Poisson-Nernst-Planck Models of Nonequilibrium Ion Electrodiffusion through a Protegrin Transmembrane Pore

Abstract

Protegrin peptides are potent antimicrobial agents believed to act against a variety of pathogens by forming nonselective transmembrane pores in the bacterial cell membrane. We have employed 3D Poisson-Nernst-Planck (PNP) calculations to determine the steady-state ion conduction characteristics of such pores at applied voltages in the range of −100 to +100 mV in 0.1 M KCl bath solutions. We have tested a variety of pore structures extracted from molecular dynamics (MD) simulations based on an experimentally proposed octomeric pore structure. The computed single-channel conductance values were in the range of 290–680 pS. Better agreement with the experimental range of 40–360 pS was obtained using structures from the last 40 ns of the MD simulation, where conductance values range from 280 to 430 pS. We observed no significant variation of the conductance with applied voltage in any of the structures that we tested, suggesting that the voltage dependence observed experimentally is a result of voltage-dependent channel formation rather than an inherent feature of the open pore structure. We have found the pore to be highly selective for anions, with anionic to cationic current ratios (I_Cl−/I_K+) on the order of 10³. This is consistent with the highly cationic nature of the pore but surprisingly in disagreement with the experimental finding of only slight anionic selectivity. We have additionally tested the sensitivity of our PNP model to several parameters and found the ion diffusion coefficients to have a significant influence on conductance characteristics. The best agreement with experimental data was obtained using a diffusion coefficient for each ion set to 10% of the bulk literature value everywhere inside the channel, a scaling used by several other studies employing PNP calculations. Overall, this work presents a useful link between previous work focused on the structure of protegrin pores and experimental efforts aimed at investigating their conductance characteristics. Protegrins are small peptides with strong antimicrobial properties, believed to kill bacteria primarily by forming nonselective pores in the bacterial membrane. This nonspecific and highly effective mechanism of action has created significant excitement about the use of protegrins as therapeutic antibiotics. However, a lack of understanding of the fundamental processes that lead to pore formation and bacterial death has proven to be a major bottleneck in the rational design of protegrin-based antibiotics. In the present work, we have carried out computational investigations of the diffusion of ions through a protegrin pore. We have thereby provided a connection between previous experimental and simulation work aimed at elucidating the structure of the protegrin pore and earlier experimental work investigating the ion transport characteristics of protegrin pores. The ion diffusion characteristics of protegrin pores are likely to be important in their ability to kill bacteria, as the uncontrolled flow of ions through a bacterial membrane will result in membrane depolarization and the loss of vital membrane functions. The present work thus represents an important first step in modeling and quantifying the timeline of events that lead to the killing of bacteria by protegrins. Furthermore, the computational tools that we have presented herein are easily extendible to similar systems, in particular other antimicrobial peptides.