Membrane curvature sensing and symmetry breaking of the M2 proton channel from Influenza A
- Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California, San Francisco, United States
- Graduate Group in Biophysics, University of California, San Francisco, United States
Figures
Figure 1
M2 channels and influenza egress.
(A) Structural organization of the nascent viral bud. M2 first accumulates in the host plasma membrane (PM), which is approximately flat and therefore has zero Gaussian curvature. M2 then diffuses …
Figure 2
Unrestrained simulations reveal dynamic amphipathic helix (AH) domains.
(A) RMSDs of Ca backbones over time. Yellow indicates the transmembrane (TM) domain only, red the AH domain only, and blue the full protein. Snapshots from unrestrained molecular dynamics (MD) are …
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Figure 2—source data 1
Raw double electron–electron resonance (DEER) data from Figure 7 of Kim et al., 2015 (green curves in panel B).
- https://cdn.elifesciences.org/articles/81571/elife-81571-fig2-data1-v2.xlsx
Figure 3
Influence of lipid packing on bilayer tension and shape.
Comparison of tension and structural features of simulated membranes with the initial packing (left, panels A, C) versus the rebalanced leaflets (right, panels B, D). (A) Lateral pressure profile of …
Figure 4
M2 membrane deformation patterns from simulation.
(A) Structures for restrained-protein simulations. Extracellular loops in green, transmembrane (TM) domain in yellow, amphipathic helix (AH) domain in blue (polar/charged) and white (hydrophobic). …
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Figure 4—source data 1
Structure of the parallel amphipathic helix (pAH) model.
- https://cdn.elifesciences.org/articles/81571/elife-81571-fig4-data1-v2.zip
Figure 5
Surface height and thickness heatmaps for three different channel configurations.
Compressive deflections are negative/shown in bright colors. Expansive deflections are positive/dark colors. The same scale is used for the upper and lower leaflets to highlight the greater amount …
Figure 6
Leaflet thicknesses and position of the bilayer midplane.
Upper and lower leaflet thicknesses are plotted as time-averaged surface values in the top and middle rows, with lighter shades of blue denoting regions of leaflet thinning. The height of the …
Figure 7
Lipid tilt around different M2 conformations.
The top row shows representative all-atom snapshots extracted from the protein-restrained, equilibrium simulations of 2L0J, parallel amphipathic helix (AH) domain model, and 2N70 (2, 3, and 4 in Tabl…
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Figure 7—source data 1
Full size image of lipids around 2L0J.
- https://cdn.elifesciences.org/articles/81571/elife-81571-fig7-data1-v2.pdf
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Figure 7—source data 2
Full size image of lipids around the parallel amphipathic helix (AH) domain model.
- https://cdn.elifesciences.org/articles/81571/elife-81571-fig7-data2-v2.pdf
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Figure 7—source data 3
Full size image of lipids around 2N70.
- https://cdn.elifesciences.org/articles/81571/elife-81571-fig7-data3-v2.pdf
Figure 8
Mean deflection and tilt as a function of distance from the protein center.
Mean deflection (A) and tilt (B) as a function of radial distance from the protein center for restrained simulations. Points are colored by local density, such that bright spots reflect highly …
Figure 9
Boundary conditions extracted from molecular dynamics (MD) simulations.
(A) Parallel amphipathic helix (AH) domain M2 protein in a lipid bilayer. The molecular surface is shown with hydrophobic residues in white and charged and polar residues in blue. The mean …
Figure 10
Continuum model membrane deformations compared to molecular dynamics (MD) surfaces.
Left column: MD upper and lower leaflet mean positions. Right column: continuum model minimum energy upper and lower leaflet surfaces for a flat membrane (200 Å by 200 Å membrane with zero …
Figure 11
C2 symmetry broken conformations are stabilized in membranes with negative Gaussian curvature.
(A) Transfer free energy ΔΔG(K) for moving M2 from a flat region to a region with Gaussian curvature K = ±1/Rc2, where Rc is the radius of curvature (top X-axis). Solid lines at negative K show ΔΔG …
Appendix 1—figure 1
Leaflet surfaces (left and middle columns) and bilayer thicknesses (right column) for the original restrained 2L0J simulation and restrained Repack simulations 1–4.
The upper leaflet has 200 lipids, and the lower leaflet lipid count is indicated in parentheses.
Appendix 1—figure 2
Leaflet tilt surfaces for the original restrained 2L0J simulation and restrained Repack simulations 1–4.
The upper leaflet has 200 lipids, and the lower leaflet lipid count is indicated in parentheses.
Appendix 1—figure 3
Leaflet thicknesses for the original restrained 2L0J simulation and restrained Repack simulations 1–4.
The upper leaflet has 200 lipids, and the lower leaflet lipid count is indicated in parentheses.
Appendix 1—figure 4
Amphipathic helix (AH) domain mobility in Repack 4, unrestrained 2L0J simulations.
(A) Trajectory RMSDs for the AH domain. Independent replicates are color coded. (B) Trajectory RMSDs for the transmembrane (TM) domain. (C) I51–I51 distance distributions from unrestrained …
Appendix 1—figure 5
Boundary conditions extracted from molecular dynamics (MD) simulations.
(A, B) Membrane–protein boundary information for the fourfold 2L0J structure. (C, D) Membrane–protein boundary information for the twofold 2N70 structure. Upper and lower bounds of the mean …
Appendix 1—figure 6
Influence of cholesterol enrichment on membrane curvature sensing by different M2 channel conformations.
Membrane parameters from Table 2 were used to calculate the membrane bending energy for moving from a flat membrane region to regions of differing curvature. (A) A 0% cholesterol membrane with 28.5 …
Appendix 1—figure 7
Membrane shapes which approximate an ideal spherical cap or saddle.
(A) Dash–dotted red: circle of radius R = 200 Å. Dashed blue: quadratic approximation of circle, valid for . Solid black: the m = 0 analytic biharmonic solution finite at the origin behaves …
Tables
Table 1
List of simulations.
| ID | Label | Gromacs | Length (ns) | PDBID | Bilayer # lipids | Restraints |
|---|---|---|---|---|---|---|
| 1 | Unrestrained 1 | 2020.6 | 2829 | 2L0J | 200 upper; 150 lower | No |
| 2 | 2L0J 1 | 2020.6 | 3808 | 2L0J | 200 upper; 150 lower | Yes |
| 3 | pAH 1 | 2020.6 | 3760 | Parallel AH | 200 upper; 150 lower | Yes |
| 4 | 2N70 1 | 2020.6 | 1727 | 2N70 | 200 upper; 150 lower | Yes |
| 5 | 2L0J Repack 1 | 2020.6 | 2740 | 2L0J | 200 upper; 158 lower | Yes |
| 6 | 2L0J Repack 2 | 2020.6 | 2500 | 2L0J | 200 upper; 166 lower | Yes |
| 7 | 2L0J Repack 3 | 2020.6 | 2890 | 2L0J | 200 upper; 174 lower | Yes |
| 8 | 2L0J Repack 4 – Final | 2020.6 | 5000 | 2L0J | 200 upper; 183 lower | Yes |
| 9 | Unrestrained 2 | 2020.6 | 2650 | 2L0J | 200 upper; 183 lower | No |
| 10 | Unrestrained 3 | 2020.6 | 3000 | 2L0J | 200 upper; 183 lower | No |
| 11 | Unrestrained 4 | 2020.6 | 3000 | 2L0J | 200 upper; 183 lower | No |
| 12 | Unrestrained 5 | 2020.6 | 3000 | 2L0J | 200 upper; 183 lower | No |
| 13 | pAH Repack Final | 2020.6 | 3000 | Parallel AH | 200 upper; 183 lower | Yes |
| 14 | 2N70 Repack Final | 2020.6 | 3000 | 2N70 | 200 upper; 183 lower | Yes |
Table 2
Default elastic membrane material properties.
| Parameters | % cholesterol | Values | Reference |
|---|---|---|---|
| Membrane thickness (LC) | 0 | 28.5 Å | Argudo et al., 2017 |
| 30 | 35 Å | This manuscript | |
| 50 | 37 Å | Scaling from Ferreira et al., 2013 | |
| Surface tension (α) | 0 | 3.0 × 10−13 N/Å | Latorraca et al., 2014 |
| 30 | 3.0 × 10−13 N/Å | “ ” | |
| 50 | 3.0 × 10−13 N/Å | “ ” | |
| Bending modulus (KC) | 0 | 29 kBT | Average value described in Methods |
| 30 | 65 kBT | Scaling from Henriksen et al., 2006 | |
| 50 | 68 kBT | Scaling from Pan et al., 2009 | |
| Gaussian modulus (KG) | 0 | −26 kBT | Relation from Hu et al., 2012 |
| 30 | −56 kBT | “ ” | |
| 50 | −61 kBT | “ ” | |
| Areal compression modulus (Ka) | 0 | 2.13 × 10−11 N/Å | Henriksen et al., 2006 |
| 30 | 3.55 × 10−11 N/Å | “ ” | |
| 50 | 3.73 × 10−11 N/Å | Scaling described in Methods |
Appendix 1—table 1
Leaflet properties for restrained 2L0J simulations with varying lipid numbers.
| Simulation | Area per lipid (Å2) | Thickness at box edges (Å) | Tension (mN/m) | |||
|---|---|---|---|---|---|---|
| (lower lipid #) | Upper leaflet | Lower leaflet | Upper leaflet | Lower leaflet | Upper leaflet | Lower leaflet |
| Original (150)* | 42.5 | 49.9 | 18.5 | 16.3 | −10.8 | 24.6 |
| Repack 1 (158) | 43.8 | 49.0 | 18.2 | 15.8 | −13.1 | 20.2 |
| Repack 2 (166) | 44.4 | 47.4 | 17.9 | 16.4 | −11.8 | 13.2 |
| Repack 3 (174) | 45.2 | 46.1 | 17.8 | 17.0 | −9.6 | 7.6 |
| Repack 4 (183)† | 46.4 | 45.1 | 17.4 | 17.2 | −3.8 | 8.0 |
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*
The original restrained 2L0J simulation used a semi-isotropic Berendsen barostat for pressure coupling. All repacked simulations, and extension simulations for Gromacs-LS calculations, use a Parrinello–Rahman barostat. Other simulation parameters were identical for all simulations.
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†
Lipid ratio used for all subsequent 2L0J analysis.
