Coarse grain lipid–protein molecular interactions and diffusion with MsbA flippase

Abstract

Coarse-grained (CG) modeling has proven effective for simulating lipid bilayer dynamics on scales of biological interest. Modeling the dynamics of flexible membrane proteins within the bilayer, on the other hand, poses a considerable challenge due to the complexity of the folding or conformational landscape. In the present work, the multiscale coarse-graining method is applied to atomistic peptide-lipid "soup" simulations to develop a general set of CG protein-lipid interaction potentials. The reduced model was constructed to be compatible with recent solvent-free CG models developed for protein-protein folding and lipid-lipid model bilayer interactions. The utility of the force field was demonstrated by molecular dynamics simulation of the MsbA ABC transporter in a mixed DOPC/DOPE bilayer. An elastic network was parameterized to restrain the MsbA dimer in its open, closed and hydrolysis intermediate conformations and its impact on domain flexibility was examined. Conformational stability enabled long-time dynamics simulation of MsbA freely diffusing in a 25 nm membrane patch. Three-dimensional density analysis revealed that a shell of weakly bound "annular lipids" solvate the membrane accessible surface of MsbA and its internal substrate-binding chamber. The annular lipid binding modes, along with local perturbations in head group structure, are a function of the orientation of grooves formed between transmembrane helices and may influence the alternating access mechanism of substrate entry and translocation.

Model parameters for simulation of physiological lipids

“…The sidechain‐centric model of Hills et al is used to represent protein–protein interactions, which maintains a similar mapping of heavy atoms to CG sites. Tabulated lipid–protein protein interactions were developed previously using MS‐CG . Transmembrane peptide is weakly biased to α‐helical structure by assigning harmonic springs ( K = 150 kJ mol −1 nm −2 ) between α‐carbons pairs within 10.5 Å separated by two or more bonds.…”

“…To explore the phase properties of various CG bilayers, simulations are conducted at constant surface tension to determine the equilibrated area per lipid. Minimal changes are made to the model scheme so that protein‐lipid potentials previously developed by Ward et al remain compatible for simulations of membrane proteins . Stable CG bilayer simulations of realistic geometry are demonstrated for membranes containing DOPC, DOPE, 1‐palmitoyl‐2‐oleoyl‐phosphatidyl‐choline (POPC), 1‐palmitoyl‐2‐oleoyl‐phosphatidyl‐ethanolamine (POPE), phosphatidylglycerol (POPG), cholesterol (Chol), and cardiolipin (CL).…”

Lipid somersaults: Uncovering the mechanisms of protein-mediated lipid flipping

“…Furthermore, current models for ABC-type translocases propose an alternating opening of lateral entry and exit pathways for the transported phospholipid substrate to the central cavity formed by the transmembrane helices. Coarse-grained modelling has revealed lipid binding to the ABC transporter MsbA within the grooves formed between transmembrane helices [193]. Similarly, scramblases appear to display such potential grooves.…”

Investigating the dynamic nature of the ABC transporters: ABCB1 and MsbA as examples for the potential synergies of MD theory and EPR applications

“…A large range of conformations were accessible at room temperature, in line with the observation of a more closed and dynamic state of the nucleotide free MsbA measured using EPR. The behavior of lipid surrounding MsbA in three conformations [74] showed that a ring of annular lipid formed, which was not homogeneous. Distortions of the membrane bilayer structure were observed and also lipid molecules reaching into the substrate binding site.…”