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arXiv · 2206.14552

Translocation of a single Arg9 peptide across a DOPC/DOPG(4:1) model membrane using the weighted ensemble method

Seungho Choe
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Abstract

It is difficult to observe a spontaneous translocation of cell-penetrating peptides(CPPs) within a short time scale (e.g., a few hundred ns) in all-atom molecular dynamics(MD) simulations because the time required for the translocation of usual CPPs is on the order of minutes or so. In this work, we report a spontaneous translocation of a single Arg$_9$(R9) across a DOPC/DOPG(4:1) model membrane within an order of a few tens ns scale by using the weighted ensemble(WE) method. We identify how water molecules and the orientation of Arg$_9$ play a role in translocation. We also show how lipid molecules are transported along with Arg$_9$. In addition, we present free energy profiles of the translocation across the membrane using umbrella sampling and show that a single Arg$_9$ translocation is energetically unfavorable. We expect that the WE method can help study interactions of CPPs with various model membranes within MD simulation approaches.

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Seungho Choe. 2022-06-29. Translocation of a single Arg9 peptide across a DOPC/DOPG(4:1) model membrane using the weighted ensemble method. https://arxiv.org/abs/2206.14552

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