The influence of the acyl chains in PIPn–protein interactions is often missed in structural studies by the utilization of soluble, short-chain versions of PIPn, the conformational dynamics of longer chains and the lack of a membrane context. (A–E) Examples of protein–PIPn interactions adapted from the Protein Data Bank, where the protein backbone is shown interacting with PIPn of diverse acyl chain composition (in spacefill representation: carbon, grey; phosphorus, orange; oxygen, red). The original lipid ligand is indicated, although shorter versions are represented in the structures of PITPα (B) and GIRK2 (C) where the PIPn acyl chains were not fully solved. Although the interaction with PIPn-binding domains is often restricted to the phosphorylated inositol ring (A), its presentation relative to the membrane surface could be affected by the acyl chain length/saturation. The PIPn acyl chains can directly interact with hydrophobic residues inserted in the membrane in transmembrane proteins such as GIRK2 (C). Interestingly, the activation of certain members of this family of ion channels by PIPn was largely dependent of their acyl chains [80]. The influence of the acyl chains could be more evident in PIPn–protein interactions that involve the extraction of the whole lipid from the membrane (B,D,E). In these proteins, the polar head can be buried in the protein (B), with the acyl chains occupying two hydrophobic channels, but can also be exposed to the solvent (E), which could be indicative of a major binding contribution for the acyl chains. (A) PX domain from p40phox bound to di-C4-PI3P (PDB 1H6H) [124]. (B) PITPα complexed to PI from bovine liver (PDB 1UW5) [125]. (C) G protein-gated inward rectifier K+ channel GIRK2 in complex with sodium and di-C8-PI(4,5)P₂ (PDB 3SYA) [126]. (D) Osh6p in complex with brain PI4P (4PH7) [127]. (E) nuclear receptor SF-1 bound to di-C16:0-PIP3 (PDB 4QJR) [92].