Accurate, high-coverage assignment of in vivo protein kinases to phosphosites from in vitro phosphoproteomic specificity data

Abstract

Phosphoproteomic experiments routinely observe thousands of phosphorylation sites. To understand the intracellular signaling processes that generated this data, one or more causal protein kinases must be assigned to each phosphosite. However, limited knowledge of kinase specificity typically restricts assignments to a small subset of a kinome. Starting from a statistical model of a high-throughput, in vitro kinase-substrate assay, I have developed an approach to high-coverage, multi-label kinase-substrate assignment called IV-KAPhE (“In vivo-Kinase Assignment for Phosphorylation Evidence”). Tested on human data, IV-KAPhE outperforms other methods of similar scope. Such computational methods generally predict a densely connected kinase-substrate network, with most sites targeted by multiple kinases, pointing either to unaccounted-for biochemical constraints or significant cross-talk and signaling redundancy. I show that such predictions can potentially identify biased kinase-site misannotations within families of closely related kinase isozymes and they provide a robust basis for kinase activity analysis.

The substrate quality of CK2 target sites has a determinant role on their function and evolution

“…Most trivially, a small number could be explained by literature curation errors from databases of kinase-substrate relationships (KSRs) such as PhosphoSitePlus and Signor (Hornbeck et al 2015;Needham et al 2019;Licata et al 2020;Invergo 2022;Bachman, Gyori, and Sorger 2022). A potentially larger number of motifs are minimal in the primary structure but can be reconstituted as full motifs when the target sequence folds in three dimensions to accommodate the substrate-binding pockets of the kinase (Chihao Duarte et al 2014;Oliveira et al 2016).…”