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Mechanics of severing for large microtubule complexes revealed by coarse-grained simulations
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10.1063/1.4819817
/content/aip/journal/jcp/139/12/10.1063/1.4819817
http://aip.metastore.ingenta.com/content/aip/journal/jcp/139/12/10.1063/1.4819817

Figures

Image of FIG. 1.
FIG. 1.

The two MT PF structures used in our bending simulations are depicted. The green letters on top of the various monomers indicate the identity of the protein chains, which are used to discuss the depolymerization behavior and bending angles obtained from the simulations. In this and all other figures, the α-tubulin monomers are in blue, while the β-tubulin monomers are in red.

Image of FIG. 2.
FIG. 2.

The FECs and pathways for bending of a single PF and of the 3 PFs complex with 29 fixed positions, under forces applied to 3 positions at their plus end. Panel (a) consists of the FECs corresponding to the two pathways for rupture in the 3 PFs complex (red and blue curves), and the corresponding FEC for the single PF structure (dark green curve). It reveals that the force/energy required to depolymerize a PF is significantly reduced when moving from the single PF to the 3 PFs complex. Panel (b) shows the depolymerization behavior for the 3 PFs complex system, which follows one of two pathways: removal of 1 or 3 dimers from the central PF.

Image of FIG. 3.
FIG. 3.

The time evolution of the various interdimer bending angles for two PF structures. The colors for each interface are chosen so that the same color on both plots indicates the interface is in the same position along the PF. HC and VO are closest to the fixed end of the PF, while BE and JC are closest to the pulled end of the PF. Panel (a) shows the interdimer interface angles for the 4-dimer single PF structure. The arrows indicate where various simulation events occur in relation to the behavior of the angles. Panel (b) is similar to (a), only for the bending of the 3 PFs complex with the 63 fixed positions that results in the removal of the maximal fragment (3 dimers) from the central PF (Pathway 3 described in the text). For this system, there are three clear transitions as the lateral contacts for each dimer break sequentially before the rupture of the longitudinal interface.

Image of FIG. 4.
FIG. 4.

The rupture pathways for the 3 PFs complex with 63 fixed positions under a bending force applied to 3 positions at its plus end. Panel (a) depicts the three possible pathways for the 3 PFs complex, under conditions mimicking an intact MT lattice. The major pathway is the removal of a single dimer from the central PF. Panel (b) shows the FECs and the main events leading to the depolymerization event. The labeled events are as follows: (I) dimer CD laterals break for all pathways, (II) dimer IJ laterals break for pathways 2 and 3, (III) interface JC breaks for pathway 1, (IV) dimer OP laterals break for pathway 3, (V) interface PI breaks for pathway 2, and (VI) interface VO breaks for pathway 3.

Image of FIG. 5.
FIG. 5.

The comparison between the behavior of a single PF and of the 3 PFs complex, when fixing the minus end and pulling only 2 positions (345 and 420) at the plus end. Panel (a) shows the FECs, which reveal the same decrease in required force as observed for pulling 3 positions. Panel (b) shows the 3 PFs complex simulation, which results in the removal of 3 dimers from the central PF. The single PF structure pathways are depicted in panel (b) of Fig. S5 in the supplementary material.

Image of FIG. 6.
FIG. 6.

The comparison between the behavior of a single PF and of the 3 PFs complex, when fixing both the minus and the plus ends and pulling 3 positions of a central dimer. Panel (a) depicts the FEC, which indicates that the force required to break the 3 PFs complex is again lower than for the single PF. However, for both structures the rupture force when pulling at the center is significantly higher than the force required to break when pulling at the plus end. Panel (b) shows the depolymerization behavior for the 3 PFs complex. Panel (b) in Fig. S7 of the supplementary material shows the equivalent behavior for the single PF.

Image of FIG. 7.
FIG. 7.

The comparison between the FEC for the 3 PFs complex with 63 fixed positions from Fig. 4 and the FECs for other single and 3-PF setups discussed in the main text. This figure shows the changes in the rigidity of the central PF in a 3 PFs complex starting from an intact MT lattice, all the way to the isolated PF case.

Image of FIG. 8.
FIG. 8.

Similar to Fig. 5 , only that in this case both ends of the two structures are fixed and we pulled on 2 positions (345, 420) from a central dimer. Panel (a) shows the comparative FECs for the single PF and 3 PFs complex. The depolymerization behavior for the 3 PFs complex is depicted in panel (b), while the equivalent behavior for the single PF is shown in panel (b) of Fig. S8 of the supplementary material.

Tables

Generic image for table
Table I.

Work and bending k-values for select simulations.

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/content/aip/journal/jcp/139/12/10.1063/1.4819817
2013-09-05
2014-04-18
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Mechanics of severing for large microtubule complexes revealed by coarse-grained simulations
http://aip.metastore.ingenta.com/content/aip/journal/jcp/139/12/10.1063/1.4819817
10.1063/1.4819817
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