| Implicit Solvent Model Studies of the Interactions of the Influenza Hemagglutinin Fusion Peptide with Lipid Bilayers Biophysical Journal, Volume 80, Issue 2, 1 February 2001, Pages 643-655 Dalit Bechor and Nir Ben-Tal Abstract The “fusion peptide”, a segment of ∼20 residues of the influenza hemagglutinin (HA), is necessary and sufficient for HA-induced membrane fusion. We used mean-field calculations of the free energy of peptide-membrane association (Δ) to deduce the most probable orientation of the fusion peptide in the membrane. The main contributions to Δ are probably from the electrostatic (Δ) and nonpolar (Δ) components of the solvation free energy; these were calculated using continuum solvent models. The peptide was described in atomic detail and was modeled as an -helix based on spectroscopic data. The membrane’s hydrocarbon region was described as a structureless slab of nonpolar medium embedded in water. All the helix-membrane configurations, which were lower in Δ than the isolated helix in the aqueous phase, were in the same (wide) basin in configurational space. In each, the helix was horizontally adsorbed at the water-bilayer interface with its principal axis parallel to the membrane plane, its hydrophobic face dissolved in the bilayer, and its polar face in the water. The associated Δ value was ∼−8 to −10kcal/mol (depending on the rotameric state of one of the phenylalanine residues). In contrast, the Δ values associated with experimentally observed oblique orientations were found to be near zero, suggesting they are marginally stable at best. The theoretical model did not take into account the interactions of the polar headgroups with the peptide and peptide-induced membrane deformation effects. Either or both may overcompensate for the Δ difference between the horizontal and oblique orientations. Abstract | Full Text | PDF (1615 kb) |
| Continuum Solvent Model Calculations of Alamethicin-Membrane Interactions: Thermodynamic Aspects Biophysical Journal, Volume 78, Issue 2, 1 February 2000, Pages 571-583 Amit Kessel, David S. Cafiso and Nir Ben-Tal Abstract Alamethicin is a 20-amino acid antibiotic peptide that forms voltage-gated ion channels in lipid bilayers. Here we report calculations of its association free energy with membranes. The calculations take into account the various free-energy terms that contribute to the transfer of the peptide from the aqueous phase into bilayers of different widths. The electrostatic and nonpolar contributions to the solvation free energy are calculated using continuum solvent models. The contributions from the lipid perturbation and membrane deformation effects and the entropy loss associated with peptide immobilization in the bilayer are estimated from a statistical thermodynamic model. The calculations were carried out using two classes of experimentally observed conformations, both of which are helical: the NMR and the x-ray crystal structures. Our calculations show that alamethicin is unlikely to partition into bilayers in any of the NMR conformations because they have uncompensated backbone hydrogen bonds and their association with the membrane involves a large electrostatic solvation free energy penalty. In contrast, the x-ray conformations provide enough backbone hydrogen bonds for the peptide to associate with bilayers. We tested numerous transmembrane and surface orientations of the peptide in bilayers, and our calculations indicate that the most favorable orientation is transmembrane, where the peptide protrudes ∼4Å into the water-membrane interface, in very good agreement with electron paramagnetic resonance and oriented circular dichroism measurements. The calculations were carried out using two alamethicin isoforms: one with glutamine and the other with glutamate in the 18th position. The calculations indicate that the two isoforms have similar membrane orientations and that their insertion into the membrane is likely to involve a 2-Å deformation of the bilayer, again, in good agreement with experimental data. The implications of the results for the biological function of alamethicin and its capacity to oligomerize and form ion channels are discussed. Abstract | Full Text | PDF (589 kb) |
| Continuum Solvent Model Studies of the Interactions of an Anticonvulsant Drug with a Lipid Bilayer Biophysical Journal, Volume 80, Issue 6, 1 June 2001, Pages 2536-2545 Amit Kessel, Boaz Musafia and Nir Ben-Tal Abstract Valproic acid (VPA) is a short, branched fatty acid with broad-spectrum anticonvulsant activity. It has been suggested that VPA acts directly on the plasma membrane. We calculated the free energy of interaction of VPA with a model lipid bilayer using simulated annealing and the continuum solvent model. Our calculations indicate that VPA is likely to partition into the bilayer both in its neutral and charged forms, as expected from such an amphipathic molecule. The calculations also show that VPA may migrate (flip-flop) across the membrane; according to our (theoretical) study, the most likely flip-flop path at neutral pH involves protonation of VPA pending its insertion into the lipid bilayer and deprotonation upon departure from the other side of the bilayer. Recently, the flip-flop of long fatty acids across lipid bilayers was studied using fluorescence and NMR spectroscopies. However, the measured value of the flip-flop rate appears to depend on the method used in these studies. Our calculated value of the flip-flop rate constant, 20/s, agrees with some of these studies. The limitations of the model and the implications of the study for VPA and other fatty acids are discussed. Abstract | Full Text | PDF (388 kb) |
Copyright © 1982 The Biophysical Society. All rights reserved.
Biophysical Journal, Volume 37, Issue 1, 217-225, 1 January 1982
doi:10.1016/S0006-3495(82)84671-7
Research Article
D.D. Thomas, D.J. Bigelow, T.C. Squier and C. Hidalgo
We have used spin labels and electron paramagnetic resonance (EPR) to study the correlation between the rotational dynamics of protein and lipid in sarcoplasmic reticulum (SR) membranes. A short-chain maleimide spin label was used to monitor the submillisecond rotational mobility of the Ca-ATPase enzyme (using saturation transfer EPR); a free fatty acid spin label was used to monitor the submicrosecond rotational mobility of the bulk lipid hydrocarbon chains (using conventional EPR); and a fatty acid spin label derivative (long-chain maleimide) attached to the enzyme was used to monitor the mobility of hydrocarbon chains adjacent to the protein (i.e., boundary lipid). In the native SR membranes, the protein was highly mobile (effective correlation time 50 microseconds). The spectra of the hydrocarbon probes both contained at least two components. For the unattached probe, the major component indicated nearly as much mobility as in the absence of protein (effective rotational correlation time 3 ns), while a minor component, corresponding to 25–30% of the total signal, indicated strong immobilization (effective correlation time greater than or equal to 10 ns). For the attached hydrocarbon probe, the major component (approximately 70% of the total) was strongly immobilized, and the mobile component was less mobile than that of the unattached probe. When the lipid-to-protein ratio was reduced 55% by treatment with deoxycholate, protein mobility decreased considerably, suggesting protein aggregation. A concomitant increase was observed in the fraction of immobilized spin labels for both the free and attached hydrocarbon probes. The observed hydrocarbon immobilization probably arises in part from immobilization at the protein-lipid boundary, but protein-protein interactions that trap hydrocarbon chains may also contribute. When protein aggregation was induced by glutaraldehyde crosslinking, submillisecond protein mobility was eliminated, but there was no effect on either hydrocarbon probe. Thus protein aggregation does not necessarily cause hydrocarbon chain immobilization.