Structure and dynamics of Penetratin’s association and translocation to a lipid bilayer

Abstract

Penetratin belongs to the important class of small and positively charged peptides, capable of entering cells. The determination of the optimal peptidic structure for translocation is challenging; results obtained so far are varied and dependent on several factors. In this work, we review the dynamics of association of Penetratin with a modeled dioleoyl-phosphatidylcholine (DOPC) lipid membrane using molecular dynamics simulations with last generation force fields. Penetratin’s structural preferences are determined using a Markov state model. It is observed that the peptide retains a helical form in the membrane associated state, just as in water, with the exception of both termini which lose helicity, facilitating the interaction of terminal residues with the phosphate groups on the membrane’s outer layer. The optimal orientation for insertion is found to be with the peptide’s axis forming a small angle with the interface, and with R1 stretching toward the bilayer. The interaction between arginine side-chains and phosphate groups is found to be greater than the corresponding to lysine, mainly due to a higher number of hydrogen bonds between them. The free energy profile of translocation is qualitatively studied using Umbrella Sampling. It is found that there are different paths of penetration, that greatly differ in size of free energy barrier. The lowest path is compatible with residues R10 to K13 leading the way through the membrane and pulling the rest of the peptide. When the other side is reached, the C-terminus overtakes those residues, and finally breaks out of the membrane. The peptide’s secondary structure during this traversal suffers some changes with respect to the association structure but, overall, conserves its helicity, with both termini in a more disordered state.

pVEC hydrophobic N‐terminus is critical for antibacterial activity

“…The force applied on the peptide starts to increase as the peptide gets closer to the membrane. Positively charged residues, particularly arginines, make the first contact with the bilayer phosphate heads, a behavior that has been observed for other CPPs . Force reaches its maximum value when the N‐terminus reaches the bilayer core (Figure B; at z around 0 Å).…”

“…Our SMD simulations for pVEC and del5 pVEC peptides suggest that both peptides translocate through the POPE bilayer in a similar manner, of the force applied on the peptide, the formation of the water pore, and ion distribution during the peptide translocation. The arginine residues are important during the adsorption stage of both peptides, which has been observed for insertion of other CPPs, as well . After the adsorption stage, the peptides are parallel to the bilayer surface and they are both guided into the bilayer by their N‐terminus.…”

“…Transient pore formation because of melittin was observed in synthetic membranes using time‐lapse fluorescence imaging, but little pore formation was observed in live bacterial cells . Translocation of penetratin did not involve pore formation nor hydration of the peptide . The effect and mechanism of pore formation are 2 research topics that are examined extensively, but the current methodologies fail to provide a full picture because of time, resource, or resolution limitations .…”

“…Furthermore, it was reported that even with sampling times that exceeded 20 microseconds, it was still not possible to obtain a fully converged free energy profile for CPP insertion . For the peptide to find the best path to move through the lipids without deforming it, very long simulations should be carried out …”

“…Ile and Leu, the most hydrophobic residues, preferred to reside in the bilayer core, with free energy values around −20 kJ/mol at the bilayer center . On the other hand, cationic residues were found to have critical involvement during adsorption on the membrane . Arginine, common to many AMPs and CPPs, was stabilized by the presence of a surrounding water droplet, and arginine‐rich peptides formed channels where fatty acid protonation/deprotonation in the bilayer contributes to uptake .…”