Identifying the Structural and Evolutionary Constraints of Post-Translational Modifications

The objective of this work is to investigate structural and evolutionary constraints on post-translational modification (PTM) sites and their flanking regions beyond the phosphoproteome. An analysis of 21 PTM types including phosphorylation, acetylation, ubiquinitation, and methylation was conducted based on 400,000 high quality, in vivo PTM sites from PhosphoSitePlus. State of the art computational methods and cloud-based computing aided in the large-scale secondary structure prediction of the entire human proteome and generation of millions of global pairwise alignments between orthologs in 143 eukaryote species ranging from chimpanzee to yeast. We found that the majority of PTMs exhibit a significantly higher level of accessibility and prefer the localization in unstructured regions of a protein. Furthermore, we found that PTMs are more conserved at both the protein and residue level when compared with their unmodified counterparts. The conservation pattern of flanking residues, critical for transferase recognition, agrees with the evolutionary profile observed for PTM sites. Our study provides previously unknown insight into structural and evolutionary constraints of PTMs, laying the foundation for future work such as mutation effect prediction models.