Implicit Membrane Investigation of the Stability of Antimicrobial Peptide β-Barrels and Arcs

Abstract

Previous simulations showed that the β-hairpin antimicrobial peptide (AMP) protegrin-1 can form stable octameric β-barrels and tetrameric arcs (half barrels) in both implicit and explicit membranes. Here, we extend this investigation to several AMPs of similar structure: tachyplesin, androctonin, polyphemusin, gomesin, and the retrocyclin θ-defensin. These peptides form short β-hairpins stabilized by 2–3 disulfide bonds. We also examine synthetic β-sheet peptides selected from a combinatorial library for their ability or inability to form pores in lipid membranes. When heptameric, octameric, and decameric β-barrels and tetrameric arcs of these peptides were embedded in preformed neutral or anionic lipid pores (i.e., pores in neutral or anionic membranes, respectively), a variety of behaviors and membrane binding energies were observed. Due to the cationic charge of the peptides, more favorable transfer energies and more stable binding were observed in anionic than neutral pores. The synthetic peptides bound very strongly and formed stable barrels and arcs in both neutral and anionic pores. The natural AMPs exhibited unfavorable or marginally favorable binding energy and kinetic stability in neutral pores, consistent with the lower hemolytic activity of some of them compared with protegrin-1. Binding to anionic pores was more favorable, but significant distortions of the barrel or arc structures were sometimes noted. These results are discussed in light of the available experimental data. The diversity of behaviors obtained makes it unlikely that the barrel and arc mechanisms are valid for the entire family of β-hairpin AMPs.

Transmembrane Pore Structures of β-Hairpin Antimicrobial Peptides by All-Atom Simulations

“…Further, tachyplesin showed lower overall tendency towards mutual interaction than protegrin did: larger oligomers than dimers of tachyplesin did not form at all. This result verifies our previous implicit membrane simulations showing that tachyplesin is unstable as a β-barrel 43 . In contrast, protegrin (which had the ability to form stable β-barrels in 43 ) showed the ability to form new associations between peptides within the pore (i.e., the trimer in Fig.…”

“…Our previous structural comparison 43 indicated the differences in hydrophobic residue packing between these two peptides’ putative pore structures. Although both peptides show “imperfect amphipathicity,” which concentrates the hydrophobic side chains on one face, the central region of the hairpin between the two disulfide bonds is longer in tachyplesin than protegrin, and this lengthened portion in tachyplesin contains two arginine side chains (R5 and R14) that face the same direction as both disulfide bonds (i.e., into the pore lumen).…”

“…After importing the PDB file for protegrin-1 into CHARMM, the peptide’s energy was minimized in water, followed by 200 ps of MD simulation with the Verlet integrator (time step: 2 fs, temperature: 298.5 K; used for all implicit simulations, following 43 ). Subsequent energy minimization then yielded the monomeric structure used for oligomerization.…”

“…During equilibration, we imposed intermolecular β-sheet hydrogen bonds using CHARMM’s NOE facility, following 43 . To generate the tilted structure of the sheared β-barrels, the hydrogen bonding pattern was shifted by two residues only once for each pair of peptides, and the other half of the hydrogen bonding junctions remained as in an unsheared β-sheet.…”

“…This paper describes all-atom molecular dynamics (MD) simulations of protegrin oligomers performed using the Anton 2 supercomputer. We also check the results against those for β-hairpin AMP tachyplesin 49 , whose β-barrel formation was assessed as unstable (in contrast to that of protegrin) in a previous implicit membrane investigation 43 . To examine whether and how protegrin oligomerizes on membrane surfaces en route to pore formation, we performed one group of simulations of protegrin oligomers on 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC):1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1′-rac-glycerol) (POPG) bilayer surfaces.…”