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. 2015 Sep 1;109(5):922–935. doi: 10.1016/j.bpj.2015.07.040

Figure 4.

Figure 4

Time dependence of the reaction coordinate Zmin of a β2e subunit (1–143) binding to membrane phospholipids, from a multiscale MD simulation of β2e. (A) Reconstructed structure of a β2e N-terminal domain (yellow cartoon) near the plasma membrane (cyan sticks and red and green balls). (B and C) Reaction coordinates Zmin for a β2e subunit (1–143) as a function of time for (B) the 100 ns ATMD simulation, which shows the initial decrease of Zmin during the 100 ns period, and (C) the 1.5 μs CGMD simulation, which shows the overall convergence of Zmin to ∼20 Å in the long time limit. (D) The free-energy landscape in a thermal energy unit –ln p[Zmin] is plotted as a function of Zmin for the 100 ns ATMD (red line) and 1.5 μs CGMD (blue line) simulations. The position of the minimum of –ln p[Zmin], i.e., the most probable value of the reaction coordinate, shows the overall convergence to ∼20 Å. The scale of free energy –ln p[Zmin] is in the thermal energy unit. To see this figure in color, go online.