Free Energy Analyses of Cell-Penetrating Peptides Using the Weighted Ensemble Method.

Seungho Choe

doi:10.3390/membranes11120974

Abstract

Cell-penetrating peptides (CPPs) have been widely used for drug-delivery agents; however, it has not been fully understood how they translocate across cell membranes. The Weighted Ensemble (WE) method, one of the most powerful and flexible path sampling techniques, can be helpful to reveal translocation paths and free energy barriers along those paths. Within the WE approach we show how Arg (nona-arginine) and Tat interact with a DOPC/DOPG(4:1) model membrane, and we present free energy (or potential mean of forces, PMFs) profiles of penetration, although a translocation across the membrane has not been observed in the current simulations. Two different compositions of lipid molecules were also tried and compared. Our approach can be applied to any CPPs interacting with various model membranes, and it will provide useful information regarding the transport mechanisms of CPPs.

Highlights

Cell-penetrating peptides (CPPs) have been extensively studied for a long time since they are capable of transporting various cargoes into cells [1]
An Molecular dynamics (MD) simulation is still one of valuable tools to study protein-lipid interactions, and it can provide us with detailed information such as the contribution of electrostatic energy between CPPs and the membranes, effects of water molecules, etc
In our previous work [10], we found that the electrostatic interaction between Arg9 and a DOPC/DOPG(4:1) membrane plays a role at the initial stage of translocation

Summary

Introduction

Cell-penetrating peptides (CPPs) have been extensively studied for a long time since they are capable of transporting various cargoes (e.g., proteins, peptides, DNAs, and even small drugs) into cells [1]. An MD simulation is still one of valuable tools to study protein-lipid interactions, and it can provide us with detailed information such as the contribution of electrostatic energy between CPPs and the membranes, effects of water molecules, etc. Due to the short time scale achieved in current MD simulations, people have been using biased simulations (e.g., umbrella sampling [11–13], steered MD simulations [14]) to study CPPs and their interactions with membranes. It turns out that the WE method is very effective for studying interactions between CPPs and membranes and for obtaining free energy barriers in the current study. We simulate two different lipid compositions, DOPC/DOPE(4:1) and DOPC lipids, respectively, to see if the surface charge of model membranes affects the penetration of CPPs. the free energy barriers between CPPs and model membranes can be obtained using the WE simulation data, and these free energy calculations will be helpful to understand the transport mechanisms of CPPs

Equilibrium Simulations

Weighted Ensemble (WE) Simulations

WE Simulations Show Much-Enhanced Penetration within a Short Amount of Time

The Free Energy Profiles Based on the WE Simulation Data Show

Different Lipid Compositions Slightly Affect the PMF Profiles of Arg9