The Integration of Proteome-Wide PTM Data with Protein Structural and Sequence Features Identifies Phosphorylations that Mediate 14-3-3 Interactions

被引:7
作者
Egbert, C. M. [1 ]
Warr, L. R. [2 ]
Pennington, K. L. [1 ,3 ]
Thornton, M. M. [4 ]
Vaughan, A. J. [1 ]
Ashworth, S. W. [1 ]
Heaton, M. J. [2 ]
English, N. [5 ]
Torres, M. P. [5 ,6 ]
Andersen, J. L. [1 ]
机构
[1] Brigham Young Univ, Dept Chem & Biochem, Fritz B Burns Canc Res Lab, Provo, UT 84604 USA
[2] Brigham Young Univ, Dept Stat, Provo, UT USA
[3] Longwood Univ, Dept Biol & Environm Sci, Farmville, VA USA
[4] Brigham Young Univ, Dept Comp Sci, Provo, UT USA
[5] Georgia Inst Technol, Quantitat Biosci Program, Atlanta, GA USA
[6] Georgia Inst Technol, Sch Biol Sci, Atlanta, GA USA
关键词
INTRINSIC DISORDER; NITRATE REDUCTASE; CRYSTAL-STRUCTURE; LIGAND-BINDING; HUMAN CDC25C; DNA-DAMAGE; LOCALIZATION; DEPHOSPHORYLATION; SURVIVAL; SITES;
D O I
10.1016/j.jmb.2022.167890
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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 phosphoserines/threonines that mediate 14-3-3 binding, which are difficult to distinguish from other phosphosites 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 pro-tein 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. (C) 2022 The Author(s).
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页数:17
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