From sequence to structural analysis in protein phosphorylation motifs

Biocomputing Group, Department of Biochemical Science A Rossi Fanelli, Sapienza University of Rome, P le Aldo Moro 5, Rome, Italy.
Frontiers in Bioscience (Impact Factor: 3.52). 01/2011; 16(4):1261-75. DOI: 10.2741/3787
Source: PubMed


Phosphorylation is the most widely studied post-translational modification occurring in cells. While mass spectrometry-based proteomics experiments are uncovering thousands of novel in vivo phosphorylation sites, the identification of kinase specificity rules still remains a relatively slow and often inefficacious task. In the last twenty years, many efforts have being devoted to the experimental and computational identification of sequence and structural motifs encoding kinase-substrate interaction key residues and the phosphorylated amino acid itself. In this review, we retrace the road to the discovery of phosphorylation sequence motifs, examine the progresses achieved in the detection of three-dimensional motifs and discuss their importance in the understanding of regulation and de-regulation of many cellular processes.

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    • "Phosphoresiduebinding domains are common functional modules distributed widely among cellular signaling proteins. Numerous studies have identified and investigated phosphoresidue binding domains in various proteins (Via et al., 2011; Reinhardt and Yaffe, 2013) such as SH2 and PTB domains for phosphotyrosine (Pawson et al., 2001), 14-3-3 domains for phosphorserine (Yaffe et al., 1997), and FHA domains for phosphothreonine (Durocher et al., 2000). Usually these domains contain arginine or lysine residues in their binding regions to form hydrogen bonds with phosphates, and may have neighboring residues (e.g., hydrophobic residues for phosphotyrosine ) which help to recognize phosphorylated site, or any specific residues in the binding motifs (Liang and Van Doren, 2008; Johnson et al., 2010). "
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    ABSTRACT: Phosphorylation offers a dynamic way to regulate protein activity and subcellular localization, which is achieved through its reversibility and fast kinetics. Adding or removing a dianionic phosphate group somewhere on a protein often changes the protein's structural properties, its stability and dynamics. Moreover, the majority of signaling pathways involve an extensive set of protein-protein interactions, and phosphorylation can be used to regulate and modulate protein-protein binding. Losses of phosphorylation sites, as a result of disease mutations, might disrupt protein binding and deregulate signal transduction. In this paper we focus on the effects of phosphorylation on protein stability, dynamics, and binding. We describe several physico-chemical mechanisms of protein regulation through phosphorylation and pay particular attention to phosphorylation in protein complexes and phosphorylation in the context of disorder-order and order-disorder transitions. Finally we assess the role of multiple phosphorylation sites in a protein molecule, their possible cooperativity and function.
    Frontiers in Genetics 08/2014; 5:270. DOI:10.3389/fgene.2014.00270
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    • "Netphos [12] was the first predictor to use neural networks in 1999, outperforming phosphorylation site identification based on sequence motifs alone. Besides the primary sequence, the structural context is also important in determining whether a site is phosphorylated or not [15,16]. Indeed several predictors such as DISPHOS [17] and PHOSIDA [18] include the predicted structural characteristics of the putative phosphorylation sites. "
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    ABSTRACT: Protein phosphorylation modulates protein function in organisms at all levels of complexity. Parasites of the Leishmania genus undergo various developmental transitions in their life cycle triggered by changes in the environment. The molecular mechanisms that these organisms use to process and integrate these external cues are largely unknown. However Leishmania lacks transcription factors, therefore most regulatory processes may occur at a post-translational level and phosphorylation has recently been demonstrated to be an important player in this process. Experimental identification of phosphorylation sites is a time-consuming task. Moreover some sites could be missed due to the highly dynamic nature of this process or to difficulties in phospho-peptide enrichment. Here we present PhosTryp, a phosphorylation site predictor specific for trypansomatids. This method uses an SVM-based approach and has been trained with recent Leishmania phosphosproteomics data. PhosTryp achieved a 17% improvement in prediction performance compared with Netphos, a non organism-specific predictor. The analysis of the peptides correctly predicted by our method but missed by Netphos demonstrates that PhosTryp captures Leishmania-specific phosphorylation features. More specifically our results show that Leishmania kinases have sequence specificities which are different from their counterparts in higher eukaryotes. Consequently we were able to propose two possible Leishmania-specific phosphorylation motifs.We further demonstrate that this improvement in performance extends to the related trypanosomatids Trypanosoma brucei and Trypanosoma cruzi. Finally, in order to maximize the usefulness of PhosTryp, we trained a predictor combining all the peptides from L. infantum, T. brucei and T. cruzi. Our work demonstrates that training on organism-specific data results in an improvement that extends to related species. PhosTryp is freely available at
    BMC Genomics 12/2011; 12(1):614. DOI:10.1186/1471-2164-12-614 · 3.99 Impact Factor
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    • "Because of the transient nature of phosphorylation events, phosphorylation sites tend to lie on the surface of proteins. Many studies [see Via et al. (35) for a summary] have shown that the substrate specificity is not only dependent on the primary sequence of the motif hosting the phosphorylation site, but also on its structural conformation. "
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    ABSTRACT: The Phospho.ELM resource ( is a relational database designed to store in vivo and in vitro phosphorylation data extracted from the scientific literature and phosphoproteomic analyses. The resource has been actively developed for more than 7 years and currently comprises 42 574 serine, threonine and tyrosine non-redundant phosphorylation sites. Several new features have been implemented, such as structural disorder/order and accessibility information and a conservation score. Additionally, the conservation of the phosphosites can now be visualized directly on the multiple sequence alignment used for the score calculation. Finally, special emphasis has been put on linking to external resources such as interaction networks and other databases.
    Nucleic Acids Research 01/2011; 39(Database issue):261-267. DOI:10.1093/nar/gkq1104 · 9.11 Impact Factor
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