A membrane insertion code for intrinsically disordered proteins

Membrane association of intrinsically disordered proteins (IDPs) mediates various cellular functions including membrane remodeling and signal transduction. Whereas membrane association through amphipathic helices and polybasic motifs is well understood, sequence determinants for deep membrane insertion of aromatic residues are still poorly characterized. Here, we decipher the sequence code for membrane insertion of aromatic-centered motifs. For an initial set of 10 9-residue aromatic-centered sequences, all-atom molecular dynamics simulations and the positioning of proteins in membranes (PPM) method produced very similar membrane insertion propensities. Applying PPM to a full library of 1.2 x 106 sequences with an F, W, or Y residue flanked by L, R, G, N, or E at four positions on either side, we found that aliphatic (L) and basic (R) residues favor membrane insertion, whereas acidic (E) and polar (N) residues disfavor it. Guided by these rules, we developed a mathematical model dubbed AroMIP to predict the membrane insertion propensities of aromatic-centered motifs. AroMIP achieves 91.2%, 92.0%, and 99.7% accuracies for F-, W-, and Y-centered motifs, respectively, in disordered regions of the human proteome and is available as a web server at https://zhougroup-uic.github.io/AroMIP/. The present work provides the sequence basis and a mechanistic understanding of how IDPs employ aromatic-centered motifs to drive membrane insertion, and enriches the tools for the study of IDP-membrane association. Significance StatementMembrane insertion of short motifs, along with membrane tethering of amphipathic helices and membrane binding of polybasic motifs, is a major mode of membrane association and mediates diverse functions including membrane remodeling and signal transduction. Here we used three complementary approaches to decipher the sequence code of membrane insertion, culminating in a sequence-based method, AroMIP, for predicting membrane-insertion propensities. Aromatic sidechains have the intrinsic ability to insert deeply into the acyl chain region of membranes; at flanking positions, they strongly stabilize the inserted state. Aliphatic and basic residues are medium to modest promoters of membrane insertion. AroMIP has >90% accuracy and identifies important motifs for regulating functions of intrinsically disordered proteins via membrane insertion.