Large-scale state-dependent membrane remodeling by a transporter protein
- National Heart, Lung and Blood Institute, National Institutes of Health, United States
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, United States
Figures
Figure 1 with 1 supplement
Structure of the GltPh trimer in the outward- and inward-facing states.
(A) View from the extracellular space, with the three protomers in the outward-facing conformation (PDB 2NWL). The ‘scaffold’ (blue) mediates all protein-protein interactions between protomers. The …
Figure 1—figure supplement 1
Molecular simulation systems.
(A) Coarse-grained representation of all-inward GltPh (yellow surface) in a model POPC membrane (298 K), viewed from the extracellular space. Phosphate and choline groups are highlighted with orange …
Figure 2 with 2 supplements
Changes in membrane morphology induced by the conformational cycle of GltPh.
The results are based on coarse-grained MD simulations of the transporter in a POPC bilayer at 298K. (A) Deflection of the membrane mid-plane for each of the primary states in the cycle. The …
Figure 2—video 1
Changes in membrane morphology induced by the conformational cycle of GltPh.
Structure of all-outward GltPh (represented as in Figure 1) alongside a calculated density map for the lipid bilayer alkyl chains within 10 Å of the protein surface (yellow), based on CG simulations …
Figure 2—video 2
Changes in membrane morphology induced by the conformational cycle of GltPh.
Structure of all-inward GltPh (represented as in Figure 1) alongside a calculated density map for the lipid bilayer alkyl chains within 10 Å of the protein surface (yellow), based on CG simulations …
Figure 3
Membrane deformation induced by all-inward GltPh in coarse-grained MD simulations in a POPC bilayer at 298 K, with and without an applied membrane tension of increasing magnitude (as indicated).
The deflection of the membrane mid-plane was calculated and represented as in Figure 2A. From left to right, the standard error of the data (N = 3) across each map is, on average, 0.6 Å, 0.7 Å, 0.4 …
Figure 4 with 2 supplements
Membrane deformation induced by all-inward GltPh in coarse-grained MD simulations in different bilayers.
The data for POPC, POPE, and 2:1 POPE:POPG were obtained at 298 K; the data for DPPC were obtained at 323 K. The deflection of the membrane mid-plane was calculated and represented as in Figure 2A. …
Figure 4—figure supplement 1
Changes in bilayer thickness induced by the conformational cycle of GltPh.
The plots quantify the thickness of the hydrophobic core of the membrane, as defined by the lipid alkyl chains, in either the all-outward or all-inward states of the transporter. Data are shown for …
Figure 4—figure supplement 2
Changes in lipid-chain tilt induced by the conformational cycle of GltPh.
The plots quantify the mean second-rank order parameter of the C-C bonds along the lipid alkyl chains, for either the outer or inner layers of the lipid bilayer (upper and lower panels, …
Figure 5 with 2 supplements
Membrane deformation induced by all-inward GltPh, based on large-scale all-atom simulations in DPPC at 323 K.
(A) Deflection of the membrane mid-plane relative to a flat surface, calculated exactly as in Figure 2A. The standard error of the data (N = 3 trajectories, 150 ns each) across the deflection map …
Figure 5—figure supplement 1
Evaluation of potential biases resulting from conversion of coarse-grained molecular configurations into an all-atom representation.
(A, B) All-atom simulation of the relaxation of an artificial 10 Å deflection in the membrane mid-plane. Given the large system size of the all-atom simulation system for all-inward GltPh …
Figure 5—video 1
Membrane deformation induced by all-inward GltPh in large-scale all-atom simulations.
The structure of the protein is represented as in Figure 1, and shown alongside a calculated density map for the lipid bilayer alkyl chains within 10 Å from the protein surface (yellow). The density …
Figure 6 with 1 supplement
Energetics of solvation and evolutionary conservation of the GltPh lipid interface.
(A) Molecular systems used to evaluate the change in the free energy of polar/hydrophobic solvation that results from membrane bending, for all-inward GltPh. The solvent-accessible surface area of …
Figure 6—figure supplement 1
Energetics of polar and hydrophobic solvation of the GltPh lipid interface.
Panels (A), (B) and (C) display information analogous to that shown in Figure 6, but for the X-ray structure of all-inward GltPh (PDB 3KBC).
Figure 7 with 1 supplement
Estimate of the free-energy cost associated with the membrane deformation caused by all-inward GltPh, from direct potential-of-mean-force calculations.
(A) Simulated membrane deformation, in the absence of the protein, induced by application of the Multi-Map method in combination with umbrella sampling, for a coarse-grained POPC lipid bilayer at …
Figure 7—figure supplement 1
Comparison of membrane-bending free-energy values calculated with the Multi-Map method and with the Helfrich-Canham theory, for the same ensembles of molecular configurations.
(A) The PMF curves shown in Figure 7 are correlated with energy profiles calculated with the Helfrich-Canham equation. Calculation of the latter requires two inputs: the assumed bending modulus kc …
Figure 8
Membrane deformation induced by the Na+-dicarboxylate symporter VcINDY, based on coarse-grained MD simulations in POPC at 298 K.
(A) Structure of the VcINDY dimer in the outward-facing state, viewed along the membrane perpendicular from the extracellular space. The protein is represented as GltPh in Figure 1. (B) Deflection …
