Global approaches for the elucidation of phosphoinositide-binding proteins

Best, Michael D.

doi:10.1016/j.chemphyslip.2013.10.014

Cited by 13 publications

(13 citation statements)

References 92 publications

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“…Synthetic PIPs have also been useful for rapid screening of PIP-binding (Rowland et al 2012) and cellular identification of PIP-binding proteins using PIP-activity probes and proteomics (Rowland et al 2011). In fact, this is an emerging area of research and new assays to globally investigate PIP-binding proteins are nicely reviewed by Michael Best in this special issue (Best 2013). …”

Section: Phosphoinositide-bindingmentioning

confidence: 99%

“…Furthermore, proteomics and lipidomics has increased our awareness of the large number of PIP-binding proteins in nature (van Meer 2005; Clark et al 2011; Rowland et al 2011; Best 2013; Catimel et al 2013; Oxley et al 2013) some of which have potential therapeutic value or unique PIP-binding properties. The future research on PIP-binding interactions will encompass more interdisciplinary studies of both computational predictions and validations of these conjectures.…”

Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

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Cellular and molecular interactions of phosphoinositides and peripheral proteins

Stahelin

Scott

Frick

2014

Chemistry and Physics of Lipids

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Anionic lipids act as signals for the recruitment of proteins containing cationic clusters to biological membranes. A family of anionic lipids known as the phosphoinositides (PIPs) are low in abundance, yet play a critical role in recruitment of peripheral proteins to the membrane interface. PIPs are mono-, bis-, or trisphosphorylated derivatives of phosphatidylinositol (PI) yielding seven species with different structure and anionic charge. The differential spatial distribution and temporal appearance of PIPs is key to their role in communicating information to target proteins. Selective recognition of PIPs came into play with the discovery that the substrate of protein kinase C termed pleckstrin possessed the first PIP binding region termed the pleckstrin homology (PH) domain. Since the discovery of the PH domain, more than ten PIP binding domains have been identified including PH, ENTH, FYVE, PX, and C2 domains. Representative examples of each of these domains have been thoroughly characterized to understand how they coordinate PIP headgroups in membranes, translocate to specific membrane docking sites in the cell, and function to regulate the activity of their full-length proteins. In addition, a number of novel mechanisms of PIP-mediated membrane association have emerged, such as coincidence detection – specificity for two distinct lipid headgroups. Other PIP-binding domains may also harbor selectivity for a membrane physical property such as charge or membrane curvature. This review summarizes the current understanding of the cellular distribution of PIPs and their molecular interaction with peripheral proteins.

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Section: Phosphoinositide-bindingmentioning

confidence: 99%

Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

Cellular and molecular interactions of phosphoinositides and peripheral proteins

Stahelin

Scott

Frick

2014

Chemistry and Physics of Lipids

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“…6 and 5PP-InsP 5 Affinity Reagents. Affinity-based probes have been widely used by the inositol community, in particular, to identify interactions between phosphatidyl inositols and their protein targets (27)(28)(29)(30)(31). Furthermore, immobilized InsP 6 has enabled the identification of two enzymes involved in InsP biosynthesis (12,32,33) and allowed for affinity capture of the Ku protein, a required factor for nonhomologous end joining (34).…”

Section: Significancementioning

confidence: 99%

Inositol polyphosphates intersect with signaling and metabolic networks via two distinct mechanisms

Chong

Perlman

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

116

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Inositol-based signaling molecules are central eukaryotic messengers and include the highly phosphorylated, diffusible inositol polyphosphates (InsPs) and inositol pyrophosphates (PP-InsPs). Despite the essential cellular regulatory functions of InsPs and PP-InsPs (including telomere maintenance, phosphate sensing, cell migration, and insulin secretion), the majority of their protein targets remain unknown. Here, the development of InsP and PP-InsP affinity reagents is described to comprehensively annotate the interactome of these messenger molecules. By using the reagents as bait, >150 putative protein targets were discovered from a eukaryotic cell lysate (Saccharomyces cerevisiae). Gene Ontology analysis of the binding partners revealed a significant overrepresentation of proteins involved in nucleotide metabolism, glucose metabolism, ribosome biogenesis, and phosphorylation-based signal transduction pathways. Notably, we isolated and characterized additional substrates of protein pyrophosphorylation, a unique posttranslational modification mediated by the PP-InsPs. Our findings not only demonstrate that the PP-InsPs provide a central line of communication between signaling and metabolic networks, but also highlight the unusual ability of these molecules to access two distinct modes of action.inositol pyrophosphates | affinity reagents | protein pyrophosphorylation | signal transduction | metabolism S ignal transduction pathways and metabolic circuits are essential for cell homeostasis and survival. These two types of networks have historically been viewed as separate entities, but it is becoming increasingly clear that they must be coordinately regulated. Indeed, growth factor-stimulated signaling pathways can promote the metabolic activity of the cell (1). Conversely, the activity of signaling proteins can be controlled by specific metabolites (2), either by allosteric mechanisms or via nutrient-sensitive covalent modifications, such as acetylation (3) and glycosylation (4).The highly phosphorylated inositol polyphosphates (InsPs), and in particular the inositol pyrophosphates (PP-InsPs), are primed to provide additional junctures between signaling and metabolic networks (5-7). A cascade of phosphorylation reactions converts the secondary messenger inositol trisphosphate (InsP 3 ) to the fully phosphorylated inositol hexakisphosphate (InsP 6 ) (8). Subsequent action of inositol hexakisphosphate kinases (IP6Ks) and diphosphoinositol pentakisphosphate kinases (PPIP5Ks) furnishes the PP-InsP messengers, a unique class of signaling molecules containing one or two high-energy phosphoanhydride bonds (Fig. 1A) (6,7,9). A number of studies have indicated a central role for PP-InsPs in metabolic reprogramming and phosphorylation-based signaling at the cellular and organismal level. For example, the biochemical properties of the IP6Ks confer an "energy sensing" function onto these enzymes (10). Because the IP6Ks have a K m for ATP between 1.0 and 1.4 mM-concentrations that are similar to the intracellular ATP levels-t...

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“…The discovery of additional protein domains or regions that bind to phosphatidylinositides is important for understanding the mechanisms by which they regulate cellular processes. Various techniques have been utilized to identify proteins that bind phosphatidylinositides (reviewed in [49]), including protein microarrays [12], affinity purification [50], neomycin nuclear extraction [51], a yeast growth rescue assay [52], λgt11-based expression cloning [53], quantitative mass spectrometry [54], and an in vitro transcription/translation-based expression cloning assay [55]. In addition to cytosolic membrane phosphatidylinositides, an independent pool of phosphatidylinositides and enzymes involved in their synthesis exists in the nucleus.…”

Section: Phosphatidylinositide-binding Proteins and The Mystery Of mentioning

confidence: 99%

Utilizing Yeast Surface Human Proteome Display Libraries to Identify Small Molecule-Protein Interactions

Bidlingmaier

Liu

2015

Methods in Molecular Biology

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The identification of proteins that interact with small bioactive molecules is a critical but often difficult and time-consuming step in understanding cellular signaling pathways or molecular mechanisms of drug action. Numerous methods for identifying small molecule-interacting proteins have been developed and utilized, including affinity-based purification followed by mass spectrometry analysis, protein microarrays, phage display, and three-hybrid approaches. Although all these methods have been used successfully, there remains a need for additional techniques for analyzing small molecule-protein interactions. A promising method for identifying small molecule-protein interactions is affinity-based selection of yeast surface-displayed human proteome libraries. Large and diverse libraries displaying human protein fragments on the surface of yeast cells have been constructed and subjected to FACS-based enrichment followed by comprehensive exon microarray-based output analysis to identify protein fragments with affinity for small molecule ligands. In a recent example, a proteome-wide search has been successfully carried out to identify cellular proteins binding to the signaling lipids PtdIns(4,5)P2 and PtdIns(3,4,5)P3. Known phosphatidylinositide-binding proteins such as pleckstrin homology domains were identified, as well as many novel interactions. Intriguingly, many novel nuclear phosphatidylinositide-binding proteins were discovered. Although the existence of an independent pool of nuclear phosphatidylinositides has been known about for some time, their functions and mechanism of action remain obscure. Thus, the identification and subsequent study of nuclear phosphatidylinositide-binding proteins is expected to bring new insights to this important biological question. Based on the success with phosphatidylinositides, it is expected that the screening of yeast surface-displayed human proteome libraries will be of general use for the discovery of novel small molecule-protein interactions, thus facilitating the study of cellular signaling pathways and mechanisms of drug action or toxicity.

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Global approaches for the elucidation of phosphoinositide-binding proteins

Cited by 13 publications

References 92 publications

Cellular and molecular interactions of phosphoinositides and peripheral proteins

Cellular and molecular interactions of phosphoinositides and peripheral proteins

Inositol polyphosphates intersect with signaling and metabolic networks via two distinct mechanisms

Utilizing Yeast Surface Human Proteome Display Libraries to Identify Small Molecule-Protein Interactions

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