Host Cell Membrane Capture by the SARS-CoV-2 Spike Protein Fusion Intermediate

SARS-CoV-2 unleashes the spike fusionintermediate to entercells. Simulations reveal 3 base hinges mediating giant fluctuationsthat enable target cell capture after similar to 2 ms and may triggerrefolding.Cell entry by SARS-CoV-2 is accomplished by the S2 subunitof thespike S protein on the virion surface by capture of the host cellmembrane and fusion with the viral envelope. Capture and fusion requirethe prefusion S2 to transit to its potent fusogenic form, the fusionintermediate (FI). However, the FI structure is unknown, detailedcomputational models of the FI are unavailable, and the mechanismsand timing of membrane capture and fusion are not established. Here,we constructed a full-length model of the SARS-CoV-2 FI by extrapolatingfrom known SARS-CoV-2 pre- and postfusion structures. In atomisticand coarse-grained molecular dynamics simulations the FI was remarkablyflexible and executed giant bending and extensional fluctuations dueto three hinges in the C-terminal base. The simulated configurationsand their giant fluctuations are quantitatively consistent with SARS-CoV-2FI configurations measured recently using cryo-electron tomography.Simulations suggested a host cell membrane capture time of similar to 2ms. Isolated fusion peptide simulations identified an N-terminal helixthat directed and maintained binding to the membrane but grossly underestimatedthe binding time, showing that the fusion peptide environment is radicallyaltered when attached to its host fusion protein. The large configurationalfluctuations of the FI generated a substantial exploration volumethat aided capture of the target membrane, and may set the waitingtime for fluctuation-triggered refolding of the FI that draws theviral envelope and host cell membrane together for fusion. These resultsdescribe the FI as machinery that uses massive configurational fluctuationsfor efficient membrane capture and suggest novel potential drug targets.