Cell entry by SARS-CoV-2 is accomplished by the S2 subunit
of the
spike S protein on the virion surface by capture of the host cell
membrane and fusion with the viral envelope. Capture and fusion require
the prefusion S2 to transit to its potent fusogenic form, the fusion
intermediate (FI). However, the FI structure is unknown, detailed
computational models of the FI are unavailable, and the mechanisms
and timing of membrane capture and fusion are not established. Here,
we constructed a full-length model of the SARS-CoV-2 FI by extrapolating
from known SARS-CoV-2 pre- and postfusion structures. In atomistic
and coarse-grained molecular dynamics simulations the FI was remarkably
flexible and executed giant bending and extensional fluctuations due
to three hinges in the C-terminal base. The simulated configurations
and their giant fluctuations are quantitatively consistent with SARS-CoV-2
FI configurations measured recently using cryo-electron tomography.
Simulations suggested a host cell membrane capture time of ∼2
ms. Isolated fusion peptide simulations identified an N-terminal helix
that directed and maintained binding to the membrane but grossly underestimated
the binding time, showing that the fusion peptide environment is radically
altered when attached to its host fusion protein. The large configurational
fluctuations of the FI generated a substantial exploration volume
that aided capture of the target membrane, and may set the waiting
time for fluctuation-triggered refolding of the FI that draws the
viral envelope and host cell membrane together for fusion. These results
describe the FI as machinery that uses massive configurational fluctuations
for efficient membrane capture and suggest novel potential drug targets.