Asymmetric Nature of MscL Opening Revealed by Molecular Dynamics Simulations

The bacterial mechanosensitive channel, MscL, opens in
response
to elevated membrane tension during osmotic shock. Some mutations,
like L17A and V21A, can reduce the activation tension threshold, thus
offering an approach to study the mechanism of MscL gating. We employed
all-atom molecular dynamics to simulate the L17A, V21A double mutant
of MscL under a tension of 30 mN/m. Under these conditions, the closed
state initially adopts a funnel-like conformation. Subsequently, five
chains of MscL undergo sequential transitions into asymmetric states
(S1, S2, etc.). Within its “open” fragment, the S1 state
is similar to the expanded state of Methanosarcina
acetivorans MscL and has a conductance 10 times lower
than the open state. We applied committor analysis and a nonlinear
regression model to construct a reaction coordinate for the transition
between the closed and the S1 state as a linear combination of interatomic
distances and contacts. The main contributions to the reaction coordinate
are (1) the disruption of the “cytoplasmic” contact
sites between the considered chain and two adjacent chains, (2) the
delipidation of the lipid-binding pocket, formed by the I82, V86,
and V22 residues, and (3) pulling the two neighboring chains apart
via the tension sensors. The free energy profile along the reaction
coordinate was calculated using the umbrella sampling approach. The
S1 state is approximately 5 kJ/mol more favorable than the closed
state under tension. The height of the free energy barrier for the
transition toward the S1 state is approximately 10 kJ/mol, which is
in reasonable agreement with the corresponding average transition
time, estimated to be 133 ± 13 ns. The results and approach can
be employed to elucidate the wild-type protein gating mechanism.