Intrinsic disorder mediates the diverse regulatory functions of the Cdk inhibitor p21

Abstract

Traditionally, well-defined three-dimensional structure was thought to be essential for protein function. However, myriad biological functions are performed by highly dynamic, intrinsically disordered proteins (IDPs). IDPs often fold upon binding their biological targets and frequently exhibit “binding diversity” by targeting multiple ligands. We sought to understand the physical basis of IDP binding diversity and herein report that the cyclin-dependent kinase (Cdk) inhibitor, p21Cip1, adaptively binds to and inhibits the various Cdk/cyclin complexes that regulate eukaryotic cell division. Based on results from NMR spectroscopy, and biochemical and cellular assays, we show that structural adaptability of a helical sub-domain within p21 termed LH enables two other sub-domains termed D1 and D2 to specifically bind conserved surface features of the cyclin and Cdk subunits, respectively, within otherwise structurally distinct Cdk/cyclin complexes. Adaptive folding upon binding is likely to mediate the diverse biological functions of the thousands of IDPs present in eukaryotes.

Tyrosine Phosphorylation of the p21 Cyclin-dependent Kinase Inhibitor Facilitates the Development of Proneural Glioma

“…3A). This indicates that the phosphorylation state of p21 does not affect binding, consistent with recent studies by Kriwacki and co-workers (33).…”

“…Neither mutation altered binding of p21 to cyclin-CDK complexes (Fig. 5B), which requires subdomains D1 and LH and the ␤-hairpin and ␤-strand of subdomain D2 (14,33,35). These mutations did not alter the subcellular localization of the protein (Fig.…”

“…5A), consistent with the notion that these interactions are necessary for complete inhibition. Residual inhibitory activity in the Y76E mutant might be due to structural distortion of the CDK (2,33). Neither mutation altered binding of p21 to cyclin-CDK complexes (Fig.…”

The CDK4/CDK6 inhibitor PD0332991 paradoxically stabilizes activated cyclin D3-CDK4/6 complexes

“…p21 and p27 bind the CDK moiety of cyclin-CDK complexes by inserting their 3 10 helix into the catalytic ATP-binding cleft, thus inhibiting the activity. [57][58][59] It is therefore likely that PD0332991, as a high affinity ATP-competitive drug, would also compete for p21/p27 binding to CDK4 and CDK6. Moreover, PD0332991 appeared to somehow mimic the effect of p21 binding as a stabilizing factor for cyclin D3-CDK4/6 complexes.…”

Disorder-function relationships for the cell cycle regulatory proteins p21 and p27

“…Nonetheless, studies of well characterized examples do provide insights into ' disorder-function relationships ' from which general concepts have emerged. Domains within the cell cycle regulatory IDPs, p21 Cip1 (p21) and p27 Kip1 (p27), bind several different cyclin-dependent kinase (Cdk)/cyclin complexes through structural adaptation to accommodate similar but topologically distinct binding sites (Wang et al , 2011 ). This system illustrates the ability of a disordered domain to bind promiscuously to multiple targets, a feature exhibited by many IDPs.…”