Fig. 2
Structure of melittin-double-stranded DNA (dsDNA) complexes from molecular simulations. a Side and top views of the melittin protofibril self-assembled in the presence of dsDNA. The cross-sectional dimensions of the protofibril is 2.7 nm × 2.7 nm. The helical pitch of the protofibril is 3.28 nm per turn. Top (b) and side (c) views of an 8 × 8 melittin-dsDNA square lattice from molecular dynamics simulations. Columnar dsDNA is colored red, and the melittin protofibril is colored green (N to C terminus polarity) and teal (C to N terminus polarity). Random polarity of the melittin protofibril is assumed. The inter-dsDNA spacing from the molecular model obtained from simulation is d = 3.64 nm, which agrees well with the predicted inter-dsDNA spacing from small-angle X-ray scattering (SAXS). The out-of-plane lattice parameter of c = 3.28 nm also agrees with the simulated pitch of the melittin protofibril. d There is good agreement between the observed structure factor peaks from SAXS with peaks recovered from theoretical X-ray scattering of the lattice model in b and c from CRYSOL58
