For those focusing on the behavior of proteins in membranes, rather than the lipids themselves, the membrane is simply a heterogeneous solvent. Therefore, including in the energy function the solvation free energy of the protein in this heterogeneous solvent provides a thermodynamically valid approach to model protein-membrane interactions. Several years ago we extended the EEF1 aqueous implicit solvation model to membranes by introducing a second set of solvation parameters pertaining to a nonpolar solvent and adjusting electrostatic interactions in the membrane interior (Ref. 1). This model was named IMM1 and was later supplemented with a Gouy-Chapman term describing counterion-screened electrostatic interactions of a solute with negatively charged membrane lipids (Ref. 2). The updated model was tested on peptides that bind to anionic membranes and was found to give peptide locations, configurations, and binding energies consistent with experimental data.
The model has been extended to account for aqueous pores (Ref. 3,5), transmembrane voltage (Ref. 4), the membrane dipole potential (Ref. 6), lateral pressure effects (Ref. 7), and curved membranes (Ref. 8). The latter has been applied to several membrane curvature sensing proteins (Ref. 9,10).
References
- Lazaridis, T. “Effective energy function for proteins in lipid membranes”, Proteins, 52:176-192 (2003)
- Lazaridis, T. “Implicit solvent simulations of peptide interactions with anionic lipid membranes”, Proteins, 58:518-27 (2005)
- Lazaridis, T. “Structural Determinants of Transmembrane Beta-Barrels”, J. Chem. Theory Comput., 1:716-22 (2005)
- Mottamal, M., Lazaridis, T. “Voltage-dependent energetics of alamethicin monomers in the membrane”, Biophys. Chem. , 122:50-7 (2006)
- Mihajlovic, M., Lazaridis, T. “Antimicrobial peptides bind more strongly to membrane pores”, BBA-Biomembranes , 1798:1494-1502 (2010)
- Zhan H., Lazaridis, T. “Influence of the membrane dipole potential on peptide binding to lipid bilayers”, Biophys Chem, 161:1-7 (2012)
- Zhan H., Lazaridis, T. “Inclusion of Lateral Pressure/Curvature Stress Effects in Implicit Membrane Models”, Biophysical J, 104:643-54 (2013)
- Nepal B., Leveritt J. III, Lazaridis T. “Membrane curvature sensing by amphipathic helices: Insights from implicit membrane modeling”, Biophysical J, 114:2128 (2018)
- Nepal B., Sepehri A., Lazaridis T. “Mechanisms of negative membrane curvature sensing and generation by ESCRT III subunit Snf7”, Pro. Sci., 29:1473-85 (2020)
- Nepal B., Sepehri A., Lazaridis T. “Mechanism of negative membrane curvature generation by I-BAR domains”, Structure, 29:1440-1452 (2021)