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The three-stage "minimal" kinetic scheme with first and second reversible steps of substrate binding and with following irreversible peptide cleavage step adequately described experimental data.
The microtubular cytoskeleton may participate mainly in later stages of invadopodia extension or subsequent cell migration rather than the early steps of substrate invasion per se[ 26, 193].
One of the referee's concerns is that the authors over-interpret the steps of substrate release and binding, given the lack of an apo structure.
The closed conformation is stabilized by hydrogen bonds between the cofactor and the peptide backbone, whereas stabilization of the open form may be advantageous during the initial steps of substrate binding since it is believed to slow down product dissociation.
Although the steps of substrate capture and product release are essential in the enzymatic process, complete atomic-level descriptions of these steps are difficult to obtain because of the transient nature of the intermediate conformations, which makes them largely inaccessible to standard structure determination methods.
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This behavior is found to be limited to films on small-angle steps, suggesting the incorporation of defects near the steep steps of substrates.
Note that only the step of substrate unfolding requires energy from ATP hydrolysis, while ATP-binding alone can support all the other steps required for protein degradation (e.g., complex assembly, gate opening, translocation, and proteolysis).
NMR spin relaxation studies performed by Kern and coworkers linked the motions of several residues with the substrate turnover step in cyclophilin A, and also indicated that the rate of enzyme conformational changes coincides with the rate-limiting step of substrate turnover [14], [20], [26].
The step of substrate recognition has been studied in ClpA from E. coli.
4) Although not necessary, have the authors considered experiments to show that the initial binding step of substrate is unaffected by the N44A mutation, as would be predicted since the ground state is unaffected?
4) Although not necessary, have the authors considered experiments to show that the initial binding step of substrate is unaffected by the N44A mutation, as would be predicted since the ground state is unaffected? 1) One weakness identified by the reviewers is that it is only a speculation that the ligand is more loosely bound in the "unlocked" state.
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