Computational prediction of the optimal oligomeric state for membrane‐inserted β‐barrels of protegrin‐1 and related mutants

Abstract

Protegrin-1 is a widely studied 18-residue β-hairpin antimicrobial peptide. Evidence suggests that it acts via a β-barrel pore formation mechanism, but the exact number of peptides comprising the pore state is unknown. In this study, we performed molecular dynamics simulations of β-barrels of protegrin and three related mutants (v14v16l, v14v16a, and r4n) in NCNC parallel topology in implicit membrane pores of varying radius and curvature for oligomeric numbers 6–14. We then identified the optimal pore radius and curvature values for all constructs and determined the total effective energy and the translational and rotational entropic losses. These, along with an estimate of membrane deformation free energy from experimental line tension values, provided an estimate of the overall energetics of formation of each pore state. The results indicated that oligomeric numbers 7–13 are generally stable, allowing the possibility of a heterogeneous pore state. The optimal oligomeric state for protegrin is the nonamer, shifting to higher numbers for the mutants. Protegrin, v14v16l, and r4n are stable as membrane-inserted β-barrels, but v14v16a seems much less so because of its decreased hydrophobicity.

The unusual conformation of cross‐strand disulfide bonds is critical to the stability of β‐hairpin peptides

“…Similar distortions of β-sheet conformations were reported in other simulations studies of PG-1 in water or in the presence of micelles but were not related to possible issues with the ability of the force field to describe correctly the conformation of the peptide [99,102,103,107,110]. Lazardis and co-workers [57,104,105,111,115] carried out a number of This article is protected by copyright. All rights reserved.…”

“…Given the high sequence and structural similarity among β-AMPs, it is likely that the same observations would apply to MD simulations of thantanin, arenicins, tachyplesins, polyphemusins and androctonin. There have been a number of MD simulation studies of β-AMPs and in particular of PG-1 [57,[99][100][101][102][103][104][105][106][107][108][109][110][111][112][113] (reviewed in [114]). Interestingly, only one of these studies contained a quantitative analysis of β-sheet content.…”

“…This might be due to several reasons. First, the majority of these studies reported simulations of PG-1 or β-AMPs in the presence of micelles [112,113], implicit membrane models [104,106,111,115], or explicit lipid bilayers [57,[99][100][101][102][103]105,[107][108][109][110]. The main aim of these simulations was thus not to study the conformation of the peptide in solution but rather its interaction with lipids or lipid mimetics, its orientation in the membrane, and the stability of pores of varying sizes and topologies.…”

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

“…After imposition of the β-sheet hydrogen bonds, further equilibration MD was run for 200 ps, followed by minimization. The NOE constraints were removed, and then the individual tetramers and octamers were placed with the more hydrophobic side facing an anionic implicit pore with radius R o = 12 Å and curvature k = 15 Å, the optimal pore geometry for protegrin octamers found in ref . The decamer barrel employed the optimal decameric implicit pore geometry of R o = 16 Å and k = 20 Å .…”

“…Pre-formed β-barrels of several similar β-hairpin AMPs in NCNC parallel topology were found to be much less stable than those of protegrin 43 . We also studied protegrin NCNC parallel β-barrels of 6–14 peptides: although the nonamer had the lowest energy, a range of pore sizes 7–13 peptides had relatively consistent favorability 48 . Those results were consistent with the predictions of the solid-state NMR study 25 , which suggested an octamer, but inconsistent with 29 , which suggested a larger pore.…”