Free Energy Calculations for the Peripheral Binding of Proteins/Peptides to an Anionic Membrane. 1. Implicit Membrane Models

Abstract

The binding of peptides and proteins to the surface of complex lipid membranes is important in many biological processes such as cell signaling and membrane remodeling. Computational studies can aid experiments by identifying physical interactions and structural motifs that determine the binding affinity and specificity. However, previous studies focused on either qualitative behaviors of protein/membrane interactions or the binding affinity of small peptides. Motivated by this observation, we set out to develop computational protocols for bimolecular binding to charged membranes that are applicable to both peptides and large proteins. In this work, we explore a method based on an implicit membrane/solvent model (generalized Born with a simple switching in combination with the Gouy-Chapman-Stern model for a charged interface), which we expect to lead to useful results when the binding does not implicate significant membrane deformation and local demixing of lipids. We show that the binding free energy can be efficiently computed following a thermodynamic cycle similar to protein-ligand binding calculations, especially when a Bennett acceptance ratio based protocol is used to consider both the membrane bound and solution conformational ensembles. Test calculations on a series of peptides show that our computational approach leads to binding affinities in encouraging agreement with experimental data, including for the challenging example of the bringing of flexible MARCKS-ED peptides to membranes. The calculations highlight that for a membrane with a significant fraction of anionic lipids, it is essential to include the effect of ion adsorption using the Stern model, which significantly modifies the effective surface charge. This implicit membrane model based computational protocol helps lay the groundwork for more systematic analysis of protein/peptide binding to membranes of complex shape and composition.

Anionic Phospholipids Stabilize RecA Filament Bundles in Escherichia coli

“…Similar to our previous observations, the vertical differential solvation free energies (ΔΔ W slv ) of RecA binding to the membrane correlate with Δ F bind and overestimate this parameter (Zhang et al, 2014). The calculated binding affinity for the parallel binding conformation of RecA to the membrane is substantially stronger than the perpendicular mode by ~5 kcal/mol.…”

“…We computed the binding free energies of the two binding conformations using the GBSW-GCS model and the thermodynamic cycle described recently (Zhang et al, 2014), which demonstrated that this methodology accurately predicts the binding free energy of peptides with membranes. We tested several mutants that were designed based on the observed RecA/membrane binding interface, which involves mainly the DNA binding loop L2 and the N-terminal helix; to a lesser extent, the C-terminal domain also contributes to binding in the parallel binding conformation.…”

“…The vertical differential solvation free energy of the protein at the membrane surface vs. in bulk solution. As discussed in (Zhang et al, 2014), this quantity correlates with binding free energy when the system does not undergo significant conformational transitions upon binding. c . Binding free energy of the protein calculated using the protocol established in (Zhang et al, 2014) based on a specific thermodynamic cycle and the Bennett Acceptance Ratio (BAR) approach (Bennett, 1976).…”

“…As discussed in (Zhang et al, 2014), this quantity correlates with binding free energy when the system does not undergo significant conformational transitions upon binding.…”

Biophysical investigations with MARCKS-ED: dissecting the molecular mechanism of its curvature sensing behaviors

“…Phe residues, due to their elevated hydrophobicity, are found closer to the bilayer center (magenta curve) at ~± 12 Å. Implicit membrane simulations by Zhang, Yetiraj and Cui [38] likewise report this trend for the MARCKS-ED peptide where the charged and polar residues are found in the high dielectric constant region and the Phe residues are found close to the dielectric boundary. In comparison to Ellena et al [18] ~5-10 Å below the lipid phosphate was where they observed the Phe residues in the presence of Phosphatidylinositol 4,5-bisphosphate (PIP 2 ).…”