Cell membranes act as semi-permeable barriers, often restricting the entry of large or hydrophilic molecules. Nonetheless, certain amphiphilic molecules, such as antimicrobial and cell-penetrating peptides, can cross these barriers. In this study, we demonstrate that specific properties of transmembrane proteins/peptides can enhance membrane permeation of amphiphilic peptides. Using coarse-grained molecular dynamics with free-energy calculations, we identify key translocation-enhancing attributes of transmembrane proteins/peptides: a continuous hydrophilic patch, charged residues preferably in the membrane center, and aromatic hydrophobic residues. By employing both coarse-grained and atomistic simulations, complemented by experimental validation, we show that these properties not only enhance peptide translocation but also speed up lipid flip-flop. The enhanced flip-flop reinforces the idea that proteins such as scramblases and insertases not only share structural features but also operate through identical biophysical mechanisms enhancing the insertion and translocation of amphiphilic molecules. Our insights offer guidelines for the designing of translocation-enhancing proteins/peptides that could be used in medical and biotechnological applications.

CEITEC Central European Institute of Technology Masaryk University Brno Czech Republic

CEITEC Central European Institute of Technology Masaryk University Brno Czech Republic; National Centre for Biomolecular Research Faculty of Science Masaryk University Brno Czech Republic

CEITEC Central European Institute of Technology Masaryk University Brno Czech Republic; National Centre for Biomolecular Research Faculty of Science Masaryk University Brno Czech Republic; Department of Condensed Matter Physics Faculty of Science Masaryk University Brno Czech Republic

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