56 / 119
Emerging Concepts in Ion Channel Biophysics
Poster Abstracts
51
37-POS
Board 37
Characterizing the Permeation and Na
+
/Ca
2+
Selectivity Mechanism of NaChBac Channel:
a Computational Study
Carlo Guardiani
, Igor Khovanov.
Warwick University, Coventry, United Kingdom.
NaChBac was the first discovered sodium voltage dependent channel, yet computational studies
are still limited due to the lack of a crystal structure. In this work a pore-only construct built
using the NavMs template was investigated using unbiased Molecular Dynamics and
Metadynamics. When the system is simulated in NaCl the Selectivity Filter becomes stably
occupied by two ions and frequent events of access of a third ion can be observed. The Potential
of Mean Force (PMF) from metadynamics shows a single deep minimum due to the presence of
an energy barrier that prevents permeation by a single Na
+
ion. This hypothesis was confirmed
by a 2D-metadynamics simulation where 2 Na
+
ions were biased to explore the SF. The analysis
of the resulting PMF revealed a knock-on permeation mechanism involving two, but possibly
also three ions. Conversely, when the channel is simulated in CaCl2 the SF becomes occupied by
a single ion that remains blocked inside. There are two reasons for the inability of Ca
2+
to
permeate NaChBac. First of all, the free energy of binding of Ca
2+
to the SF, that we computed
through the free energy perturbation approach, is 3.5 times higher than that of Na+, leading to a
stronger attraction to the glutamates of the EEEE-ring. Second, using metadynamics simulations
with a fixed ion and a mobile ion, we showed that a Ca
2+/
Ca
2+
knock-on mechanism can not
occur due to the high repulsion energy that the resident ion exerts on a second, potentially
incoming ion. Our work thus, provides an alternative scenario with respect to the traditional view
of the Ca-exclusion model that postulates the inability of Ca
2+
to bind to the Selectivity Filter of
sodium channels.