Translocation of a single Arg$$_9$$ peptide across a DOPC/DOPG(4:1) model membrane using the weighted ensemble method

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$$_9$$ 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$$_9$$ 9 play a role in translocation. We also show how lipid molecules are transported along with Arg$$_9$$ 9 . In addition, we present free energy profiles of the translocation across the membrane using umbrella sampling and show that a single Arg$$_9$$ 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.

Design and Discovery of New Collagen V-Derived FGF2-Blocking Natural Peptides Inhibiting Lung Squamous Cell Carcinoma In Vitro and In Vivo

“…The dynamic GUV leakage assays serve as an effective method to monitor real-time membrane permeabilization and deformation caused by active molecules, which are commonly employed for investigating molecule–membrane interactions. , GUVs composed of DOPC, DOPG (at a mol ratio of 4:1; previously utilized , ) and labeled with 1 mol % RhB-PE were prepared using the conventional electro-forming method and immobilized on a glass substrate through biotin–streptavidin binding. Calcein, a water-soluble and membrane-impermeable fluorophore, was introduced into the solution for evaluating membrane permeability.…”

Unravelling the Cell-Penetrating Potential of Endogenous Opioid Neuropeptide Dynorphin A through Computational Dissection of Membrane Disruption Principles

“…In parallel, CPP showed various translocation mechanisms: Arg9 seems to translocate through a transient pore formation [69,70], a mechanism shared by DynA WT. On the other hand, DynA L5S and TP2 may involve direct translocation (through a quick and transient pore or without pore formation) of a monomeric peptide, leading to a minimum leakage.…”

Leaflet-Dependent Effect of Anionic Lipids on Membrane Insertion by Cationic Cell-Penetrating Peptides

“…Experimental and computational studies of other arginine-containing peptides have shown that trans-leaflet flip-flop can be induced by peptide membrane insertion. 41,42 If NAF-1 44−67 induces trans-leaflet flip-flop, a cooperative insertion enhancement could occur when an inner leaflet > outer leaflet anionic lipid gradient is present. For example, if the outer leaflet and inner leaflet are 30 and 50 mol % PA, respectively, permeating NAF-1 44−67 could flip some PA lipids to the OL.…”

“…In an unperturbed bilayer, the time scale of lipid flip-flop is very slow, on the order of hours to days with a large ∼20–30 kcal mol –1 free energy barrier. − However, when NAF-1 44–67 forms a membrane defect, this barrier may be reduced, neutralizing any gradient between the leaflets. Experimental and computational studies of other arginine-containing peptides have shown that trans-leaflet flip-flop can be induced by peptide membrane insertion. , If NAF-1 44–67 induces trans-leaflet flip-flop, a cooperative insertion enhancement could occur when an inner leaflet > outer leaflet anionic lipid gradient is present. For example, if the outer leaflet and inner leaflet are 30 and 50 mol % PA, respectively, permeating NAF-1 44–67 could flip some PA lipids to the OL.…”