Microtubule assembly governed by tubulin allosteric gain in flexibility and lattice induced fit
- Max Planck Institute for Biophysical Chemistry, Germany
Figures
Figure 1
Allosteric and lattice models of MT assembly represented by a three-dimensional thermodynamic cycle.
GTP- (orange) and GDP-dimers (blue) can be free (no box), MT-cap-bound (dotted box), or integrated into the MT body (solid box). The dimmed states denote energetically unfavored states.
Figure 2 with 4 supplements
PCA on the set of experimental structures.
(A) Projection of the set onto the plane constituted by the first and second largest-amplitude conformational modes. Each structure is represented by a point on this plane. Known experimental …
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Figure 2—source data 1
Coordinates of the PDB structures projected onto conformational modes 1 and 2.
- https://doi.org/10.7554/eLife.34353.005
Figure 2—figure supplement 1
A simplified 2D example of the principal component analysis (PCA).
Given a set of observations, each being a point on a plane described by only two coordinates (left panel), the method calculates ‘collective’ coordinates on this plane that account for as much of …
Figure 2—video 1
Merged set of the analyzed PDB structures played in consecutive order.
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Figure 2—video 2
Structural motion along conformational mode 1.
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Figure 2—video 3
Structural motion along conformational mode 2.
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Figure 3 with 1 supplement
Simulated tubulin ensembles in two nucleotide states (left vs.right panel) plotted as in Figure 2A,B.
Experimental structures are shown as black squares, whereas the simulated ensembles are shown as green (started from straight conformation) or pink (started from kinked conformation) point clouds. …
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Figure 3—source data 1
Coordinates of the merged GTP-tubulin ensemble started from a straight structure (PDB ID: 3JAT, two independent simulations) projected onto conformational modes 1 and 2 (left panel, green).
- https://doi.org/10.7554/eLife.34353.011
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Figure 3—source data 2
Coordinates of the merged GTP-tubulin ensemble started from kinked structures (PDB IDs: 5JQG, 5FNV) projected onto conformational modes 1 and 2 (left panel, pink).
- https://doi.org/10.7554/eLife.34353.012
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Figure 3—source data 3
Coordinates of the merged GDP-tubulin ensemble started from a straight structure (PDB ID: 3JAS, two independent simulations) projected onto conformational modes 1 and 2 (right panel, green).
- https://doi.org/10.7554/eLife.34353.013
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Figure 3—source data 4
Coordinates of the merged GDP-tubulin ensemble started from kinked structures (PDB IDs: 4ZOL, 4ZHQ) projected onto conformational modes 1 and 2 (right panel, pink).
- https://doi.org/10.7554/eLife.34353.014
Figure 3—figure supplement 1
Convergence of the simulated ensembles assessed by overlaying point clouds originating from different independent simulations (two independent simulations per bound nucleotide per curvature state).
The data are plotted as in Figure 2A,B and Figure 3. Dynamics of the simulated dimers stared from the straight MT conformations (PDB ID: 3JAT and 3JAS) during the -ns equilibration phase are shown …
Figure 4 with 3 supplements
Free energy profiles derived from the projections of the simulated ensembles onto a plane, where the x-axis denotes the position along the ensemble separation RC and the y-axis denotes an orthogonal coordinate describing the largest-amplitude bending motion in the combined TUB + TUB ensemble.
Experimental structures used for the free simulations are highlighted with gray dashed lines and green (straight structures) and pink squares (kinked structures).
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Figure 4—source data 1
Coordinates of the PDB structures projected onto the ensemble separation and common bending coordinates (GTP).
- https://doi.org/10.7554/eLife.34353.018
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Figure 4—source data 2
Coordinates of the merged GTP-tubulin ensemble started from a straight structure (PDB ID: 3JAT, two independent simulations) projected onto the ensemble separation and common bending coordinates (GTP).
- https://doi.org/10.7554/eLife.34353.019
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Figure 4—source data 3
Coordinates of the merged GTP-tubulin ensemble started from kinked structures (PDB ID: 5JQG, 5FNV) projected onto the ensemble separation and common bending coordinates (GTP).
- https://doi.org/10.7554/eLife.34353.020
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Figure 4—source data 4
Coordinates of the PDB structures projected onto the ensemble separation and common bending coordinates (GDP).
- https://doi.org/10.7554/eLife.34353.021
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Figure 4—source data 5
Coordinates of the merged GDP-tubulin ensemble started from a straight structure (PDB ID: 3JAS, two independent simulations) projected onto the ensemble separation and common bending coordinates (GDP).
- https://doi.org/10.7554/eLife.34353.022
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Figure 4—source data 6
Coordinates of the merged GDP-tubulin ensemble started from kinked structures (PDB ID: 4ZOL, 4ZHQ) projected onto the ensemble separation and common bending coordinates (GDP).
- https://doi.org/10.7554/eLife.34353.023
Figure 4—figure supplement 1
A 2D example of the ensemble separation search.
Given a system with two energy minima in the 2D conformational space (state 1 and 2), the method aims at rotating the coordinate system such that the x-axis coincides with the axis along which the …
Figure 4—figure supplement 2
Dot products of the three-dimensional ensemble separation vector with vectors of higher dimensions for the tubulin ensembles in two different nucleotide states.
With the increasing number of PCA eigenvectors in the search space, the ensemble separation vector becomes independent of the search space dimension. This yields the minimal search space in which …
Figure 4—video 1
Structural motion along the ensemble separation RC.
https://doi.org/10.7554/eLife.34353.024
Figure 5 with 2 supplements
Nucleotide-dependent motions of tubulin bending.
(A) Molecular representation of the twist-bend and splay-bend tubulin bending motions derived from the TUB and TUB simulated ensembles. The anchor point around the H8 helix is indicated with …
Figure 5—figure supplement 1
Functional mode analysis of the TUB and TUB ensembles.
(A) Straight (reference) and kinked tubulin structures aligned by -subunit. The RMSD to the reference increases as the tubulin conformation deviates from the straight conformation, irrespective of …
Figure 5—video 1
Side-by-side comparison of the twist-bend (green) and splay-bend (pink) conformational motions.
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Figure 6 with 1 supplement
Free energy profiles along the bending RCs defined for the TB and SB bending motions calculated for GTP- and GDP-tubulin.
Smaller (larger) values on the x-axis correspond to straighter (more kinked) dimer conformations. Squares denote the positions of the starting PDB structures in the GTP- (black) and GDP-state (gray) …
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Figure 6—source data 1
Free energy values (second and third columns, mean +/- SD) along the TB bending coordinate (first column) for GTP-tubulin.
- https://doi.org/10.7554/eLife.34353.030
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Figure 6—source data 2
Free energy values (second and third columns, mean +/- SD) along the TB bending coordinate (first column) for GDP-tubulin.
- https://doi.org/10.7554/eLife.34353.031
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Figure 6—source data 3
Free energy values (second and third columns, mean +/- SD) along the SB bending coordinate (first column) for GTP-tubulin.
- https://doi.org/10.7554/eLife.34353.032
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Figure 6—source data 4
Free energy values (second and third columns, mean +/- SD) along the SB bending coordinate (first column) for GDP-tubulin.
- https://doi.org/10.7554/eLife.34353.033
Figure 6—figure supplement 1
Convergence properties and robustness of the error evaluation with respect to the method used.
(A) Unnormalized individual umbrella histograms, each derived from a restrained simulation of at least 120 ns or longer. (B) Error evaluation using a block average method (Zhu and Hummer, 2012). The …
Figure 7 with 1 supplement
Dynamics and energetics of GTP-tubulin along the ensemble separation RC.
(A) Collective mode of motion along the ensemble separation RC represented as a linear interpolation between the TUB and TUB simulated ensembles. The largest-amplitude intrinsic rearrangements …
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Figure 7—source data 1
Free energy values (second and third columns, mean +/- SD) along the ensemble separation coordinate (first column).
- https://doi.org/10.7554/eLife.34353.036
Figure 7—figure supplement 1
Convergence properties and robustness of the error evaluation with respect to the method used.
(A) Unnormalized individual umbrella histograms, each derived from a restrained simulation of at least 120 ns or longer. The region around the barrier at nm was sampled more extensively. (B) …
Figure 8
The proposed, combined model of MT assembly represented by a thermodynamic cycle.
Here, TB and SB denote not only the different modes of tubulin bending but also the belonging to the respective free energy basin, i.e. anchor point state.
Additional files
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Transparent reporting form
- https://doi.org/10.7554/eLife.34353.038
