Figure 6. Analysis of our simulations mimics experimental biochemical measurements of Gag dimerization as a function of time, agreeing for moderately stable lattices.

(A) Percent of tagged Gag molecules that have formed a dimer (involving a SNAP-tag and HALO-tag plus linker) as a function of time. Here, 10% of Gag monomers were initially tagged either HALO or SNAP. As the hexamer stability ΔG_hex increases, the dimerization yield dramatically slows. The dashed lines are linear fits of the last 1s of the curves. Results averaged over all 60 traces per parameter set. (B) Yield of dimers formed at 3 min estimated via simple linear extrapolation. Our results represent an upper bound. Dashed black line is the experimental measurement of the dimer formation at 3 min given 10% tagged populations. Fast (black), moderate (red), and slower (cyan) rate constants. With the most stable lattices and slowest rates, dimer yield is too low compared to experiment. (C) Dimer yield as we increase the population of initially tagged Gag monomers from 5% to 40%. Red is simulated yield at 20 s (to avoid extrapolation assumptions), and black is experimental yield at 3 min. We normalize the yield by the value at tagged Gag = 10%, given the different time points used.