State-specific morphological deformations of the lipid bilayer explain mechanosensitive gating of MscS ion channels
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, United States
- Department of Biochemistry and Molecular Biology, University of Chicago, United States
Figures
Figure 1
Structure of a putatively open conformation of wild-type MscS in a lipid nanodisc.
(A) Left, structure of the MscS heptamer (in cartoon representation) fitted on the 3.1 Å resolution cryo-electron microscopy (EM) map (transparent surface). Each protomer is shown in a different …
Figure 2 with 1 supplement
Comparison of closed and open structures of MscS in lipid nanodiscs.
(A) Left, the open structure of MscS in PC14:1 lipid nanodiscs (blue cartoons) is superimposed onto that of the closed state (red), previously determined in PC18:1 nanodiscs (PDB ID 6PWN, and …
Figure 2—figure supplement 1
Cryo-electron microscopy (EM) map and structural model of open-state MscS in PC14:1 lipid nanodiscs, highlighting putative sites of lipid interaction atop the C-terminus of TM2, involving residue R88.
Lipids at these sites were more clearly discerned in the closed state in PC18:1 nanodiscs (Reddy et al., 2019), and referred to as ‘hook’ lipids.
Figure 3
Comparison of alternate conformations of open MscS obtained in different experimental conditions.
(A) Overlay comparing helices TM1 and TM2 in the closed state (green tube and white cartoons) and in the putatively open states obtained in PC14:1 nanodiscs (this work, cyan), in PC10:0 nanodiscs …
Figure 4 with 2 supplements
Closed-state MscS induces drastic perturbations of the lipid bilayer.
The figure summarizes the results from multiple simulations of the closed structure of MscS in different membrane compositions and using different forcefield representations (Table 1). The …
Figure 4—figure supplement 1
Lipid solvation of hydrophobic cavities outside the membrane drives the formation of inner-leaflet protrusions in closed-state MscS.
The figure shows three different views of a fragment of the closed MscS structure comprising TM1, TM2, and TM3a (from left to right) in two alternative representations (top and bottom). Residues are …
Figure 4—figure supplement 2
Relaxation of the closed-state MscS structure in all-atom simulations.
(A) To preclude large-scale changes in fold that might develop in the 10-μs timescale due to cumulative forcefield inaccuracies, a restraining potential was applied to all and angles in the …
Figure 5 with 1 supplement
Molecular structure of the membrane perturbations induced by MscS in the closed state.
(A) Instantaneous configurations of the lipid bilayer in single snapshots of two of the molecular dynamics (MD) trajectories calculated for closed-state MscS in POPC …
Figure 5—figure supplement 1
Molecular structure of the membrane perturbations induced by MscS in the closed state.
The figure reports results for multiple simulations of closed- and open-state MscS in membranes of different size and lipid composition using either coarse-grained or all-atom representations (Table …
Figure 6
Lipids in inner-leaflet protrusions exchange with lipids in the bulk membrane.
(A) Close-up of one of the hydrophobic cavities that drive the formation of membrane protrusions in closed-state MscS. To identify which lipids reside in these protrusions and for how long, we …
Figure 7
Persistence of lipid protrusions across increasing lateral tension conditions despite changes in global membrane properties.
The figure summarizes the results from simulations of the closed structure of MscS under different membrane tensions. (A) The cryo-electron microscopy (EM) structure of MscS in the closed state …
Figure 8 with 2 supplements
Membrane perturbations are largely eliminated upon MscS channel opening.
The figure summarizes the results from a 20-µs simulation of open MscS in a POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) membrane, using a coarse-grained representation. (A) The …
Figure 8—figure supplement 1
Change in protein-lipid interfacial area during gating is much smaller than what could be inferred from change of in-plane cross-sectional area.
(A) To evaluate the area of the protein surface exposed to the membrane, we quantified the number of coarse-grained (CG) particles in the channel within 6.5 Å of any lipid particle, for each …
Figure 8—figure supplement 2
Changes in membrane morphology upon gating of MscS.
The figure summarizes results from simulations of alternative open conformations of wild-type and mutagenized MscS in POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine; Wang et al., 2008; Pliota…
Figure 9
MSL1 gating causes morphological changes in membrane akin to those observed for MscS.
The figure summarizes the results from simulations of closed and open states of MSL1 in a POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) membrane, using a coarse-grained representation (Tabl…
Figure 10
Conceptualization of the membrane deformation model of mechanosensation proposed in this study.
Lateral tension increases the open-state probability of MscS because membrane stretching increases the energetic cost of the deformations in the lipid bilayer that stabilize the closed conformation …
Tables
Table 1
Molecular simulation systems evaluated in this study of McsS and MSL1 mechanosensation.
| MscS coarse grained* | MscS all atom† | MSL1coarse grained* | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Closed WT POPC | Closed WT POPC §d | Closed WT DMPC | Closed WT PC:PG | Open WT POPC | Open A106V POPC | Open D67R1 POPC | Closed WT POPC | Closed WT DMPC | Closed WT POPC | Open WT POPC | |
| Protein | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| POPC | 2057 | 755 | 0 | 1651 | 686 | 737 | 740 | 755 | 0 | 2001 | 1916 |
| POPG | 0 | 0 | 0 | 407 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| DMPC | 0 | 0 | 768 | 0 | 0 | 0 | 0 | 0 | 768 | 0 | 0 |
| Na+ | 855 | 328 | 340 | 1265 | 328 | 328 | 328 | 314 | 326 | 855 | 855 |
| Cl– | 862 | 335 | 347 | 865 | 335 | 356 | 349 | 335 | 347 | 890 | 883 |
| Water ‡ | 75,938 | 28,123 | 29,000 | 75,501 | 28,200 | 28,372 | 28,299 | 115,170 | 118,774 | 76,076 | 76,549 |
| Total atoms or particles | 106,364 | 41,871 | 41,392 | 106,352 | 41,120 | 41,603 | 41,524 | 476,183 | 476,473 | 106,012 | 105,248 |
| System size (nm) | 26.5×26.5×18.7 | 16.9×16.9×17.9 | 16.3×16.3×19.1 | 26.3×26.3×19.0 | 16.9×16.9×17.9 | 16.9×16.9×17.9 | 16.9×16.9×17.9 | 15.9×15.9×19.9 | 15.4×15.4×21.1 | 26.5×26.5×18.7 | 26.5×26.5×18.7 |
| Time (μs) | 20 | 20 | 20 | 20 | 20 | 20 | 20 | 10 | 8 | 80 | 20 |
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POPC: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine; WT: wild type; DMPC:1–2-dimyristoleoyl-sn-glycero-3-phosphocholine; POPG:1–2-palmitoyl-2-oleoylglycero-3-phosphoglycerol.
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*
MARTINI 2.2 forcefield.
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†
CHARMM36m forcefield.
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‡
One CG water particle is equivalent to four AA water molecules.
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§
Five additional 10 μs simulations were carried out for this system under applied lateral tensions of 0, 0.5. 2.5, 5.0, and 10 mN/m.
Additional files
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Supplementary file 1
Cryo-electron microscopy (EM) data acquisition and model refinement statistics.
EM maps and atomic models have been deposited in the Electron Microscopy Data Bank (accession number EMD-27337) and the Protein Data Back (entry code 8DDJ).
- https://cdn.elifesciences.org/articles/81445/elife-81445-supp1-v2.docx
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MDAR checklist
- https://cdn.elifesciences.org/articles/81445/elife-81445-mdarchecklist1-v2.docx
