posted on 2021-06-10, 13:05authored byNisha Bhattarai, Prabin Baral, Bernard S. Gerstman, Prem P. Chapagain
The
novel coronavirus (SARS-CoV-2) pandemic that started in late
2019 is responsible for hundreds of millions of cases worldwide and
millions of fatalities. Though vaccines are available, the virus is
mutating to form new strains among which are the variants B.1.1.7
and B.1.351 that demonstrate increased transmissivity and infectivity.
In this study, we performed molecular dynamics simulations to explore
the role of the mutations in the interaction of the virus spike protein
receptor binding domain (RBD) with the host receptor ACE2. We find
that the hydrogen bond networks are rearranged in the variants and
also that new hydrogen bonds are established between the RBD and ACE2
as a result of mutations. We investigated three variants: the wild-type
(WT), B.1.1.7, and B.1.351. We find that the B.1.351 variant (also
known as 501Y.V2) shows larger flexibility in the RBD loop segment
involving residue K484, yet the RBD–ACE2 complex shows higher
stability. Mutations that allow a more flexible interface that can
result in a more stable complex may be a factor contributing to the
increased infectivity of the mutated variants.