Protein conformational transitions coupled to binding in molecular recognition of unstructured proteins: Hierarchy of structural loss from all‐atom Monte Carlo simulations of p27 Kip1 unfolding–unbinding and structural determinants of the binding mechanism

Conformational transitions coupled to binding are studied for the p27 Kip1 protein which undergoes a functional disorder–to–order folding transition during tertiary complex formation with the phosphorylated cyclin A–cyclin‐dependent kinase 2 (Cdk2) binary complex. Temperature–induced Monte Carlo simulations of p27 Kip1 unfolding–unbinding carried out from the crystal structure of the tertiary complex have revealed a systematic trend in the hierarchy of structural loss for p27 Kip1 and a considerable difference in mobility of p27 Kip1 secondary structure elements. The most persistent interactions of p27 Kip1 at the intermolecular interface during unfolding–unbinding simulations are formed by β‐hairpin and β–strand that on average maintain their structural integrity considerably longer than other p27 Kip1 elements. We have found that the ensemble of unfolded p27 Kip1 conformations is characterized by transitions between mostly unbound, collapsed conformations and entropically favorable p27 Kip1 conformations, which are weakly bound to the cyclin A side of the binary complex. The results of this study are consistent with the experimental evidence pointing to this region of the intermolecular interface as a potential initiation docking site during binding reaction and may reconcile conflicting experimental hypotheses on the recognition of substrate recruitment motifs. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004