Figure 5.
Free energy profiles along three reaction coordinates at T = 0.85 TC. The continuous lines are spline fits to the free energy data (crosses). To obtain free energy differences between two states, we estimate the reversible work that has be done to go from one state to the other. For this purpose, we fix the z coordinate of a specific residue in order to compute the canonical average of the force and then apply Eq. 2 (see Appendix). The free energy of the native state is defined to be equal to 0. (a) Free energy as a function of the z coordinate of the 58th residue (z = 0 corresponds to the middle of the membrane) starting from HV; this forces the second helix to cross the membrane as the protein goes from HV to N; the local minimum at z ≃ 20 corresponds to a state topologically equivalent to HV, with the helix containing the 58th residue fully formed on the membrane interface but without any contact with the first helix (in HV some of the interhelices contacts are already formed); (b) the 5th residue is translocated across the membrane with the protein starting from state HI and proceeding to HV; (c) the same as in b, but the initial state is I (see Fig. 2a).