Effect of pH on the influenza fusion peptide properties unveiled by constant-pH molecular dynamics simulations combined with experiment

Abstract

The influenza virus fusion process, whereby the virus fuses its envelope with the host endosome membrane to release the genetic material, takes place in the acidic late endosome environment. Acidification triggers a large conformational change in the fusion protein, hemagglutinin (HA), which enables the insertion of the N-terminal region of the HA2 subunit, known as the fusion peptide, into the membrane of the host endosome. However, the mechanism by which pH modulates the molecular properties of the fusion peptide remains unclear. To answer this question, we performed the first constant-pH molecular dynamics simulations of the influenza fusion peptide in a membrane, extending for 40 µs of aggregated time. The simulations were combined with spectroscopic data, which showed that the peptide is twofold more active in promoting lipid mixing of model membranes at pH 5 than at pH 7.4. The realistic treatment of protonation introduced by the constant-pH molecular dynamics simulations revealed that low pH stabilizes a vertical membrane-spanning conformation and leads to more frequent contacts between the fusion peptide and the lipid headgroups, which may explain the increase in activity. The study also revealed that the N-terminal region is determinant for the peptide’s effect on the membrane.

Molecular mechanisms of the influenza fusion peptide: insights from experimental and simulation studies

“…Conformations adopted by the IFP and their effect in the membrane. The conformations were obtained in constant‐pH MD simulations [66] starting from two distinct conformations (labeled as horizontal and vertical) obtained using a self‐assembly approach [37]. (A) Illustration of a lipid tail protrusion event promoted by interaction of a lipid with the peptide N terminus, observed in the constant‐pH MD simulations performed at pH 5 starting from the horizontal conformation [66] (this snapshot corresponds to the 114th ns of replicate 4).…”

“…The conformations were obtained in constant‐pH MD simulations [66] starting from two distinct conformations (labeled as horizontal and vertical) obtained using a self‐assembly approach [37]. (A) Illustration of a lipid tail protrusion event promoted by interaction of a lipid with the peptide N terminus, observed in the constant‐pH MD simulations performed at pH 5 starting from the horizontal conformation [66] (this snapshot corresponds to the 114th ns of replicate 4). (B) Illustration of a lipid tail protrusion event promoted by interaction of a lipid with the peptide N terminus, observed in the constant‐pH MD simulations performed at pH 5 starting from the vertical conformation [66] (this snapshot corresponds to the 597th ns of replicate 4).…”

“…The simulations show that the N‐terminal G1 interacts strongly with the phosphate groups, which results in head group intrusion and lipid tail protrusion (an illustration of this effect is shown in Fig. 2) [36–38,66]. Interestingly, both simulation and experimental studies have shown that having a free NH 3 + terminal is crucial for the IFP effect on the membrane [20,42,56,66].…”

Transient Excursions to Membrane Core as Determinants of Influenza Virus Fusion Peptide Activity

“…On the other hand, measurements based on attenuated total reflection Fourier-transform infrared spectroscopy (ATR-FTIR) or spin-label electron paramagnetic resonance (EPR) suggest that peptides insert obliquely into the external membrane leaflet with the N-helix tilted on average ∼50 degrees with respect to bilayer normal [9,10,17,18], which results in buried N-terminal group and solvent-facing kink region. Moreover, recent molecular dynamics (MD) simulations indicated the possibility of fully transmembrane peptide placement which can be achieved owing to local membrane thinning caused by aqueous solvent attraction towards hydrophilic residues on both hairpin poles [19][20][21][22].…”

Modulatory Effects of Acidic pH and Membrane Potential on the Adsorption of pH-Sensitive Peptides to Anionic Lipid Membrane

“…This method was firstly proposed by Baptista et al [33], using Poisson-Boltzmann equations and a continuum electrostatic model. Recently, Lousa and coworkers [34] applied this method to investigate the interaction of influenza virus fusion peptide, revealing important implications of protonated states on the orientation of this peptide in the lipid membrane. Different strategies such as different water models [35] and T-REX [36], available in the AMBER software [37], brought more molecular details for these systems.…”