Fig 1.
Structure of spike glycoprotein with bound linoleate (LA) molecules. (A) Side view of the spike trimer, comprising Chain A (blue), Chain B (pink), and Chain C (green). The structure is shown in the simulation water box with glycans in the 3D-SNFG cartoon representation. (B) Top view of the spike trimer, highlighting the receptor-binding domain (RBD) and N-terminal domain (NTD). Each RBD contains a bound LA molecule (magenta), with the corresponding subunit indicated as A, B, or C, noted as subscripts. (C) Close-up view of the free fatty acid (FFA) binding pocket within the RBD, illustrating the specific interaction of LA within the pocket.
Fig 2.
Linoleate (LA) dissociation pathways.
(A) The RMSD of LA relative to the initial equilibrated structure for each successful dissociation simulation. A successful dissociation is defined by a ligand RMSD greater than 30 Å. The simulation time before and after the dashed line indicates the GaMD preparation and production run, respectively. (B) Representative trajectories depicting two distinct dissociation pathways: Path A (green) and Path B (orange). The ligand trajectory is shown by individual beads, representing the center of mass coordinates of LA over the simulation time.
Table 1.
List of successful spike-LA dissociation simulations.
The subscript and superscript of RBD indicate the domains that contain bound and boosted LAs, respectively. σL,nb and σD represent the user-defined upper limit of the standard deviation of the boost potential added to the nonbonded ligand potential terms and to the rest of the potential terms, respectively (details are in S1 Text).
Fig 3.
Dynamic opening and closing of the FFA binding pocket.
(A) Ligand dissociation along Path A involves LA passing through the open gate formed by the α1 and α3 helices. The opening of the gate is measured by the distance between E340 on α1 and A372 on α3. (B) Ligand dissociation along Path B occurs when α1 and α3 move closer, resulting a closed gate and allowing the ligand to move between α1 and β-sheets. The distance between E340 and A372 for a Path A (C) and Path B (D) changes over the simulation time.
Fig 4.
PMF profile of LA dissociation.
The 2D PMF plot illustrates ligand RMSD and gate distance changes, indicating the intermediate conformations during LA unbinding processes. Arrows show the LA snapshots, starting in the fully bound state and moving along either Path A or Path B. A dual arrow indicates the transition of LA between dissociation paths at intermediate stages I-1A and I-1B.
Fig 5.
Dynamics of the glycan at N343.
(A) In the case of dissociation along Path A, the N343 glycan extends into the solvent, moving away from the α1 and α3 helices. This allows LA to traverse through the open gate created by the α1 and α3 helices. (B) Conversely, during dissociation along Path B, the N343 glycan moves towards the α1 and α3 helices, restricting LA from progressing through Path A. Measurement of the dihedral angle of residue N343 is shown for Path A (C) and Path B (D), spanning the simulation duration.