A new reaction coordinate to study the translocation pathway of cell-penetrating peptides across lipid bilayers: The cases of transportan-10 and penetratin

Abstract

Translocation pathway of cell-penetrating peptides remains elusive, as it is hard to observe by experimental and theoretical studies, which limits their effective use. Furthermore, lipid dynamics influence the translocation pathway, which is often overlooked due to its slow timescale. Current studies lack the effect of multiple peptides on the translocation process. Therefore, in this work, we employ the umbrella sampling technique with a preferential lipid–peptide interaction term in the reaction coordinate to explore the translocation activity of penetratin and transportan-10 (TP10) peptides in a heterogeneous membrane. In experiments, they follow different pathways according to their concentration, but the cause of this difference is unknown. We considered single and multiple (two and four) peptide translocation processes to understand the differences. Self-aggregation process is taken into account for multiple peptides. The interaction between peptides and peptides–lipids is found to be important for a proper overview of the translocation process. Peptide translocation was found to be related to the dynamics of the lipids, which change during the translocation process, making the system complex to study. In the case of multiple penetratin translocation, the anionic lipids were found to aggregate on the positive curvature of the upper leaflet, helping fold the membrane. Lipid composition of the TP10 multiple peptide case was found random. The increased mass and size of the solute in this case helped attain a radius more than the threshold value, leading to pore formation. Free energy barriers of single TP10 and penetratin are found to be 45.4 ± 2 and 33.7 ± 0.8 kJ mol?1, respectively. © 2025 Author(s).