The Role of Dynamic Protein Complexes in the Ubiquitin-Proteasome Pathway

Abstract

Intrinsically disordered proteins (IDPs) have been implicated in the regulation of many important cellular processes, such as regulation of cell cycle progression, of transcription and of translation. IDPs are thought to function primarily in the mediation of protein-protein interactions, but detailed analysis of the molecular mechanisms that render disorder beneficial in protein interactions is required. According to a common view, IDPs are usually thought to undergo disorder-to-order transitions upon interaction with their binding partners. It is becoming increasingly clear that predominantly disordered protein complexes are functionally relevant. We have shown previously that the intrinsically disordered cyclin dependent kinase (CDK) inhibitor Sic1 interacts with the substrate adapter, Cdc4, of its ubiquitin ligase via multiple phosphorylated binding motifs in a dynamic complex. Cdc4 is the substrate recognition subunit of a culin ubiquitin ligase and targets Sic1 for degradation at the G1/S phase transition of the yeast cell cycle. Individual binding motifs in Sic1 are ordered transiently without a global disorder-to-order transition upon binding Cdc4. The dynamic complex allows for engagement of several phosphorylation sites in a dynamic interface resulting in an affinity that depends on the number of phosphorylation sites in an ultrasensitive manner. The dynamic nature of the complex allows for ‘counting’ of phosphorylation sites via largely electrostatic interactions. The Sic1-Cdc4 interaction therefore acts as a sensor of the concentration of active kinase and the cell cycle status. We continue to use NMR spectroscopy and other biophysical methods to study dynamic interactions in the ubiquitin proteasome pathway with the objective of unraveling nature's repertoire of disorder in protein function. The combination of disorder with multi-site phosphorylation may serve as a general means to set thresholds in regulated protein-protein interactions.