Twist is the key to the gating of mechanosensitive ion channel NOMPC
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, China
Figures
Figure 1 with 4 supplements
Force distribution during the push-to-open gating process of NOMPC.
(a) The simulation systems of NOMPC. The NOMPC molecule was divided into two subsystems, denoted by the orange and purple rectangular boxes, for molecular dynamics (MD) simulations. The interface between the linker helices (LH) and the TRP domains is shown in a circular inset (bottom view). (b) The membrane-parallel (purple line) and membrane-normal (yellow line) components of the net forces on the TRP domain exerted by the LH domain. The error bars denote the standard deviations from two compressive trajectories (CI-1/2) and two free trajectories (FI-1/2). (c) The net forces on the TRP domain exerted by the LH domain. The gray quiver on each residue showed the net force exerted by the LH domain. The black shows the resultant force on the residues of the TRP domain. Two major points of force application, E1571 and R1581, are marked. represents the inward force component. The data were averaged for the four subunits by rotationally symmetrized around the protein center.
Figure 1—figure supplement 1
Kinematic analysis of the push-to-open trajectory CI-1.
(a) The simulation systems and domain structures. (b) The pore dilation process in the push-to-open trajectory. (c) The motion tendency of the LH domain. The purple arrows represent each α-C, and the orange arrows represent the mass center of the LH domain. The data were averaged for the four subunits by rotationally symmetrized around the protein center. (d) The rotation of the TRP domain, projected in the XY plane (light purple line, positive values a clockwise rotation viewing from the intracellular side) and Z direction (dark purple line, the positive value meant a tilt-up rotation from intracellular side to extracellular side), respectively.
Figure 1—figure supplement 2
The pairwise force distribution analysis (FDA) results of the push-to-open trajectory CI-1 between the AR29 domain, the LH domain, and the TRP domain.
The size and color of each marker denote the magnitude of the corresponding pairwise FDA results labeled in the two sides. The circle marker and square marker show the FDA results between AR29-LH and TRP-LH, respectively.
Figure 1—figure supplement 3
The force distribution analysis (FDA) results of the push-to-open trajectories between the LH domain and the TRP domain on the XY plane (TRP).
A superimposed quiver plot of the FDA results for each residue of the TRP domain, exerted by the LH domain, was calculated from the trajectories FI-1/2 and CI-1/2.
Figure 1—figure supplement 4
The force distribution analysis (FDA) results of the push-to-open trajectory CI-1 between the TRP and transmembrane (TM) domain.
(a) The scalar FDA of the TM domain exerted by the TRP domain. The size of each marker indicates the magnitude of the corresponding pairwise interaction in FDA. The TM domain is subdivided into four regions with strong interactions, which are illustrated by circles of distinct colors: mint green for S1, violet for the S2-S3 linker, pink for the S4-S5 linker, and yellow for S6. (b) The quiver plot illustrates the membrane-normal component of the net-FDA of the TM domain exerted by the TRP domain. (c) Intracellular view and (d) side view of the structure. The regions of significant interactions are highlighted using the same color code as in (a).
Figure 2 with 3 supplements
A membrane-parallel torsion force can open NOMPC.
(a, b) The side view (a) and bottom view (b) of the net-FDA of the E1571 and R1581 on the TRP domain exerted from the LH domain, which was decomposed into the membrane-parallel and membrane-normal components. represents membrane-normal forces pointing into the membrane. (c, d) The transmembrane pore size evolution in the simulations with membrane-parallel forces (c) or membrane-normal forces (d), three replicates for each condition (trajectories: MPI-1/2/3, MNI-1/2/3, see ‘Methods’).
Figure 2—figure supplement 1
Water molecules around the pore region.
(a) A snapshot of trajectory MPI-1 at 800 ns. The pore was dilated so water molecules (red) could spontaneously pass through. (b) The number of water molecules in the gate region around I1554, which was the narrowest part. We counted the water molecules whose oxygen atom was within 4 Å in the Z-direction from the α-C of I1554.
Figure 2—figure supplement 2
The transmembrane pore size evolution in the simulations with (a) half or (b) one-third magnitude of original membrane-parallel force, three replicates for each condition (trajectories: MPI-h1/2/3, MPI-t1/2/3).
Figure 2—figure supplement 3
Secondary structure analysis of the TRP domain in the trajectory MPI-1.
The vertical coordinates denote all residue IDs of the TRP domains across the four chains. The analysis was conducted with DSSP.
Figure 3 with 2 supplements
Torsional mechanical properties of the AR bundle.
(a) The sketch of the steered molecular dynamics simulation. The dotted arrows reveal the direction of twisting. (b) The relationships between the torque on AR1-8 (left Y-axis), the length of the AR domain (right Y-axis), and the rotational angle of AR1-8. This was calculated from the rotating trajectories RII (0–4).
Figure 3—figure supplement 1
The torque (a) and rotational angle (b) versus time of trajectory RII, respectively.
The black line illustrates the trajectory RII-0 (the second step of the rotation of system II), while the other colored lines starting from a circle depict the third step of the rotation of system II at every 2.5° rotation for a duration of 100 ns in the trajectory RII-1/2/3/4. The solid line corresponds to the data of the AR1-8, whereas the dotted line corresponds to the LH domain (Figure 3).
Figure 3—figure supplement 2
Torsional mechanical properties of the AR bundle.
(a) The sketch of the steered molecular dynamics simulation. The dotted arrows reveal the direction of twisting. (b) The relationships between the torque on AR1-8 (left Y-axis), the length of the AR domain (right Y-axis), and the rotational angle of AR1-8. This was calculated from the rotating trajectories RII-fast (0–4). The torque (c) and rotational angle (d) versus time of trajectory RII-fast, respectively. The black line illustrates the trajectory RII-fast-0 (the second step of the rotation of system II), while the other colored lines starting from a circle depict the third step of the rotation of system II at every 2.5° rotation for a duration of 100 ns in the trajectory RII-fast-1/2/3/4. The solid line corresponds to the data of the AR1-8, whereas the dotted line corresponds to the LH domain. The fitted torsion coefficient from RII-fast is (2.31 × 0.44) × 103 kJ mol−1 rad−1 and the compression-twist coupling coefficient, , is (1.67±0.14) nm rad−1.
Figure 4 with 2 supplements
Force transmission along the AR domain.
(a) The quiver plot of net-FDA (XY planar) of each AR unit exerted from the ith AR unit shows the force transmission from the intracellular terminal to the transmembrane side of the AR domain viewing from AR1 toward AR29. represents the outward Z-component force. (b) The distribution of the pairwise residue-residue net-FDA within AR9 to AR29 (weak interaction under 5 pN neglected). The inset shows local information over 70 pN. (c) The representative interaction heatmaps (AR13-AR15) show the magnitude of non-bonded pairwise residue-residue net-FDA (left) and hydrogen bonds occupancy (right). (d) The Pearson correlation coefficient (PCC) between net-FDA and hbonds in AR units. The inset shows the mean value and standard deviation of Intra-AR (diagonal) and Inter-AR (sub-diagonal) PCCs.
Figure 4—figure supplement 1
Location of AR13-15 in the AR spring.
Figure 4—figure supplement 2
Secondary structure analysis of the force-acting AR units in the trajectory RII-0.
The vertical coordinates denote all residue IDs of the AR9-AR11 units of one chain. The analysis was conducted with DSSP.
Figure 5
A schematic diagram of the twist-to-open model.
The side view (left) and bottom view (right) of the twist-to-open model. Both the compression and clockwise twisting of the AR domain can generate a membrane-parallel twisting force on the TRP domain, which is the key component for gating.
Figure 6 with 1 supplement
Conformational changes of the TRP domain in various TRP channels with resolved closed- and open-state cryo-EM structures.
(a) The membrane-parallel rotational angle of the TRP helix (a positive value indicates clockwise rotation when viewed from the intracellular side). (b) The tilt angle of the TRP domain relative to the membrane surface (a positive value indicates tilt-up). S1-S4 helices were aligned for analysis. (c) and (d) represent the rotational and tilting conformational changes of the TRP domain upon gating, respectively. In the majority of the studied cases, the TRP domain rotates clockwise (c). The exception of counterclockwise rotation is observed for HsTRPA1. (Please refer to Table 1 for the protein structures used in this analysis).
Figure 6—figure supplement 1
Rotation of the TRP domain of TRPV1 under torsional or pushing forces.
(a) Structure of squirrel TRPV1. (b) Overlay of TRPV1 conformations at 0 ns (gray) and 500 ns (red) under torsional force, as viewed from the intracellular side. The dark red denotes the AR1-2 units, while the light red indicates the TRP domain. (c) Rotation of AR1-2 units (dark red, rotating around the center of TRPV1) and the TRP domain (light red, self-rotating) under torsional force. (d) Similar to (b), but under pushing force. (e) Rotation of the TRP domain under pushing force (light red, self-rotating).
Tables
Table 1
PDB ID of resolved cryo-EM structures used in Figure 6.
| Protein | State description | PDB ID |
|---|---|---|
| RnTRPV1 | apo→open (+RTX/DkTx) | 5IRZ, 7L2L, 5IRX; Gao et al., 2016; Zhang et al., 2021 |
| RnTRPV1 | apo→open (+RTX,4°→25°C) | 5IRZ, 7RQU, 7RQX, 7RQZ; Gao et al., 2016; Kwon et al., 2022 |
| RnTRPV1 | apo→open (+capsaisin,48°C) | 5IRZ, 7LPD, 7LPE; Gao et al., 2016; Kwon et al., 2021 |
| RnTRPV2 | apo→open (+2APB,agonist) | 6U84, 7N0N; Pumroy et al., 2019; Pumroy et al., 2022 |
| HsTRPV3 | apo→open (+THCV) | 8V6K, 8V6M, 8V6L; Nadezhdin et al., 2024 |
| HsTRPV3 | apo→open (+2-APB) | 8V6K, 8V6O, 8V6N; Nadezhdin et al., 2024 |
| MmTRPV3 | apo→open (42 °) | 7MIM, 7MIL, 7MIO; Nadezhdin et al., 2021b |
| HsTRPV4 | apo→open (+4a-PDD) | 8T1B, 8T1D; Nadezhdin et al., 2023b |
| HsTRPV4 | close→open (−antagonist, +agonist) | 8FC7, 8FC9, 8FCB; Kwon et al., 2023 |
| OcTRPV5 | apo→open (+CoA) | 7T6J, 8FHI; Fluck et al., 2022; Lee et al., 2023 |
| DmTRPA1 | close→sensitized (warm) | 7YKR, 7YKS; Wang et al., 2023 |
| HsTRPA1 | close→open (inhibitor:A96; agonist:IA) | 6V9Y, 6V9X; Zhao et al., 2020 |
| DrTRPM2 | apo→open (+ADPR, Ca2+) | 6DRK,6DRJ; Huang et al., 2018 |
| SrTRPM2 | apo→open (+ADPR, Mg2+) | 8SRJ,8SRD; Huang et al., 2024 |
| NvTRPM2 | close→pre-open (+ADPR, Ca2+) | 6CO7,9JJE; Zhang et al., 2018; Tóth et al., 2024 |
| HsTRPM4 | cold close→warm open (+DVT,Ca2+) | 9B92, 9B8W, 9B8Y; Hu et al., 2024 |
| DrTRPM5 | apo→open (+Ca2+) | 7MBP, 7MBS; Ruan et al., 2021 |
| MmTRPM7 | apo→open (+agonist) | 8SI2, 8SI5; Nadezhdin et al., 2023a |
| MmTRPM8 | apo→open (+cooling agonist) | 8E4P, 8E4L; Yin et al., 2022 |
Table 2
Molecular dynamics simulation systems.
| System I | System II | |
|---|---|---|
| Protein | TM, LH, AR29 | LH, AR1-AR29 |
| Box size | 145 × 145 × 145 Å3 | 290 × 193 × 200 Å3 |
| Atom number | 314,352 | 1,134,213 |
| Membrane | 492 POPC | / |
| Ions | 0.15 M NaCl | 0.15 M NaCl |
| Water number | 71,968 | 354,567 |
Table 3
Simulation trajectories of system I.
| Trajectory (label) | MPI-1/2/3 |
|---|---|
| Pulling group | Side chain of 1571 and 1581 |
| Force vector of each chain (kJ mol−1 nm−1) | On 1571: (3.4, 69.4, 0.0) On 1581: (13.1, 91.5, 0.0) |
| Simulation time | 800 ns × 3 replicates |
| Trajectory (label) | MPI-h1/2/3 |
| Pulling group | Side chain of 1571 and 1581 |
| Force vector of each chain (kJ mol−1 nm−1) | On 1571: (1.7, 34.7, 0.0) On 1581: (6.6, 45.8, 0.0) |
| Simulation time | 1000 ns × 3 replicates |
| Trajectory (label) | MPI-t1/2/3 |
| Pulling group | Side chain of 1571 and 1581 |
| Force vector of each chain (kJ mol−1 nm−1) | On 1571: (1.1, 23.1, 0.0) On 1581: (4.4, 30.5, 0.0) |
| Simulation time | 1000 ns × 3 replicates |
| Trajectory (label) | MNI-1/2/3 |
| Pulling group | Side chain of 1571 and 1581 |
| Force vector of each chain (kJ mol−1 nm−1) | On 1571: (0.0, 0.0, 28.3) On 1581: (0.0, 0.0, 61.2) |
| Simulation time | 800 ns × 3 replicates |
-
The force vectors are described in an X'Y'Z' coordinate system for each subunit. The positive direction of the X'-axis is oriented parallel to the TRP helix, pointing from the center of the pore towards the membrane. The positive direction of the Y'-axis is perpendicular to the TRP helix. The positive direction of the Z'-axis is perpendicular to the membrane, pointing towards the extracellular direction. The X'Y'Z' coordinate system follows the right-hand rule.
Table 4
Simulation trajectories of system II.
| Trajectory (label) | RII-0 | RII-1/2/3/4 | RII-fast-0 | RII-fast-1/2/3/4 |
|---|---|---|---|---|
| Rotation group 1 | LH | LH | LH | LH |
| Rotation group 2 | AR1-8 | AR1-8 | AR1-8 | AR1-8 |
| Rotational speed (°/ns) | 0.05 | 0 | 0.1 | 0 |
| Simulation time (ns) | 200 | 200 | 100 | 100 |
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Twist is the key to the gating of mechanosensitive ion channel NOMPC
eLife 13:RP102941.
https://doi.org/10.7554/eLife.102941.3
