Mathematical modeling of microtubule dynamic instability: new insight into the link between gtp-hydrolysis and microtubule aging

2018 ◽  
Vol 52 (6) ◽  
pp. 2433-2456 ◽  
Author(s):  
Ayuna Barlukova ◽  
Diana White ◽  
Gérard Henry ◽  
Stéphane Honoré ◽  
Florence Hubert
Keyword(s):  
Dynamic Instability ◽  
Dynamic Properties ◽  
Model Parameters ◽  
Microtubule Dynamic ◽  
Gtp Hydrolysis ◽  
Unique Type ◽  
Microtubule Targeting Agents ◽  
Age Dependent ◽  
Type Of Behavior ◽  
Insight Into

Microtubules (MTs) are protein polymers that exhibit a unique type of behavior referred to as dynamic instability. That is, they undergo periods of growth (through the addition of GTP-tubulin) and shortening (through the subtraction of GDP-tubulin). Shortening events are very fast, where this transition is referred to as a catastrophe. There are many processes that regulate MT dynamic instability, however, recent experiments show that MT dynamics may be highly regulated by a MTs age, where young MTs are less likely to undergo shortening events than older ones. In this paper, we develop a novel modeling approach to describe how the age of a MT affects its dynamic properties. In particular, we extend on a previously developed model that describes MT dynamics, by proposing a new concept for GTP-tubulin hydrolysis (the process by which newly incorporated GTP-tubulin is hydrolyzed to lower energy GDP-tubulin). In particular, we assume that hydrolysis is mainly vectorial, age-dependent and delayed according to the GTP-tubulin incorporation into the MT. Through numerical simulation, we are able to show how MT age affects certain properties that define MT dynamics. For example, simulations illustrate how the aging process leads to an increase in the rate of GTP-tubulin hydrolysis for older MTs, as well as increases in catastrophe frequency. Also, since it has been found that MT dynamic instability is affected by chemotherapy microtubule-targeting agents (MTAs), we highlight the fact that our model can be used to investigate the action of MTAs on MT dynamics by varying certain model parameters.

scholarly journals A mutation uncouples the tubulin conformational and GTPase cycles, revealing allosteric control of microtubule dynamics

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Elisabeth A Geyer ◽  
Alexander Burns ◽  
Beth A Lalonde ◽  
Xuecheng Ye ◽  
Felipe-Andres Piedra ◽  
...  
Keyword(s):  
Conformational Change ◽  
Dynamic Instability ◽  
Dynamic Properties ◽  
Microtubule Dynamics ◽  
Gtpase Activity ◽  
Microtubule Dynamic ◽  
Gtp Hydrolysis ◽  
Allosteric Control

Microtubule dynamic instability depends on the GTPase activity of the polymerizing αβ-tubulin subunits, which cycle through at least three distinct conformations as they move into and out of microtubules. How this conformational cycle contributes to microtubule growing, shrinking, and switching remains unknown. Here, we report that a buried mutation in αβ-tubulin yields microtubules with dramatically reduced shrinking rate and catastrophe frequency. The mutation causes these effects by suppressing a conformational change that normally occurs in response to GTP hydrolysis in the lattice, without detectably changing the conformation of unpolymerized αβ-tubulin. Thus, the mutation weakens the coupling between the conformational and GTPase cycles of αβ-tubulin. By showing that the mutation predominantly affects post-GTPase conformational and dynamic properties of microtubules, our data reveal that the strength of the allosteric response to GDP in the lattice dictates the frequency of catastrophe and the severity of rapid shrinking.

Analysis of the Mechanism of Microtubule Dynamic Instability Using a UV Microbeam to Sever Elongating Microtubules

1988 ◽  
Vol 46 ◽  
pp. 122-123
Author(s):  
R.A Walker ◽  
S. Inoue ◽  
E.D. Salmon
Keyword(s):  
Dynamic Instability ◽  
Microtubule Dynamic ◽  
Gtp Hydrolysis ◽  
Abrupt Transition ◽  
Microtubule Associated Proteins ◽  
Asymmetrical Structure ◽  
Associated Proteins

Microtubules polymerized in vitro from tubulin purified free of microtubule-associated proteins exhibit dynamic instability (1,2,3). Free microtubule ends exist in persistent phases of elongation or rapid shortening with infrequent, but, abrupt transitions between these phases. The abrupt transition from elongation to rapid shortening is termed catastrophe and the abrupt transition from rapid shortening to elongation is termed rescue. A microtubule is an asymmetrical structure. The plus end grows faster than the minus end. The frequency of catastrophe of the plus end is somewhat greater than the minus end, while the frequency of rescue of the plus end in much lower than for the minus end (4).The mechanism of catastrophe is controversial, but for both the plus and minus microtubule ends, catastrophe is thought to be dependent on GTP hydrolysis. Microtubule elongation occurs by the association of tubulin-GTP subunits to the growing end. Sometime after incorporation into an elongating microtubule end, the GTP is hydrolyzed to GDP, yielding a core of tubulin-GDP capped by tubulin-GTP (“GTP-cap”).

scholarly journals Microtubule dynamic instability: A new model with coupled GTP hydrolysis and multistep catastrophe

BioEssays ◽  
2013 ◽  
Vol 35 (5) ◽  
pp. 452-461 ◽  
Author(s):  
Hugo Bowne‐Anderson ◽  
Marija Zanic ◽  
Monika Kauer ◽  
Jonathon Howard
Keyword(s):  
Dynamic Instability ◽  
Microtubule Dynamic ◽  
Gtp Hydrolysis ◽  
New Model

scholarly journals Abstract P-33: Structural Basis for the Growing Microtubule End Recognition by End Binding Proteins

2021 ◽  
Vol 11 (Suppl_1) ◽  
pp. S26-S26
Author(s):  
Alena Korshunova
Keyword(s):  
Amino Acids ◽  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Molecular Mechanism ◽  
Binding Proteins ◽  
Dynamic Instability ◽  
3D Structure ◽  
Structural Basis ◽  
Microtubule Dynamic ◽  
Gtp Hydrolysis

Background: Eukaryotic end binding proteins (EBs) can follow the growing microtubule end. EBs play a crucial role in microtubule dynamic instability and promote simultaneously growth rate and catastrophe frequency. It makes EB-like proteins perspective drag targets for a wide number of diseases. But the molecular mechanism of tip tracking by EB-like proteins remains unknown. Studies of mutants have revealed that the conservative amino acid Q102 (numbering relative to the human EB1 protein) plays a key role in the recognition of the growing microtubule end. However, the 3D structure studies revealed that this amino acid has no bonds with tubulin. In this work, we performed structural and phylogenetic analysis of EBs proteins to identify a possible molecular mechanism behind the plus end tracking. Methods: UCSF Chimera10 was used for structural analysis. Phylogenetic analysis was performed with MEGA X software. 3D structures of EBs and microtubules with different states of GTP hydrolysis were used (pdb 3JAK, 3JAS, 3JAT, 3JAW, 3JAL, 3JAR, 6DPU, 6DPV, 6DPW). Results: We have shown that two conservative amino acids (K100, E106) should play an important role in the recognition of the microtubule plus end in addition to Q102. It was concluded that these amino acids together form the plus-end «navigation site» of EBs. Analysis of possible interaction of the «navigation site» amino acids with microtubules in different conformational states suggested that the main mechanism of growing microtubule end recognition is not due to an affinity increase for a certain state of tubulin in microtubules at their end, but it due to a significant affinity decrease in other parts of the microtubule as a result of steric clashes. Conclusion: Thus, the results of the analysis suggested the possible molecular mechanism that provides the tip tracking by EB-like proteins and allowed us to identify the key amino acids of this mechanism.

scholarly journals Mathematical Modeling of Effect Of Microtubule-Targeted Agents On Microtubule Dynamic Instability

2018 ◽  
Vol 62 ◽  
pp. 1-16
Author(s):  
Ayuna Barlukova ◽  
Stéphane Honoré ◽  
Florence Hubert
Keyword(s):  
Mathematical Modeling ◽  
Dynamic Instability ◽  
Growth Speed ◽  
Model Parameters ◽  
Cancer Cell Migration ◽  
Targeted Agents ◽  
Potential Mechanism ◽  
Microtubule Dynamic ◽  
Drug Concentrations ◽  
Param Eters

Microtubule-targeted agents (MTAs), widely used in chemotherapy, are molecules that are able to block cancer cell migration and division. Their effect on microtubule (MT) dynamic instability is measured by their influence on observable parameters of MT dynamics such as growth speed, time-based catastrophe frequency, time-based rescue fre- quency, etc. In this paper, we propose a new mathematical model that is able to reproduce MT dynamics with an appropriate estimation of the main observable parameters. Using the experimental data on paclitaxel effect in presence of EB proteins, we fitted param- eters of the model from several drug concentrations. It enable us to understand which non-observable model parameters are able to reproduce the effect of MTAs and thus to highlight a new potential mechanism of action associated with MTAs effect in presence of EB protein.

scholarly journals Structural transitions in the GTP cap visualized by cryo-electron microscopy of catalytically inactive microtubules

2022 ◽  
Vol 119 (2) ◽  
pp. e2114994119
Author(s):  
Benjamin J. LaFrance ◽  
Johanna Roostalu ◽  
Gil Henkin ◽  
Basil J. Greber ◽  
Rui Zhang ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Conformational Changes ◽  
Total Internal Reflection ◽  
Dynamic Instability ◽  
Wild Type ◽  
Gtp Hydrolysis ◽  
Cryo Electron Microscopy ◽  
Catalytically Active ◽  
The Stability ◽  
Insight Into

Microtubules (MTs) are polymers of αβ-tubulin heterodimers that stochastically switch between growth and shrinkage phases. This dynamic instability is critically important for MT function. It is believed that GTP hydrolysis within the MT lattice is accompanied by destabilizing conformational changes and that MT stability depends on a transiently existing GTP cap at the growing MT end. Here, we use cryo-electron microscopy and total internal reflection fluorescence microscopy of GTP hydrolysis–deficient MTs assembled from mutant recombinant human tubulin to investigate the structure of a GTP-bound MT lattice. We find that the GTP-MT lattice of two mutants in which the catalytically active glutamate in α-tubulin was substituted by inactive amino acids (E254A and E254N) is remarkably plastic. Undecorated E254A and E254N MTs with 13 protofilaments both have an expanded lattice but display opposite protofilament twists, making these lattices distinct from the compacted lattice of wild-type GDP-MTs. End-binding proteins of the EB family have the ability to compact both mutant GTP lattices and to stabilize a negative twist, suggesting that they promote this transition also in the GTP cap of wild-type MTs, thereby contributing to the maturation of the MT structure. We also find that the MT seam appears to be stabilized in mutant GTP-MTs and destabilized in GDP-MTs, supporting the proposal that the seam plays an important role in MT stability. Together, these structures of catalytically inactive MTs add mechanistic insight into the GTP state of MTs, the stability of the GTP- and GDP-bound lattice, and our overall understanding of MT dynamic instability.

scholarly journals The effect of solution composition on microtubule dynamic instability

1991 ◽  
Vol 277 (3) ◽  
pp. 839-847 ◽  
Author(s):  
M J Schilstra ◽  
P M Bayley ◽  
S R Martin
Keyword(s):  
Rate Constant ◽  
Dynamic Instability ◽  
Dynamic Properties ◽  
Intrinsic Rate ◽  
Dissociation Rate ◽  
Microtubule Dynamic ◽  
Exchange Method ◽  
Dynamic Activity ◽  
Cap Model ◽  
Good Agreement

The exchange of tubulin dimer into steady-state microtubules was studied over a range of solution conditions, in order to assess the effects of various common buffer components on the dynamic instability of microtubules. In comparison with standard buffer conditions (100 mM-Pipes buffer, pH 6.5, containing 0.1 mM-EGTA, 1.8 mM-MgC12 and 1 M-glycerol), the rate and extent of exchange, and thus of dynamic instability, are suppressed by increasing the concentration of glycerol above 2 M. Exchange is enhanced by the addition of further Mg2+ (up to 17 mM) or by the addition of Ca2+ (up to 0.4 mM). Phosphate ion (150 mM) has relatively little effect on the dynamic behaviour of microtubules, as judged by the exchange method. The findings are interpreted within the framework of the Lateral Cap model for microtubule dynamic instability, in terms of the effects of these changes on the intrinsic rate constants of the system. By contrast, the extent of tubulin exchange depends selectively on the value of the dissociation rate constant for tubulin-GDP. A decrease in the extent of exchange, and hence in dynamic activity, is associated with a decreased value for this rate constant, and vice versa. The results also show good agreement of predictions of the model in treating the observed variations in the dynamic properties of individual microtubules, induced by different solution conditions.

Dynamic properties of nucleated microtubules: GTP utilisation in the subcritical concentration regime

1996 ◽  
Vol 109 (11) ◽  
pp. 2755-2766
Author(s):  
M.F. Symmons ◽  
S.R. Martin ◽  
P.M. Bayley
Keyword(s):  
Dynamic Instability ◽  
Dynamic Properties ◽  
Critical Concentration ◽  
Specific Inhibitor ◽  
Microtubule Assembly ◽  
Microtubule Dynamic ◽  
Assembly Kinetics ◽  
Microtubule Growth ◽  
Growth Features

Microtubule assembly kinetics have been studied quantitatively under solution conditions supporting microtubule dynamic instability. Purified GTP-tubulin (Tu-GTP) and covalently cross-linked short microtubule seeds (EGS-seeds; Koshland et al. (1988) Nature 331, 499) were used with and without biotinylation. Under sub-critical concentration conditions ([Tu-GTP] < 5.3 microM), significant microtubule growth of limited length was observed on a proportion of the EGS-seeds by immuno-electron microscopy. A sensitive fluorescence assay for microtubule GDP production was developed for parallel assessment of GTP utilisation. This revealed a correlation between the detected microtubule growth and the production of tubulin-GDP, deriving from the shortening phase of the dynamic microtubules. This correlation was confirmed by the action of nocodazole, a specific inhibitor of microtubule assembly, that was found to abolish the GDP release. The variation of the GDP release with tubulin concentration (Jh(c) plot) was determined below the critical concentration (Cc). The GDP production observed was consistent with the elongation of the observed seeded microtubules with an apparent rate constant of 1.5 × 10(6) M-1 second-1 above a threshold of approximately 1 microM tubulin. The form of this Jh(c) plot for elongation below Cc is reproduced by the Lateral Cap model for microtubule dynamic instability adapted for seeded assembly. The behaviour of the system is contrasted with that previously studied in the absence of detectable microtubule elongation (Caplow and Shanks (1990) J. Biol. Chem. 265, 8935–8941). The approach provides a means of monitoring microtubule dynamics at concentrations inaccessible to optical microscopy, and shows that essentially the same dynamic mechanisms apply at all concentrations. Numerical simulation of the subcritical concentration regime shows dynamic growth features applicable to the initiation of microtubule growth in vivo.

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