Figure 21. Comparison of our model of a nonamer α-Syn channel to the
structure of Lysenin. (a & b) Side and top views of ribbon
representations of an atomic scale model of the α-Syn channel. The
ribbons are colored by a rainbow spectrum beginning with red for the
N-termini and ending with magenta for the C-termini. c) Atomic-force
microscopy (AFM) image of the extracellular domain of an α-Syn channel
(Adapted from Quist et al. [21]. The ovals represent outlines of the
Nt (black) and Ct (white) β-barrel walls of the model. (c & d) Side and
top views of a cryo-EM-determined structure of Lysenin [31]. e) An
AFM image of the extracellular domains of a Lysenin channel (Adepted
with permission from Podobnik M, Savory P, Rojko N, et al [66].
Positioning the outer barrel to reduce clashes among side chains while
maintaining the radial symmetry permits H-bonding between the strands of
each barrel to be maintained while eliminating empty space between the
barrels (Figs. 22 d & f). This tight packing is possible because the
majority of side-chains between the barrels are small and the pitches of
the pleats are similar enough (7.8 and 7.0 nm) for intermeshing-pleats.
The distance between the walls of the middle and tentative outer Ct
barrel is greater (~ 1.2 nm) and the side-chains are
larger and more polar. Excluding the last four resides where the
conformation is most ambiguous, all charged side chains inside the Ct
barrel (D98, K102, E104, D115, E126, E131, D135) form at least one salt
bridge with oppositely charged side-chains of the Nt domain.