Atomistic Simulations of Ion Channels - Computational Neuroscience: A Comprehensive Approach - page 53

Figure 2.7
Electrostatic potential profiles calculated from the linear Poisson-Boltzmann equa-
tion (A-C) and the non-linear Poisson-Boltzmann equation (D-F) for three different
values of the ionic strengths and different Stern radius values (solid line 1 A, dotted
2 A, long dashed 3 A). Linear: A) 10 mM; B) 100 mM; C) 1 M; non-linear: D) 10
mM; E) 100 mM; and F) 1M. Reproduced with permission from [115].

(linearized or non-linear PB calculation) and the Stern exclusion radius (a zone in
which no ions are assumed to be present). These calculations did not consider differ-
ent choices of dielectric constants, although these are non-trivial. In the reasonable
case in Figures 2.7D, 2.7E, 2.7G PB calculations on models of the octameric channel
predict an average of 2 to 4 Cl − ions near the lysine residues as a function of ionic
strength, comparable to the numbers found from MD simulations.
These counterions lower the apparent charge of the channel, which may underlie
the decrease in selectivity observed experimentally with increasing salt concentra-
tions. We suggested that to increase the selectivity of Alm K18 channels, positive
charges could be engineered in a narrower part of the channel. Because Alm K18
is essentially a designer channel, and artificially synthesized, new versions of this
channel can be created, redesigned with the knowledge of the simulations in mind.

2.3.4 OmpF

Porins form large trimeric pores in the outer membrane of Gram-negative bacte-
ria, which passively transport small molecules down their concentration gradients.
They can either be general porins or transport specific substrates such as maltose.
OmpF is a general diffusion pore from the outer membrane of E. coli that transports