Fig. 3.
Vesicle fusion reaction mechanism and kinetics. (a) A schematic of the fusion reaction mechanism as determined by MSM. All reactions with probabilities >5% are shown with rates as calculated from the MSM transition matrix. In our simulations, fusion proceeds via a stalk-like intermediate state. We also observe a long-lived off-pathway intermediate that is hemifused, which slowly converts to the fused state (dashed line). Error estimation for calculated rates is given in Table 2, which is published as supporting information on the PNAS web site. (b) The reaction kinetics for fusion over multimillisecond time scales as determined from our simulations. The hemifused intermediate state dominates on the microsecond time scale, with a decay t1/2 of 6.3 μs. On the 10-μs time scale, the fused state dominates. (Inset) The formation of transient intermediates at early times. Dashed lines show 90% confidence bounds. (c) Free energy values calculated from the long-time scale kinetic model for each state identified via k-means clustering. Error bars denote 90% confidence intervals.