Phosphorylation is one of the most frequent protein modifications in living organisms. Phosphorylation profile has been interpreted as a “molecular barcode” to trigger protein activation, inactivation, translocation, interaction with other proteins and degradation. Phosphorylation-triggered degradation process is a common strategy for elimination of regulatory proteins including cyclin-dependent kinase inhibitors such as Sic1 in yeast and p27 in mammalian cells. Reduced p27 expression is observed in up to 60% of primary human breast cancers, which has been correlated with increased activity of a kinase family.

In this work, phosphorylation-triggered protein degradation has been modeled and analyzed in a systematic approach. Our simulation results show that while a single-site protein does not degrade in an ultrasensitive manner, multisite phosphorylation can lead to thresholding for degradation and causes a switch-like elimination. Switch-like responses are required for binary decisions in the cell cycle transitions and apoptosis. The effects of different parameters and ordering on ultrasensitivity of protein elimination in response to kinase have also been investigated. The ultrasensitivity of the response curve is at maximum when protein degrades after becoming phosphorylated on half of its total sites. With regard to ordering effect, the elimination curve of a multisite protein phosphorylated sequentially is more switch-like than that of a protein phosphorylated randomly.

Other kinds of modification such as ubiquitination, methylation and glycosilation which are involved in tuning macromolecules' stability, activity and translocation can also be explained by the model presented in this work. Generally, multi-site modification provides a precise mechanism for controlling the speed and sharpness of the output in response to an input of stimulus. By using multisite modification of a macromolecule, a gradually changing input signal can be converted into an ultrasensitive output signal. Such single-molecule based switches could also provide a powerful tool for tuning gene expression and protein activity.