14-3-3-Pred: improved methods to predict 14-3-3-binding phosphopeptides

Abstract

Motivation: The 14-3-3 family of phosphoprotein-binding proteins regulates many cellular processes by docking onto pairs of phosphorylated Ser and Thr residues in a constellation of intracellular targets. Therefore, there is a pressing need to develop new prediction methods that use an updated set of 14-3-3-binding motifs for the identification of new 14-3-3 targets and to prioritize the downstream analysis of >2000 potential interactors identified in high-throughput experiments.Results: Here, a comprehensive set of 14-3-3-binding targets from the literature was used to develop 14-3-3-binding phosphosite predictors. Position-specific scoring matrix, support vector machines (SVM) and artificial neural network (ANN) classification methods were trained to discriminate experimentally determined 14-3-3-binding motifs from non-binding phosphopeptides. ANN, position-specific scoring matrix and SVM methods showed best performance for a motif window spanning from −6 to +4 around the binding phosphosite, achieving Matthews correlation coefficient of up to 0.60. Blind prediction showed that all three methods outperform two popular 14-3-3-binding site predictors, Scansite and ELM. The new methods were used for prediction of 14-3-3-binding phosphosites in the human proteome. Experimental analysis of high-scoring predictions in the FAM122A and FAM122B proteins confirms the predictions and suggests the new 14-3-3-predictors will be generally useful.Availability and implementation: A standalone prediction web server is available at http://www.compbio.dundee.ac.uk/1433pred. Human candidate 14-3-3-binding phosphosites were integrated in ANIA: ANnotation and Integrated Analysis of the 14-3-3 interactome database.Contact: cmackintosh@dundee.ac.uk or gjbarton@dundee.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online.

AMP‐activated protein kinase: a cellular energy sensor that comes in 12 flavours

“…As an example, Figs 1B, 1C and 2B illustrate criterion (c) for the c subunits, criterion (a) for the a subunits, and criterion (d) for all three subunits, respectively. This is in keeping with the observation that the few thousand families of 2R-ohnologues retained in modern-day vertebrates are highly enriched in genes encoding regulatory proteins, including cytokines, growth factors, ion channels, receptors, G proteins, regulated metabolic enzymes, transcription factors and protein kinases [13][14][15][16]. One implication of this is that the 2R-WGD provided an evolutionary leap in cellular communication; a quadrupling of the signalling pathways available to our last common invertebrate ancestor may have enabled the great increase in complexity and variety of the vertebrates that followed.…”

Enhancement of mitochondrial biogenesis and paradoxical inhibition of lactate dehydrogenase mediated by 14‐3‐3η in oncocytomas

“…As members of the 14-3-3 family commonly function by interacting with their target proteins, and could interfere with the ubiquitination of proteins such as c-Myc [30], we hypothesized that 14-3-3η could also bind to LDHA and affect LDHA degradation through a similar mechanism. Two phosphorylated sites (CKLLIV[S]NPVD and IKLKGY[T]SWAI) in LDHA were predicted to be recognized by 14-3-3η according to 14-3-3-Pred (www.compbio.dundee.ac .uk/1433pred) [31]. Indeed, we detected an interaction between 14-3-3η and LDHA ( Figure 5C).…”

Moonlighting chaperone‐like activity of the universal regulatory 14‐3‐3 proteins

“…In practice, formation of ternary complexes mediated by 14-3-3 has been poorly documented [33,34]. At present more than 700 human phosphoproteins have been identified as potential 14-3-3 targets [12] and it is predicted that the number will be much larger [35]. Having a wide interactome, 14-3-3 proteins are involved in regulation of many vital processes such as signal transduction, cell cycle control, apoptosis, transcriptional regulation, cytoskeleton rearrangements, protein localization, trafficking and degradation, exocytosis and endocytosis, and many others [5,32,[36][37][38].…”