Insights into Membrane Protein-Lipid Interactions from Free Energy Calculations

Abstract

Integral membrane proteins are regulated by specific interactions with lipids from the surrounding bilayer.The structures of protein-lipid complexes can be determined through a combination of experimental and computational approaches, but the energetic basis of these interactions is difficult to resolve. Molecular dynamic simulations provide the primary computational technique to estimate the free energies of these interactions. We demonstrate that the energetics of protein-lipid interactions may be reliably and reproducibly calculated using three simulation-based approaches: potential of mean force calculations. alchemical free energy perturbation, and well-tempered metadynamics. We employ these techniques within the framework of a coarse-grained force field, and apply them to both bacterial and mammalian membrane protein-lipid systems. We demonstrate good agreement between the different techniques, providing a robust framework for their automated implementation within a pipeline for annotation of newly determined membrane protein structures.

Evaluating Inositol phospholipid interactions with Inward Rectifier Potassium Channels and characterising their role in Disease

“…Our recent study showed how the method could be extended to a CG protocol (CG-FEP) to assess relative protein-lipid binding free energies. This approach was in strong agreement with other free energy calculation methods such as potential of mean force calculation (PMF) and well-tempered metadynamics (WTMetaD) 6 .…”

“…Kir channels form an attractive target for applying a computational approach to compare binding affinity between phosphoinositides and also assess the impact of mutations on binding. Coarse-grained (CG) molecular dynamics (MD) simulations have previously been used to identify lipid-binding sites on ion channels [3][4][5] , as well as predicting the affinity of interactions 6 . For many years, the application of atomistic free energy perturbation (FEP) methods have been successfully applied to determine small molecule, lipid, and drug binding affinities 19 as well as to study the impact of amino acid side chain mutations 20,21 .…”

“…In this study, we use CG-FEP 6 to compare the relative binding free energies between different phospholipids and the human Kir6.2 channel, capturing the full thermodynamic cycle for the transition of PIP2 to PC, either directly or via intermediates phosphatidylinositol-4-phosphate (PI4P) and phosphatidylinositol (PI), and thereby reporting on the affinity of each interaction.…”

Defining how multiple lipid species interact with inward rectifier potassium (Kir2) channels

“…FEP calculations were performed as described in ref. 46. In brief, a pose of Kir2.2 with PIP 2 bound at both sites 1 and 2 was extracted from the equilibrium data, and the protein and PIP 2 molecules were built into a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayer using the insane protocol (64).…”

“…Further, by calculating the residence times of each interaction site, we identify their kinetic profiles, while free energy perturbation calculations (see, e.g., ref. 46) quantify the preference for PIP 2 vs. PS binding at each site. These analyses allow us to build up a picture of diverse lipid interactions on the surface of Kir2.2 channels, corresponding to the multimodal regulation of this channel by different lipid species.…”