Fig 1.
Schematics of membrane fusion stages.
The membranes are shown in blue, cell and virion environments in green and yellow, respectively. (A) Tight contact of viral and endosomal membranes. (B) Two apposed lipid bilayers. (C) Stalk, a hydrophobic lipid bridge between proximal monolayers. (D) Hemifusion diaphragm: during stalk expansion, lipids of the distal monolayers are brought into contact, thus forming a bilayer. (E) Fusion pore.
Fig 2.
Simulation snapshots of considered HAfp configurations: (A) TM hairpin, (B) surface hairpin, (C) boomerang, (D) W14 mutant.
Color coding: water oxygen atoms, blue spheres; lipid and cholesterol molecules: white spheres, HAfp: yellow ribbon; HAfp Trp14 side chain: purple.
Fig 3.
Thickness of interbilayer space averaged over 2 × 400 ns from independent MD runs.
Positions of HAfp Cα atoms every 100 ns are marked with circles; blue: residues 1, 7, 9, green: residue 14, red: residues 17, 21, 23; positions of N and C termini are marked by blue and red stars, respectively. Black dots correspond to locations of lipid tails protrusions.
Fig 4.
(A) Distributions of local (0.5 nm × 0.5 nm bins in XY plane) instantaneous interbilayer distances in considered systems. (B) Sample geometries of lipid tail protrusion and N-P contact between lipids from the opposing membranes. (C-D) Correlation between local interbilayer distance and the frequency of N-P contacts (C) or lipid tails protrusions (D). (E) Residue-based mean minimum distance profiles between HAfp and opposing membrane heavy atoms. (F) The distribution of ϕ angle (see text for definition) for surface HAfp hairpin in single and double bilayer systems. Shadows (A, E) correspond to one standard deviation.
Fig 5.
(A-B) PMF for stalk formation in (A) 310 K and (B) 350 K; vertical dashed lines indicate the moment of stalk formation assessed by the appearance of hydration discontinuity as shown in panel C. (C) Local dehydration of interbilayer space at 310 K at consecutive umbrella windows, relative to membrane-only system at ξc = 0.1 (see Methods for definition). (D) Mean angle (ϕ) between the orthogonal vector to surface-bound HAfp hairpin plane and the Z axis. Lines are guide to the eye, error bars correspond to one standard deviation.
Table 1.
Gibbs free energy (G‡, kJmol−1), entropy (ΔS, kJmol−1K−1), and enthalpy (ΔH, kJmol−1), corresponding to free energy barriers for stalk formation at 310 K and 350 K (in brackets).
TΔS is reported for 310 K.
Fig 6.
Partial atomic densities across stalk in XZ plane (upper row) and simulation snapshots along the Z axis (lower row) for TM hairpin, surface hairpin, and boomerang configurations (results for wt boomerang and W14A mutant are qualitatively the same; only the former is shown).
Black and red colors denote density of HAfp heavy atoms in hydrophobic and hydrophilic residues, respectively.
Fig 7.
(A) Statistics of distance between Cα atom of 14th HAfp residue and stalk centre of mass. (B, C) Top view along membrane normal on peptide-stalk assembly summarising the two energetically favourable models. Yellow ribbons—HAfp, green spheres—lipid carbon atoms, blue spheres—water oxygen atoms.