On the Nature of Antimicrobial Activity:  A Model for Protegrin-1 Pores

Abstract

We conducted over 150 ns of simulation of a protegrin-1 octamer pore in a lipid bilayer composed of palmitoyloleoyl-phosphatidylethanolamine (POPE) and palmitoyloleoyl-phosphatidylglycerol (POPG) lipids mimicking the inner membrane of a bacterial cell. The simulations improve on a model of a pore proposed from recent NMR experiments and provide a coherent understanding of the molecular mechanism of antimicrobial activity. Although lipids tilt somewhat toward the peptides, the simulated protegrin-1 pore more closely follows the barrel-stave model than the toroidal-pore model. The movement of ions is investigated through the pore. The pore selectively allows negatively charged chloride ions to pass through at an average rate of one ion every two nanoseconds. Only two events are observed of sodium ions crossing through the pore. The potential of mean force is calculated for the water and both ion types. It is determined that the chloride ions move through the pore with ease, similarly to the water molecules with the exception of a zone of restricted movement midway through the pore. In bacteria, ions moving through the pore will compromise the integrity of the transmembrane potential. Without the transmembrane potential as a countermeasure, water will readily flow inside the higher osmolality cytoplasm. We determine that the diffusivity of water through a single PG-1 pore is sufficient to cause fast cell death by osmotic lysis.

Cysteine deleted protegrin-1 (CDP-1): Anti-bacterial activity, outer-membrane disruption and selectivity

“…Structural studies have demonstrated that the -hairpin conformation of PG-1, although monomeric in free solution [38,39], may form oligomeric -sheet like structures in zwitterionic detergent micelles and model lipid bilayers [40,41]. It has been proposed that these oligomeric -sheet states of PG-1 can induce pore formation in bacterial membrane causing cell lysis [40][41][42][43].…”

Membrane Curvature-sensing and Curvature-inducing Activity of Islet Amyloid Polypeptide and Its Implications for Membrane Disruption

“…Peptides that employ the detergent-like carpet mechanism cause widespread defects throughout the membrane surface in a nonspecific manner (25)(26)(27)(28). Pore models, in contrast, entail monomers assembling to form a discrete oligomer in the membrane that acts as a pore with ion channellike properties (29,30) or, alternatively, peptides inducing the membrane to form a toroidal pore lined by its own phospholipids (31)(32)(33). Different studies have proposed a variety of mechanisms such as these for IAPP, including pore mechanisms (16, 34 -38).…”

Current Understanding of the Mechanisms by which Membrane-Active Peptides Permeate and Disrupt Model Lipid Membranes

“…This oligomer was later observed in MD simulations by Langham et al [113] and Jang et al [114]. Langham et al suggested that the PG-1 oligomer is aligned in a barrel-stave shaped membrane pore [113]. However, rotational-echo double resonance experiments showed only a small distance between the lipid heads and the Arg residues at both the β-turn and in the middle of the β-strand (less than 6.5 Å to the phosphorous atom of lipid head), implying a toroidal pore [115].…”

“…Their 1 H and 19 F spin diffusion NMR data showed that eight or ten PG-1 peptides self-assemble into a parallel (NCCN) n (n=4 or 5) oligomeric structure in an anionic lipid membrane pore, with an inner diameter of ~2.1 nm [111]. This oligomer was later observed in MD simulations by Langham et al [113] and Jang et al [114]. Langham et al suggested that the PG-1 oligomer is aligned in a barrel-stave shaped membrane pore [113].…”