Asymmetric Conformational Transitions in AAA plus Biological Nanomachines Modulate Direction-Dependent Substrate Protein Unfolding Mechanisms

Powerful AAA+ biological nanomachines, such as C1pY, form hexameric ring structures, which selectively process abnormal proteins targeted for degradation by unfolding and threading them through a narrow central channel. The molecular details of this process are not yet fully understood. We perform Langevin dynamics simulations using a coarse-grained model of substrate proteins (SPs), Titin 127 and its V13P variant, threading through the ClpY pore. We probe the effect of ClpY surface heterogeneity and changes in pore width on SP orientation and the direction of applied force during SP unfolding. We contrast mechanisms of SP unfolding in a restrained geometry, as in single-molecule force spectroscopy experiments, and in an unrestrained geometry, as in the in vivo degradation process. In open pore configurations, unfolding of unrestrained SPs occurs via an unzipping mechanism, which involves force application along a weak mechanical direction. In the partially closed pore, unfolding occurs via a shearing mechanism, with force application along a strong mechanical direction. By contrast, unfolding of the restrained 127 is limited to a shearing mechanism due to application of force along the strong mechanical direction. We propose that Clp nanomachine plasticity underlies direction-dependent pulling mechanisms that enable versatile SP remodeling actions.