Structural Behavior of the Peptaibol Harzianin HK VI in a DMPC Bilayer: Insights from MD Simulations

Abstract

Microsecond molecular dynamics simulations of harzianin HK VI (HZ) interacting with a dimyristoylphosphatidylcholine bilayer were performed at the condition of low peptide-to-lipid ratio. Two orientations of HZ molecule in the bilayer were found and characterized. In the orientation perpendicular to the bilayer surface, HZ induces a local thinning of the bilayer. When inserted into the bilayer parallel to its surface, HZ is located nearly completely within the hydrophobic region of the bilayer. A combination of solid-state NMR and circular dichroism experiments found the latter orientation to be dominant. An extended sampling simulation provided qualitative results and showed the same orientation to be a global minimum of free energy. The secondary structure of HZ was characterized, and it was found to be located in the 3-helical family. The specific challenges of computer simulation of nonpolar peptides are discussed briefly.

Orthogonal 19F‐Labeling for Solid‐State NMR Spectroscopy Reveals the Conformation and Orientation of Short Peptaibols in Membranes

“…In lipids with a highly positive spontaneous curvature, they can turn into a transmembrane state and assemble as a stable pore . In the case of HZ, both surface‐parallel and perpendicular alignments have been recently reported from MD simulations in DMPC, for which a deep penetration of this hydrophobic molecule towards the core of the bilayer was observed …”

“…In addition, we have resolved the structure of HZ in 50 % TFE, as well as in DPC and in SDS micelles, by solution‐state NMR spectroscopy . Furthermore, two computational models were included, which we obtained as averaged structures from two independent unrestrained all‐atom molecular dynamics (MD) simulations of HZ in a DMPC bilayer on a microsecond timescale . (The backbone torsion angles, ϕ / ψ , of all models are listed in Table S4 in the Supporting Information.)…”

“…[25,26] In the case of HZ, both surface-parallel and perpendicular alignments have been recently reported from MD simulations in DMPC,f or whichad eep penetration of this hydrophobic molecule towards the core of the bilayer was observed. [21] The observed realignment of HZ in bilayersw ith different lengths and spontaneousc urvatures can provide new mechanistic insights into the membrane-perturbing activity of HZ. Relative to many well-known antimicrobial peptides, harzianin is quite short and more hydrophobic,b esides being ap eptaibol with an unusual conformation.…”

“…This way, the backbone structure and different alignment states of the peptaibol harzianin HZ VI could be determined to overcome special challenges imposed by the short sequence and high content of Aib of this peptide. Despite its hydrophobic character and short length, HZ exhibits an alignment behavior that is also observed for longer and distinctly amphipathic sequences, such as α‐helical antimicrobial and pore‐forming peptides . In membranes with negative or low spontaneous curvature, HZ is preferentially aligned parallel to the bilayer surface, and it becomes tilted in lipids with high positive curvature.…”

“…[20] Furthermore, two computational models were included, which we obtaineda sa veraged structures from two independentu nrestrained all-atom molecular dynamics (MD) simulations of HZ in aD MPC bilayer on am icrosecond timescale. [21] (The backbone torsion angles, f/y,o fa ll models are listed in Table S4 in the Supporting Information. )…”