Turning the spotlight on protein–lipid interactions in cells

Abstract

Protein function is largely dependent on coordinated and dynamic interactions of the protein with biomolecules including other proteins, nucleic acids and lipids. While powerful methods for global profiling of protein-protein and protein-nucleic acid interactions are available, proteome-wide mapping of protein-lipid interactions is still challenging and rarely performed. The emergence of bifunctional lipid probes with photoactivatable and clickable groups offers new chemical tools for globally profiling protein-lipid interactions under cellular contexts. In this review, we summarize recent advances in the development of bifunctional lipid probes for studying protein-lipid interactions. We also highlight how in vivo photocrosslinking reactions contribute to the characterization of lipid-binding proteins and lipidation-mediated protein-protein interactions.

A facile, sensitive and quantitative membrane‐binding assay for proteins

“…We provide such a solution with PLiMAP. The choice of reagents to prepare the reporter lipid was based on the following considerations; (a) the diazirine moiety is small in size and upon photolysis by light of approximately 350 nm, which should by itself reduce photodamage to macromolecules, produce promiscuously reactive but highly short‐lived carbenes that can potentially insert into any X‐H bond (where X can be C, O, N or S) and therefore label the protein relatively nonspecifically, (b) crosslinking with proteins is more efficient in hydrophobic environments due to the absence of competing water molecules, (c) their placement at the phospholipid headgroup should render free access to and covalently modify proximal membrane‐bound proteins, (d) BODIPY dyes are bright, relatively insensitive to solvent polarity and pH change and easily detected using standard optics and (e) of the commercially available tail‐labeled fluorescent lipids, BODIPY analogs have been reported to better mimic the behavior of native phospholipids . Unlike previous reports of similar bi‐functional photoactivable lipids designed to assay specific lipid‐protein interactions (reviewed in Ref.…”

“…Unlike previous reports of similar bi‐functional photoactivable lipids designed to assay specific lipid‐protein interactions (reviewed in Ref. ), our strategy builds on the converse rationale that a generic phospholipid with a promiscuously reactive moiety at the head group should report on all types of associations with the membrane. Proteins bind membranes through specific local interactions with lipids but have an effective footprint that encompasses several lipids on the membrane, possibly explaining why such a generic crosslinker functions so well in reporting on membrane association.…”

Proteomic analysis of fatty-acylated proteins

“…This bifunctional reporter was used in mammalian cells in combination with quantitative proteomics to study S-palmitoylated IFITM3-interacting proteins and revealed known IFITM3-interacting proteins, such as VAPA, as well as novel interacting proteins, which could be key cellular factors for host resistance to virus infection. A similar method could be applied to identify interacting proteins of other fatty-acylated proteins [75] and study the role of fatty-acylation in regulating protein–protein interactions in cells.…”

Global Mapping of Protein–Lipid Interactions by Using Modified Choline‐Containing Phospholipids Metabolically Synthesized in Live Cells

“…[2] By interacting with cellular proteins, lipids modulate their subcellular localization and activities. [3] Dysregulation of such interactions leads to numerous pathological conditions. [4] Chemical tools capable of proteome-wide elucidation of protein-lipid interactions, especially those that are distinguishable among different classes of lipids (for example, protein-phospholipid interactions from other lipid interactions), are urgently needed.…”

“…Most metabolic lipids are first synthesized in endoplasmic reticulum (ER) and Golgi, then sorted to various subcellular compartments, a process with which synthetic lipids cannot easily emulate. [1][2][3] While many photoactivatable metabolites have been developed to characterize protein interactions, [10,11] few were well-suited for protein-lipid interactions and none could be used for in situ mapping of protein-phospholipid interactions exclusively. [12] A bifunctional fatty acid, pacFA (Supporting Information, Figure S2), was recently reported to be incorporated into phospholipid biosynthesis, and the resulting lipids were used to identify more than 200 putative lipid-binding proteins from mammalian cells.…”