories of the gREST_Down simulation.
(a) Schematic representation of the rotation scheme and criteria that was used to define structural changes of receptor binding domains (RBDs). First, hinge angle of each RBD is calculated. Then, if …
Figure 1—figure supplement 7
Free-energy landscape (FEL) along the hinge/twist angles in the gREST_Down w/o glycan and gREST_Up simulations.
(a, b) FEL in chains A, B, and C before (a) and after the rotation (b) in the gREST_Down w/o glycan simulation. The FELs show significant receptor binding domain (RBD) changes in chain B (or A) and …
Figure 1—video 1
Down-to-1Up transition of replica 16 in gREST_Down simulation.
Figure 1—video 2
1Up-to-2Up transition of replica 4 in gREST_Up simulation.
Figure 1—video 3
Down-to-1Up transition of replica 6 in gREST_Down w/o glycan simulation.
Figure 2 with 1 supplement
Representative receptor binding domain (RBD) conformations from molecular dynamics (MD) simulations vs. cryo-electron microscopy (cryo-EM) PDB structures.
(a) An overlay of the two free-energy landscapes at 310 K along the PC1 and PC2 obtained from gREST_Down (light blue) and gREST_Up (light cyan) simulations. The red dots represent the positions of …
Figure 2—figure supplement 1
Free-energy landscape (FEL) along the hinge/twist angles in the gREST_SSCR simulations in comparisons with the conventional molecular dynamics (cMD) simulations for receptor binding domain (RBD)/SD1 monomer and cryo-electron microscopy (cryo-EM) structures.
(a) FEL of RBDA in all three gREST_SSCR simulations. Note that these FELs are identical with those in Figure 1—figure supplement 6d (left), 6c (left), and 7b (left). 891 cryo-EM protomers are shown …
Figure 3 with 5 supplements
Accessibility of receptor binding motif (RBM).
(a) Per-residue solvent accessible surface area (SASA) values of the RBM (residues 410–510) in Down conformation (top) and their changes in Up conformations (bottom three). SASA values were …
Figure 3—figure supplement 1
Glycan shield of spike (S) protein.
(a, b) Solvent accessible surface area (SASA) of the head region of S-protein and the glycan shielded area, calculated for Down and 1U conformations at different probe radii from 1.4 to 15 Å (from a …
Figure 3—figure supplement 2
Accessibility of receptor binding motif (RBM).
Per-residue solvent accessible surface area (SASA) values of the RBM (residues 410–510) in Down (top) and three Up conformations (1U, 1UO, and 2UL, bottom three). SASA values were calculated using …
Figure 3—figure supplement 3
Glycan effect on the accessibility of receptor binding motif (RBM).
(a) Per-residue solvent accessible surface area (SASA) values of the RBM (residues 410–510) in Down conformation with and without glycan (top) and their changes (SASA w/ glycan – SASA w/o glycan, …
Figure 3—figure supplement 4
Putative interaction models with antibodies.
(a) The surface representation of receptor binding domain (RBD) epitopes for neutralizing antibodies: green: B38 (Class I), orange: C002 (Class II), blue: S309 (Class III), and pink: CR3022 (Class …
Figure 3—figure supplement 5
Comparison of Up structures from molecular dynamics (MD) simulations with cryo-electron microscopy (cryo-EM) structures.
The structures of 1U, 1UO, and 2UL from our simulations were aligned with the cryo-EM structures of spike (S) protein complexed with three types of neutralizing antibodies (nAbs): Class III (S309-S …
Figure 4 with 13 supplements
Protein-protein and protein-glycan interactions critical for Down-to-Up transition.
(a) Probability of finding the hydrogen bond (green) and contact (purple) pairs between protein residues or protein-glycans that markedly change along the transition pathway (DownSym, I2a, I3a, and …
Figure 4—figure supplement 1
Clustering for the conformations obtained from the gREST_Down simulation.
Schematic representation of the clustering steps and the resultant distributions of the hinge and twist angles are illustrated. (1) First, all conformations at 310 K were classified into eight …
Figure 4—figure supplement 2
Clustering for the conformations obtained from the gREST_Up simulation.
The scheme is almost same as in Figure 4—figure supplement 1.
Figure 4—figure supplement 3
Clustering for the conformations obtained from the gREST_Down w/o glycan simulation.
The scheme is almost same as in Figure 4—figure supplement 1.
Figure 4—figure supplement 4
Simulated single molecule fluorescence resonance energy transfer (smFRET) distance using the gREST_SSCR trajectory data.
(a) The residues used in the calculation of the smFRET-like distance are illustrated in blue. The distance was estimated based on the center of mass (COM) of the Cα atoms of the residues 425–431 in …
Figure 4—figure supplement 5
Transition pathway from Down to 1Up in the gREST_Down simulation.
(a) Top: free-energy landscapes (FELs) along the HingeA/ HingeB and HingeA/ HingeC angles, and Bottom: projection of the five main clusters [DownSym and DownLike (blue), I2a (green), I3a (purple), …
Figure 4—figure supplement 6
Comparison between targeted molecular dynamics (TMD) and gREST_SSCR simulations.
Projection of our previous TMD Down-to-Up (blue) or Up-to-Down (red) simulations (Mori et al., 2021) onto the overlapped free-energy landscape along the hinge/twist angles in the gREST_Down and …
Figure 4—figure supplement 7
Contact analysis for the main clusters in gREST_Down and gREST_Up simulations.
Probability of the residue-residue contacts in the receptor binding domain (RBD)/RBD (a), RBD/N-terminal domain (NTD) (b), and RBD/S2 interfaces (c) was analyzed for the main clusters DownSym, DownLi…
Figure 4—figure supplement 8
Hydrogen bond analysis for the main clusters in gREST_Down and gREST_Up simulations.
Probability of the residue-residue hydrogen-bonding in the receptor binding domain (RBD)/RBD (a), RBD/N-terminal domain (NTD) (b), and RBD/S2 interfaces (c) was analyzed. Hydrogen bonding pairs are …
Figure 4—figure supplement 9
Relationship between the sideway motion of RBDB and intrusion of the glycan at N343B.
Cluster centers of DownSym and DownLike (DAsym and Int1) conformations are shown to highlight the sideway motion of RBDB that allows the glycan N343 (yellow sphere) to intrude underneath RBDA. Black …
Figure 4—figure supplement 10
Glycan interaction sites in various Up conformations.
Structures of the cluster centers of top populated 1Up (1Ua, 1Ub, and 1Uc) and 1Up/open conformations (1UO) in the gREST_Up simulation are shown. For comparison, the cluster center of 1Up_like (1UL) …
Figure 4—figure supplement 11
Stability of I2a and I3a along transition pathway.
(a) Free-energy landscape (FEL) along PC1-PC2 of gREST_Down simulation shown as black contour. I2a and I3a are shown as green and purple dots, respectively. Down and one-Up cryo-electron microscopy …
Figure 4—figure supplement 12
Intermediate structures align with cryo-electron microscopy (cryo-EM) structures.
Superposition of the cartoon representation of I2a and I3a intermediate structures with D614G spike mutant cryo-EM structure of intermediate state (PDB:7KRS).
Figure 4—video 1
Protein-glycans interactions along Down-to-1Up transition pathway.
Figure 5 with 1 supplement
Selected protein-protein and protein-glycan interactions along the 1Up-to-2Up transition.
(a) Probability of finding the hydrogen bond (green) and contact (purple) pairs throughout the transition pathway (1Ua, 2UaL, and 2UbL). Where the conformational transition of RBDB induces RBDA/RBDC …
Figure 5—figure supplement 1
Free-energy landscape (FEL) in the gREST_Up and gREST_Down w/o glycan simulations.
(a) FEL along the HingeA/HingeB (middle) and HingeA/HingeC (right) as well as the projection of the top populated clusters (1Up (1Ua) and 2Up-like clusters (2UaL and 2UbL)) onto the FEL (left) in …
Figure 6 with 1 supplement
Druggable cryptic pockets in the transition intermediates.
(a) Snapshots of receptor binding domain (RBD) interface in Down symmetric (DownSym), Intermediate 2a (I2a), and 1Up-like (1UL) conformations. Chains A, B, and C in the protein are shown in red, …
Figure 6—figure supplement 1
Cryptic pockets and ligand binding in receptor binding domain (RBD).
(a) Results of the binding pocket search for I2a predicted by P2Rank software (Krivák and Hoksza, 2018). The spike protein is shown as gray surface, while all other colors represent predicted …
Tables
Table 1
Molecular dynamics (MD) simulations of spike (S) protein performed in this study.
| Name | Model | Method | Simulations length |
|---|---|---|---|
| gREST_Down | Spike Down w/ glycans | gREST_SSCR | 500 ns × 16 replicas |
| gREST_Up | Spike Up w/ glycans | gREST_SSCR | 300 ns × 16 replicas |
| gREST_Down w/o glycan | Spike Down w/o glycans | gREST_SSCR | 150 ns × 16 replicas |
| Monomer_Down | RBD/SD1 monomer Down | cMD | 300 ns × 1 run |
| Monomer_Up | RBD/SD1 monomer Up | cMD | 300 ns × 2 runs |
| cMD_Down* | Spike Down w/ glycans | cMD | 1000 ns × 1 run |
| cMD_Up* | Spike Up w/ glycans | cMD | 1000 ns × 1 run |
-
*
cMD_Down and cMD_Up are the same simulations as shown in our previous study Mori et al., 2021.
Additional files
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Supplementary file 1
List of PDBs, clusters and lignads.
(A) Cryo-electron microscopy (cryo-EM) structures used in the principal component analysis (PCA). (B) Definition of protomer coarse-grained particles representing rigid domains for PCA. (C) List of clusters for gREST_Down, gREST_Up, and gREST_Down w/o glycan simulations. (D) The receptor binding domain (RBD) interface cryptic pockets predicted by P2Rank. (E) List of the top-ranked molecules from the virtual screening of 2115 FDA approved drugs to RBD interface in I2a, I3a, and I3b intermediate structures. (F) Nilotinib binding energy to I2a, I3a, and I3b intermediates.
- https://cdn.elifesciences.org/articles/75720/elife-75720-supp1-v2.docx
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Transparent reporting form
- https://cdn.elifesciences.org/articles/75720/elife-75720-transrepform1-v2.pdf
