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Review
. 2014 Sep 30:5:315.
doi: 10.3389/fgene.2014.00315. eCollection 2014.

Exploiting holistic approaches to model specificity in protein phosphorylation

Antonio Palmeri  1 , Fabrizio Ferrè  1 , Manuela Helmer-Citterich  1
Affiliations
Review

Exploiting holistic approaches to model specificity in protein phosphorylation

Antonio Palmeri et al. Front Genet. .

Abstract

Phosphate plays a chemically unique role in shaping cellular signaling of all current living systems, especially eukaryotes. Protein phosphorylation has been studied at several levels, from the near-site context, both in sequence and structure, to the crowded cellular environment, and ultimately to the systems-level perspective. Despite the tremendous advances in mass spectrometry and efforts dedicated to the development of ad hoc highly sophisticated methods, phosphorylation site inference and associated kinase identification are still unresolved problems in kinome biology. The sequence and structure of the substrate near-site context are not sufficient alone to model the in vivo phosphorylation rules, and they should be integrated with orthogonal information in all possible applications. Here we provide an overview of the different contexts that contribute to protein phosphorylation, discussing their potential impact in phosphorylation site annotation and in predicting kinase-substrate specificity.

Keywords: cellular signaling; kinase-peptide specificity; kinase-substrate specificity; phosphorylation context; phosphorylation prediction; signaling networks; substrate recruitment.

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Figures

Figure 1
Figure 1
Specificity levels in Protein Phosphorylation. (A) Peptide specificity in a tyrosine kinase, Insulin Receptor (IR), a proline-directed kinase, Cyclin-dependent kinase 2 (CDK2), and a serine threonine kinase, cAMP-dependent protein kinase catalytic subunit alpha (PKA). Peptide preferences for each kinase are represented as sequence logos (top). The binding pockets of the three kinases have been visualized with UCSF Chimera, and the surfaces colored according to their electrostatic potential: red, positive; blue, negative; white, neutral (bottom). The structures from left to right show IR in complex with a peptide (pdb 1IR3), CDK2 in complex with a substrate peptide and cyclin A (pdb 1QMZ), which contributes to peptide specificity with a negative charged surface shown in the upper right of the figure, and PKA in complex with a peptide inhibitor (pdb 3FJQ). (B) Substrate recruitment. The kinase-substrate complexes concentration can be locally increased with docking motifs, protein interaction domains, and scaffold proteins. As an example of a docking motif, MAPK p38 bound to the docking site on its nuclear substrate MEF2A is shown on the left, colored in purple (pdb 1LEW). The protein interaction domains SH3 and SH2 domains in Src are fundamental for Src activation (inactive Src: pdb 2SRC), as shown in the cartoon in the middle (Xu et al., 1999). MAPK Fus3 in complex with a Ste5 peptide (pdb 2F49) is shown on the right.
Figure 2
Figure 2
Methodologies for the experimental identification of phosphorylation sites. In the inner circle the techniques for the detection of phosphorylation sites are reported, while the outer circle displays the major techniques for dissecting kinase-substrates interactions, both at the level of direct determination of kinase-substrate interaction (kinase activity assays, OPL, MS with ATP analogs, structural data, western blot, optogenetics) and at the contextual information generation level, i.e., the methodologies that allow the identification of interacting domain preferences, domain-peptide interactions, etc. (Y2H, Y3H, phage display, structural data, western blot, optogenetics). In the field of PTM identification, future advancements in MS will allow the monitoring of multiple PTMs co-modulation, while for kinase-substrate interactions, the use of ATP analogs coupled with MS/MS is currently the most promising high-throughput technique to link kinases to their substrates in vivo. Y2H/Y3H: yeast 2/3 hybrid system (Y3H could be deployed for the study of scaffold proteins-mediated interactions).
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References

    1. Alexander J., Lim D., Joughin B. A., Hegemann B., Hutchins J. R. A., Ehrenberger T., et al. (2011). Spatial exclusivity combined with positive and negative selection of phosphorylation motifs is the basis for context-dependent mitotic signaling. Sci. Signal. 4:ra42 10.1126/scisignal.2001796 - DOI - PMC - PubMed
    1. Barford D., Hu S. H., Johnson L. N. (1991). Structural mechanism for glycogen phosphorylase control by phosphorylation and AMP. J. Mol. Biol. 218, 233–260 10.1016/0022-2836(91)90887-C - DOI - PubMed
    1. Biondi R. M., Nebreda A. R. (2003). Signalling specificity of Ser/Thr protein kinases through docking-site-mediated interactions. Biochem. J. 372, 1–13 10.1042/BJ20021641 - DOI - PMC - PubMed
    1. Beltrao P., Albanèse V., Kenner L. R., Swaney D. L., Burlingame A., Villén J., et al. (2012). Systematic functional prioritization of protein posttranslational modifications. Cell 150, 413–425 10.1016/j.cell.2012.05.036 - DOI - PMC - PubMed
    1. Blom N., Sicheritz-Pontén T., Gupta R., Gammeltoft S., Brunak S. (2004). Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics 4, 1633–1649 10.1002/pmic.200300771 - DOI - PubMed

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