Bioinformatics Analysis Of Ubiquitination And Pupylation

Post-translational modifications (PTMs) are critical to protein maturation, protein structure and protein function. Now PTMs exist ubiquitously in vivo with dynamic diversity, making them very difficult to study with traditional methods. Recently it is becoming faster in PTMs study, for besides experimental strategy, numerous computational predictors implemented in various algorithms have been developed for post-translational modification sites prediction.Ubiquitination, a very important post-translational modification, plays a significant role in many biological processes. As a kind of E3 liagse,β-TrCP (beta-transducin repeat-containing protein) recognizes some special substrates and mediates their ubiquitination and proteasomal degradation. In this study, we designed a novel computational tool of GPS-BeTrIP 1.0 for the prediction ofβ-TrCP binding sites. In addition we selected hAnkra2, hNudc, hTrf1 from the prediction results of GPS-BeTrIP 1.0 to investigate their interactions withβ-TrCP. In vitro and in vivo experimental assays demonstrated that human hAnkra2 and hNudc are novel interacting partners ofβ-TrCP, while S280 and S284 of Ankra2 play a significant role in degradation mediated byβ-TrCP.In recent study, PUP (prokaryotic ubiquitin-like protein) was identified to function in a manner analogous to ubiquitin for proteasome-dependent degradation in prokaryotes. We designed a novel computational tool of GPS-PUP 1.0 for the prediction of pupylation sites, which was shown to have a promising performance. We also collected 238 potentially pupylated substrates for which the exact pupylation sites were still not determined. As an example application, we predicted ~85% of these proteins with at least one potential pupylation site. In addition, we annotated these potential pupylation substrates with GO (Gene Ontology). Through functional analysis, we observed that pupylation can target various substrates so as to regulate a broad array of biological processes, such as the response to stress and metabolism.Taken together, our systematic analysis of these post-translational modifications provides reliable resource and will propel the related researches into a new phase.