{"doi":"10.1016/j.jmb.2022.167890","title":"The Integration of Proteome-Wide PTM Data with Protein Structural and Sequence Features Identifies Phosphorylations that Mediate 14-3-3 Interactions","abstract":"14-3-3s are abundant proteins that regulate essentially all aspects of cell biology, including cell cycle, motility, metabolism, and cell death. 14-3-3s work by docking to phosphorylated Ser/Thr residues on a large network of client proteins and modulating client protein function in a variety of ways. In recent years, aided by improvements in proteomics, the discovery of 14-3-3 client proteins has far outpaced our ability to understand the biological impact of individual 14-3-3 interactions. The rate-limiting step in this process is often the identification of the individual phospho-serines/threonines that mediate 14-3-3 binding, which are difficult to distinguish from other phospho-sites by sequence alone. Furthermore, trial-and-error molecular approaches to identify these phosphorylations are costly and can take months or years to identify even a single 14-3-3 docking site phosphorylation. To help overcome this challenge, we used machine learning to analyze predictive features of 14-3-3 binding sites. We found that accounting for intrinsic protein disorder and the unbiased mass spectrometry identification rate of a given phosphorylation significantly improves the identification of 14-3-3 docking site phosphorylations across the proteome. We incorporated these features, coupled with consensus sequence prediction, into a publicly available web app, called \"14-3-3 site-finder\". We demonstrate the strength of this approach through its ability to identify 14-3-3 binding sites that do not conform to the loose consensus sequence of 14-3-3 docking phosphorylations, which we validate with 14-3-3 client proteins, including TNK1, CHEK1, MAPK7, and others. In addition, by using this approach, we identify a phosphorylation on A-kinase anchor protein-13 (AKAP13) at Ser2467 that dominantly controls its interaction with 14-3-3.","journal":"Journal of Molecular Biology","year":2022,"id":273379,"datarank":0.37273599746820013,"base_score":2.4849066497880004,"endowment":2.4849066497880004,"self_citation_contribution":0.37273599746820013,"citation_network_contribution":0.0,"self_endowment_contribution":0.37273599746820013,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":11,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9483,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":940416,"name":"Lynsie R. Warr","orcid":"0000-0003-4204-8689","position":1,"is_corresponding":false},{"id":694976,"name":"Katie L. Pennington","orcid":"0000-0003-2883-0025","position":2,"is_corresponding":false},{"id":940805,"name":"Michele Thornton","orcid":null,"position":3,"is_corresponding":false},{"id":940806,"name":"A.J. Vaughan","orcid":null,"position":4,"is_corresponding":false},{"id":940807,"name":"S.W. Ashworth","orcid":null,"position":5,"is_corresponding":false},{"id":940808,"name":"M.J. Heaton","orcid":null,"position":6,"is_corresponding":false},{"id":940417,"name":"Nolan English","orcid":"0000-0002-9841-0731","position":7,"is_corresponding":false},{"id":574950,"name":"Matthew P. Torres","orcid":"0000-0001-7296-4536","position":8,"is_corresponding":false},{"id":371299,"name":"Joshua L. Andersen","orcid":"0000-0003-2071-744X","position":9,"is_corresponding":false},{"id":655681,"name":"Christina M. Egbert","orcid":"0009-0007-7240-6850","position":0,"is_corresponding":true}],"reference_count":84,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T00:27:52.048702Z","pmid":"36402225","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}