Conformational changes, excess area, and elasticity of the Piezo protein-membrane nanodome from coarse-grained and atomistic simulations
- Department of Biomolecular Systems, Max Planck Institut of Colloids and Interfaces, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, Germany
Figures
Figure 1
Coarse-grained Piezo 2 nanodome in a tensionless membrane.
(a) Representative conformations and average nanodome shape, average nanodome contours, and average lipid density within quadratic membrane patches with side length nm for the constrained Piezo 2 cryo-EM structure and the relaxed Piezo 2 structure in a coarse-grained tensionless membrane. The relaxed nanodome shape is an average over conformations from the last microseconds of 10 independent simulation runs with a length of 8 μs. The nanodome shape for the constrained Piezo 2 cryo-EM structure is an average over the last microseconds of three independent simulation runs with a length of 4 μs for a harmonic force constant of 1000 kJ mol-1 nm-2 per bead. (b) Radial membrane profiles of the average nanodome shapes. The shaded areas represent the error of the mean obtained from the shape profiles of the independent runs. (c) Mean curvature along the shape profiles calculated from first and second derivatives at radial distance , which are obtained from local quadratic fits of profile segments nm. (d) Average displacement of the center of mass (COM) of 4 TM-helix units versus average radial distance. The 4 TM-helix units are numbered as in Figure 7. Only protein residues in the TM sections of the 4-TM units are included in the calculation of COMs (see Materials and methods).
Figure 2
Tension-induced flattening of the coarse-grained Piezo 2 protein-membrane nanodome.
(a) Average nanodome shapes, (b) average nanodome contours, and (c) average lipid density within quadratic membrane patches with sidelength nm at membrane tensions from 0 to 20.8 mN/m. The nanodome shapes and lipid densities are averages over conformations from the last microseconds of 10 independent simulation runs with lengths of 8 μs for and with lengths of 4 μs for . (d) Radial membrane profiles of the average nanodome shapes in (a). The shaded areas represent the error of the mean obtained from the shape profiles of the independent runs. (e) Average displacement of the center of mass (COM) of 4 TM-helix units versus average radial distance. The 4 TM-helix units are numbered as in Figure 7. Only protein residues in the TM sections of the 4-TM units are included in the calculation of COMs.
Figure 3
Flattening of the Piezo 2 protein-membrane nanodome in atomistic simulations.
(a) Average nanodome shape, (b) average nanodome contours, and (c) average lipid density in a tensionless membrane. The nanodome shapes and lipid densities are averages over conformations from the last 50 ns of 5 independent atomistic simulation runs with lengths of 300 ns. (d) Radial membrane profiles of the nanodome shapes at membrane tensions from 0 to 18 mN/m obtained from averaging over conformations from the last 50 ns of five independent atomistic simulation runs. (e) Excess area of the protein-membrane nanodome versus membrane tension from coarse-grained simulations of membrane-embedded Piezo 1 and Piezo 2 and atomistic simulations with Piezo 2. The values and errors of excess area are obtained from the extrapolations to long timescales shown in Figure 4.
Figure 4 with 1 supplement
Extrapolation of the excess area of the protein-membrane nanodome in coarse-grained simulations with (a) Piezo 2 and (b) Piezo 1 and (c) in atomistic simulations with Piezo 2 to long timescales.
In these extrapolations, the trajectories lengths are divided into five equal time intervals, and the excess area in each time interval is calculated for the nanodome shape obtained from averaging over conformations of all independent simulation runs in this time interval. The values are plotted against the inverse of the centers of the time intervals, and the values of the last three intervals are linearly fitted with the function LinearModelFit of Mathematica 13. The errors of the data points represent the error of the mean of values obtained for the individual simulation runs, and the shaded error region of the linear fits represents prediction bands with confidence level . The values with error shown in Figure 4 are determined as the extrapolated values with prediction band error at .
Figure 4—figure supplement 1
Extrapolation of the membrane bending energy of the nanodome in coarse-grained simulations with (a) Piezo 2 and (b) Piezo 1 to long timescales, akin to the extrapolations of in Figure 4.
Figure 5 with 1 supplement
Elasticity modeling of the Piezo 2 protein based on coarse-grained simulation data.
(a) Piezo 2 height change versus membrane tension in our coarse-grained simulations of membrane-embedded Piezo 2. The protein height change is defined as where is the vertical displacement of the fourth 4-TM unit of the Piezo arms relative to the channel center (see Figure 2e). (b) Excess area of the nanodome and (c) bending energy of the lipid membrane in the nanodome versus Piezo height change . The values and errors of and are obtained from extrapolating simulation results at the tension values , , , , , and mN/m to long timescales (see Figure 4, Figure 4—figure supplement 1). (d) Vertical force determined from Equation 2 and the slopes of the fitted lines in (b) and (c) at the values obtained from simulations at the tension values , , , and mN/m. The vertical force is the absolute value of the opposing and in equilibrium equal forces exerted by the Piezo protein and by the membrane at a given tension value (see text). The dashed lines result from linear fitting of data points for mN/m in (a), of data points for nm in (b) and (c), and of all data points in (d) with the function LinearModelFit of Mathematica 13. The shaded error region of the linear fit in (d) represents prediction bands with confidence level .
Figure 5—figure supplement 1
Elasticity modeling of the Piezo 1 protein based on coarse-grained simulation data.
Figure 6
Response of the Piezo 1 and Piezo 2 channels to membrane tension.
(a,b) Simulation conformations of the three TM helices 38 that line the ion channel from our coarse-grained simulations of membrane-embedded Piezo 1 at vanishing membrane tension and at the largest simulated tension mN/m. (c,d) Simulation conformations of the TM helices 38 from our coarse-grained simulations of membrane-embedded Piezo 2 at and the largest simulated tension mN/m. The 50 aligned simulation conformations in (a) to (d) are taken from the last microseconds of the 10 simulation trajectories at intervals of 0.25 μs along each trajectory (5 conformations per trajectory), with TM helices 38 depicted as spline curves of backbone beads in Mathematica 13. (e) Average distance between the backbone beads of the residues L2469 that form the outermost constriction site of the ion channel in Piezo 1 (Yang et al., 2022) versus membrane tension of our simulations. The L2469 backbone beads of the three TM helices 38 are shown as beads in (a) and (b). (f) Average tilt angle of the Piezo 1 helices 38 relative to the vertical direction of the simulation conformations in (a,b) versus membrane tension of our simulations. (g) Average distance between the backbone atoms of the residues L2473 that form the outermost constriction site of the ion channel in Piezo 2 (Yang et al., 2022) versus membrane tension . (h) Average tilt angle of the Piezo 2 helices 38 versus membrane tension . Error bars in (e) to (h) represent errors of the mean calculated from average values obtained for the 10 trajectories.
Figure 7
Structure and topology of the Piezo 2 monomer (Wang et al., 2019).
The 38 TM helices of the monomer are numbered from the N- to the C-terminus of the protein chain. The TM helices 1–36 are arranged in 9 TM units with 4 helices each. The ion channel of the Piezo 2 trimer is lined by the three TM helices 38 of the three monomers. Loops not resolved in the cryo-EM structure of the Piezo 2 trimer structure in detergent micelles are indicated by dashed lines.
Figure 8
Embedding the Piezo 2 protein into a membrane.
(a) Piezo 2 trimer with ‘lipid envelop’ placed into a planar and asymmetric membrane of area 50 nm × 50 nm. The lipid envelope was created by insertion of a Piezo 2 monomer into a planar lipid membrane and subsequent superposition of the resulting lipid-enveloped monomers on the Piezo 2 cryo-EM structure (see Materials and methods). (b) Piezo 2 trimer embedded in a continuous membrane nanodome after minimization and equilibration simulations starting from (a).
Tables
Table 1
Lipid percentages of membrane.
| POPC | POPE | CHOL | POPS | PIP2 | DPSM | |
|---|---|---|---|---|---|---|
| inner leaflet | 50 | 20 | 20 | 5 | 5 | - |
| outer leaflet | 50 | 20 | 20 | - | - | 5 |
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Conformational changes, excess area, and elasticity of the Piezo protein-membrane nanodome from coarse-grained and atomistic simulations
eLife 14:RP105138.
https://doi.org/10.7554/eLife.105138.3
