Global approaches for the elucidation of phosphoinositide-binding proteins

• This review article covers advancements in large-scale identification of phosphoinositide-binding proteins using various techniques.
• The development of affinity chromatography and optimization of this approach for global analysis is discussed.
• The use of microarray analysis as a tool for identifying phosphoinositide-binding proteins is discussed, including methods involving the immobilization of proteins, individual lipids and membrane motifs.
• Initial approach using activity-based protein profiling for the collective labeling and identification of phosphoinositides-binding proteins is described.
• Finally, various strategies for the computational prediction of phosphoinositide-binding proteins are detailed.

Phosphoinositide lipids (PIPns) control numerous critical biological pathways, typically through the regulation of protein function driven by non-covalent protein–lipid binding interactions. Despite the importance of these systems, the unraveling of the full scope of protein–PIPn interactions has represented a significant challenge due to the massive complexity associated with these events, including the large number of diverse proteins that bind to these lipids, variations in the mechanisms by which proteins bind to lipids, and the presence of multiple distinct PIPn isomers. As a result of this complexity, global methods in which numerous proteins that bind PIPns can be identified and characterized simultaneously from complex samples, which have been enabled by key technological advancements, have become popular as an efficient means for tackling this challenge. This review article provides an overview of advancements in large-scale methods for profiling protein–PIPn binding, including experimental methods, such as affinity enrichment, microarray analysis and activity-based protein profiling, as well as computational methods, and combined computational/experimental efforts.

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