Phosphorylation Variation during the Cell Cycle Scales with Structural Propensities of Proteins

Phosphorylation at specific residues can activate a protein, lead to its localization to particular compartments, be a trigger for protein degradation and fulfill many other biological functions. Protein phosphorylation is increasingly being studied at a large scale and in a quantitative manner that includes a temporal dimension. By contrast, structural properties of identified phosphorylation sites have so far been investigated in a static, non-quantitative way. Here we combine for the first time dynamic properties of the phosphoproteome with protein structural features. At six time points of the cell division cycle we investigate how the variation of the amount of phosphorylation correlates with the protein structure in the vicinity of the modified site. We find two distinct phosphorylation site groups: intrinsically disordered regions tend to contain sites with dynamically varying levels, whereas regions with predominantly regular secondary structures retain more constant phosphorylation levels. The two groups show preferences for different amino acids in their kinase recognition motifs - proline and other disorder-associated residues are enriched in the former group and charged residues in the latter. Furthermore, these preferences scale with the degree of disorderedness, from regular to irregular and to disordered structures. Our results suggest that the structural organization of the region in which a phosphorylation site resides may serve as an additional control mechanism. They also imply that phosphorylation sites are associated with different time scales that serve different functional needs. Cells employ protein phosphorylation – the addition of a phosphate group to serine, threonine or tyrosine residues – as a key regulatory mechanism for modulating protein function. Proteomics technologies can now quantify thousands of phosphorylation sites to reveal the dynamics of phosphorylation at each site in response to a biological process. It is known that phosphorylation does not occur randomly with regard to a protein's structure, but so far the relationship between the dynamics of phosphorylation and these structural properties has not been investigated. Here we relate the relative levels of phosphorylation for more than 5,000 sites through the cell cycle to the predicted structural features of the vicinity of the sites. We find that dynamic phosphorylation tends to occur in disordered regions, whereas phosphorylation sites that did not vary as much over the cell cycle are often located in defined secondary structure elements. Kinases that prefer charged amino acids in their substrate motives are more often associated with unchanging sites whereas proline-directed protein kinases phosphorylate cell cycle regulated sites in disordered regions more frequently. The structural organization of the region in which a phosphorylation site resides may therefore serve as an additional control mechanism in kinase mediated regulation.