Compared
to all-atom models, coarse-grained models enable the investigation
of the dynamics of simulation systems on a much larger length scale
and a longer time scale, which makes them suitable for studying macromolecular
systems. Hence, in this work, we performed multiple μs-scale
Martini coarse-grained molecular dynamics simulations to reveal the
interaction details between SARS-CoV-2 RBD and full-length human ACE2.
Besides, the key coarse-grained systems were backmapped into the corresponding
all-atom system for the display of structural details. Our results
indicated that the plier structure in two ends of the binding interface
plays a key role in the binding process of SARS-CoV-2 RBD with ACE2.
Furthermore, we also found that when there is no B0AT1 in the simulation
system, the N-terminus of ACE2 is more likely to approach the cell
membrane, which has a strong correlation with the subsequent fusion
of the virus with the cell membrane. These binding details of SARS-CoV-2
RBD and the ACE2 protease domain (PD) as well as the membrane orientation
thermodynamics can promote the development of therapeutic drugs and
preventive vaccines against SARS-CoV-2.
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