Is the G‑Quadruplex an Effective Nanoconductor for Ions?

We use a stepwise pulling protocol
in molecular dynamics simulations
to identify how a G-quadruplex selects and conducts Na+, K+, and NH4+ ions. By estimating
the minimum free-energy changes of the ions along the central channel
via Jarzynski’s equality, we find that the G-quadruplex selectively
binds the ionic species in the following order: K+ >
Na+ > NH4+. This order implies
that K+ optimally fits the channel. However, the features
of the
free-energy profiles indicate that the channel conducts Na+ best. These findings are in fair agreement with experiments on G-quadruplexes
and reveal a profoundly different behavior from the prototype potassium-ion
channel KcsA, which selects and conducts the same ionic species. We
further show that the channel can also conduct a single file of water
molecules and deform to leak water molecules. We propose a range for
the conductance of the G-quadruplex.