Figure 2.

Schematic representation of the two alternative scenarios of evolution of the modeled system. (a) Stalk-mediated fusion: the distance ∆H between the fusion peptides and the transmembrane domains of the fusion proteins in the membranes is assumed as the reaction coordinate; (b) Formation of the dead-end state (π-shaped structure): the reaction coordinates are the pore radius R_p and the length L of the hydrophobic part of the pore. The transmembrane domains (with the half-width of R_TM) are schematically shown as gray rectangles, the fusion peptides (with the half-width of R_FP) are represented by gray triangles. H₀ is the equilibrium distance between the membranes, ρ is the radius of the hydrophobic spot formed in the area of maximal proximity of the membranes.