Nonamer channel
Next we developed atomic scale models of the nonamer channel using S/N =
4/3 for the second β-barrel as occurs in the Lysenin structure. Upon
examining these models, however, we observed a substantial amount of
empty space between the two barrels. Reducing S/N of the middle barrel
to 2/3 (the next value permissible for 9-fold symmetry with a
three-stranded subunit) reduces the diameter of this barrel by
~1.2 nm, leaving a gap distance between the walls of the
two barrels of only 0.6 nm, the lowest gap distance we allow.