Figure 5.

The design and in silico testing of the Cpx poor-clamp and super-clamp mutants. A, The poor-clamp mutant is designed to disrupt the RQ motif within the Cpx AH, which maintains the interactions between the Cpx AH and the unraveled n-syb terminus. B, The super-clamp mutant is designed to disrupt the IK motif maintaining the interactions between the Cpx AH and the zippered part of the SNARE bundle. C, MD simulations of the native and mutated complexes show that the super-clamp mutant maintains the separation between the unraveled n-syb C terminus and the SNARE bundle, while the poor-clamp mutant does not. The graph shows the distance between C_α atoms of the C-terminal residues of n-syb and Syx over the length of the 1.2-μs MD trajectory. Trajectory points are separated by 240 ps. D, Structures of the mutated and native Cpx complexes in the end of respective MD trajectories. Note the unraveled C terminus of n-syb and the Cpx AH tightly interacting with the SV bilayer in the super-clamp mutant. In contrast, in the poor-clamp mutant, the C terminus of n-syb separated from the SV bilayer and started forming contacts with t-SNARE.