2.A.6.4.3
Protein translocase subunit SecDF.  The 3-dimensional structure is known at 3.3 Å resolution (Tsukazaki et al. 2011).  SecDF serves several functions, such as stabilizing other Sec translocon components within the membrane, maintaining the transmembrane (TM) potential, and facilitating the ATP-independent stage of the translocation mechanism. SecDF also undergoes functionally important conformational changes that involve mainly its P1-head domain, and these changes are coupled with the proton motive force (Δpmf). Using all-atom molecular dynamics simulations combined with umbrella sampling, Ficici et al. 2017 studied the P1-head conformational change and how it is coupled to the pmf. They reported potentials of mean force along a root-mean-square-distance-based reaction coordinate obtained in the presence and absence of the TM electrical potential. Their results showed that the interaction of the P1 domain dipole moment with the TM electrical field lowers the free-energy barrier in the direction of the F-form to I-form transition, two conformations that vary by the relative positioning of the P1-head subdomain—the large periplasmic domain of TtSecDF—which is suggested to undergo a hinge motion (Ficici et al. 2017).