Intrinsic Dynamics of the ClpXP Proteolytic Machine Using Elastic Network Models

Abstract

ClpXP complex is an ATP-dependent mitochondrial matrix protease that binds, unfolds, translocates, and subsequently degrades specific protein substrates. Its mechanisms of operation are still being debated, and several have been proposed, including the sequential translocation of two residues (SC/2R), six residues (SC/6R), and even long-pass probabilistic models. Therefore, it has been suggested to employ biophysical–computational approaches that can determine the kinetics and thermodynamics of the translocation. In this sense, and based on the apparent inconsistency between structural and functional studies, we propose to apply biophysical approaches based on elastic network models (ENM) to study the intrinsic dynamics of the theoretically most probable hydrolysis mechanism. The proposed models ENM suggest that the ClpP region is decisive for the stabilization of the ClpXP complex, contributing to the flexibility of the residues adjacent to the pore, favoring the increase in pore size and, therefore, with the energy of interaction of its residues with a larger portion of the substrate. It is predicted that the complex may undergo a stable configurational change once assembled and that the deformability of the system once assembled is oriented, to increase the rigidity of the domains of each region (ClpP and ClpX) and to gain flexibility of the pore. Our predictions could suggest under the conditions of this study the mechanism of the interaction of the system, of which the substrate passes through the unfolding of the pore in parallel with a folding of the bottleneck. The variations in the distance calculated by molecular dynamics could allow the passage of a substrate with a size equivalent to ∼3 residues. The theoretical behavior of the pore and the stability and energy of binding to the substrate based on ENM models suggest that in this system, there are thermodynamic, structural, and configurational conditions that allow a possible translocation mechanism that is not strictly sequential.

Allosteric communication in the gating mechanism for controlled protein degradation by the bacterial ClpP peptidase

“…To glean the collective motions of ClpP protomers underlying the gate-opening transition, we use Normal Mode Analysis (NMA) and Principal Component Analysis (PCA) (see the Methods section). These approaches have proved highly effective in studies of conformational changes and dynamics of multisubunit biomolecules, such as the ring-shaped chaperonins, ClpXP or immunoglobulin 45,[89][90][91][92] . We use these analysis methods in conjunction to obtain detailed information about the collective motions, as inter-residue couplings in NMA are restricted to an elastic network model of the native protein structure, whereas in PCA they reflect dynamic, i.e.…”