Characterization of PROPPIN-Phosphoinositide Binding by Stopped-Flow Fluorescence Spectroscopy

PROPPINs (β-propellers that bind polyphosphoinositides) are a protein family that binds preferentially phosphatidylinositol 3-phosphate (PtdIns(3)P) and phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2) via its FRRG motif. PROPPINs are involved in autophagic functions, but their molecular mechanism is still elusive. To unravel the molecular mechanism of PROPPINs, it is essential to understand the PROPPIN-phosphoinositide binding. Here, we describe a protocol to study the kinetics of the PROPPIN-phosphoinositide binding using a fluorescence resonance energy transfer (FRET) stopped-flow approach. We use FRET between fluorophore-labeled protein and fluorophore-labeled liposomes, monitoring the increase of the acceptor emission in labeled liposomes after the protein-membrane binding. Through this approach, we studied the kinetics of the PROPPIN Atg18 (Autophagy-related protein 18) from Pichia angusta (PaAtg18) and a mutant of its FRRG motif, called FTTG mutant. Stopped-flow experiments demonstrated that the main function of the FRRG motif is to retain, instead of to drive, Atg18 to the membrane, decreasing the Atg18 dissociation rate. Furthermore, this method is suitable for the study of other PI-binding proteins.