The extended apo-TtClpP was probed in a 1-μs MD simulation. In addition, the computational assay consisting of the protein with zwitterionic alanine tripeptides bound to its 14 serine active sites was examined in three independent, 1-μs MD simulations, using distinct initial conditions. These simulations are aimed at exploring how the presence of the substrate affects the flexibility of TtClpP, alongside the relevance of the alanine tripeptide as a proxy for the peptide chain that binds to the Ser97 active site.