Predicting peptide orientation in membrane interactions: a review on transmembrane and surface-bound states

Understanding the mechanism of action of antimicrobial peptides (AMPs) is a key step in developing new antimicrobial agents. This mechanism is often linked to the peptide’s orientation upon interaction with lipid membranes—whether it inserts into the membrane or remains surface-bound. Despite its importance, the literature lacks a systematic approach to predict peptide orientation based on physicochemical characteristics. This review highlights how peptide orientation at membranes can be qualitatively predicted by integrating sequence-level features, length/effective span, amphipathicity, charge distribution, and helix propensity, with membrane/environmental variables. The approach is illustrated with representative AMPs and it is discussed how external factors (pH, anionic fraction, cholesterol, ionic strength) bias surface-bound versus transmembrane regimes. The review is built upon theoretical observations and integrates structural, thermodynamic, and electrostatic parameters drawn from experimental data in the literature. While this study does not aim to provide a definitive classification, it offers a starting point that may guide experimental validation and future refinement.