Protein conformational transitions coupled to binding in molecular recognition of unstructured proteins: hierarchy of structural loss from all-atom Monte Carlo simulations of p27Kip1 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 beta-hairpin and beta-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.
Pfizer Global Research and Development, LA Jolla Laboratories, 10614 Science Center Drive, San Diego, CA 92121, USA. gennady.verkhivker@pfizer.com
Gennady M
GM
Verkhivker
D018797:Cell Cycle Proteins / Q000737:chemistry* / Q000378:metabolism; D019295:Computational Biology; D050760:Cyclin-Dependent Kinase Inhibitor p27; D009010:Monte Carlo Method; D011485:Protein Binding; D011487:Protein Conformation; D017510:Protein Folding; D025521:Tumor Suppressor Proteins / Q000737:chemistry* / Q000378:metabolism
D018797:Cell Cycle Proteins; D025521:Tumor Suppressor Proteins; D050760:Cyclin-Dependent Kinase Inhibitor p27