A New Theoretical Approach to Analyze Complex Processes in Cytoskeleton Proteins

Li, Xin; Kolomeisky, Anatoly B.

doi:10.1021/jp500268q

Cited by 4 publications

(33 citation statements)

References 30 publications

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“…However, in this case, one can utilize a better theoretical method that takes into account spatial correlation in the chemical composition of cytoskeleton proteins. 17 In our approach, we can also evaluate the influence of the lateral interactions on the mean growth velocity and dispersion of the microtubule. Let us consider the case of zero external forces.…”

Section: The Journal Of Physical Chemistry Bmentioning

confidence: 99%

“…A different method, which takes into account the hydrolysis and polymerization/depolymerization processes, is able to describe the dynamics of cytoskeleton proteins much better. 16,17,21,24,29,30 Although this approach revealed important microscopic details on complex dynamics in microtubules and actin filaments, its usefulness is diminished by neglecting the structure and interactions in these biopolymers. A computational model that includes the hydrolysis and binding/ unbinding chemical transitions for multifilament biopolymers has been introduced recently.…”

Section: ■ Introductionmentioning

confidence: 99%

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The Role of Multifilament Structures and Lateral Interactions in Dynamics of Cytoskeleton Proteins and Assemblies

Kolomeisky

2015

J. Phys. Chem. B

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Microtubules and actin filaments are biopolymer molecules that are major components of cytoskeleton networks in biological cells. They play important roles in supporting fundamental cellular processes such as cell division, signaling, locomotion, and intracellular transport. In cells, cytoskeleton proteins function under nonequilibrium conditions that are powered by hydrolysis of adenosine triphosphate (ATP) or guanosine triphosphate (GTP) molecules attached to them. Although these biopolymers are critically important for all cellular processes, the mechanisms that govern their complex dynamics and force generation remain not well explained. One of the most difficult fundamental issues is to understand how different components of cytoskeleton proteins interact together. We develop an approximate theoretical approach for analyzing complex processes in cytoskeleton proteins that takes into account the multifilament structure, lateral interactions between parallel protofilaments, and the most relevant biochemical transitions during the biopolymer growth. It allows us to fully evaluate collective dynamic properties of cytoskeleton filaments as well as the effect of external forces on them. It is found that for the case of strong lateral interactions the stall force of the multifilament protein is a linear function of the number of protofilaments. However, for weak lateral interactions, deviations from the linearity are observed. We also show that stall forces, mean velocities, and dispersions are increasing functions of the lateral interactions. Physical−chemical explanations of these phenomena are presented. Our theoretical predictions are supported by extensive Monte Carlo computer simulations.

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Section: The Journal Of Physical Chemistry Bmentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 99%

The Role of Multifilament Structures and Lateral Interactions in Dynamics of Cytoskeleton Proteins and Assemblies

Kolomeisky

2015

J. Phys. Chem. B

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“…The dynamics of the cluster distribution function S n (l,t) can be described by a set of Master equations, 16 dS n (l,t) dt …”

Section: Resultsmentioning

confidence: 99%

“…2,3,8,11,12 Another issue is that even more detailed theoretical investigations concentrate mostly on stationarystate behavior of the system. [13][14][15][16] In other words, dynamic properties of microtubules are assumed to be stationary and independent of the time. However, these theoretical views have been challenged recently by high-resolution measurements of filament length and lifetime distributions.…”

Section: Introductionmentioning

confidence: 99%

Theoretical Analysis of Microtubule Dynamics at All Times

Kolomeisky

2014

J. Phys. Chem. B

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Microtubules are biopolymers consisting of tubulin dimer subunits. As a major component of cytoskeleton they are essential for supporting most important cellular processes such as cell division, signaling, intracellular transport and cell locomotion. The hydrolysis of guanosine triphosphate (GTP) molecules attached to each tubulin subunit supports the nonequilibrium nature of microtubule dynamics. One of the most spectacular properties of microtubules is their dynamic instability when their growth from continuous attachment of tubulin dimers stochastically alternates with periods of shrinking. Despite the critical importance of this process to all cellular activities, its mechanism remains not fully understood. We investigated theoretically microtubule dynamics at all times by analyzing explicitly temporal evolution of various length clusters of unhydrolyzed subunits. It is found that the dynamic behavior of microtubules depends strongly on initial conditions. Our theoretical findings provide a microscopic explanation for recent experiments which found that the frequency of catastrophes increases with the lifetime of microtubules. It is argued that most growing microtubule configurations cannot transit in one step into a shrinking state, leading to a complex overall temporal behavior.Theoretical calculations combined with Monte Carlo computer simulations are also directly compared with experimental observations, and the good agreement is found.

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“…While the precise modeling of cytoskeletal dynamics requires considerations of experimental details, such as the two-step ATP hydrolysis within actin filaments [1,9] or the protofilament interactions in microtubules [1,10], only three factors are essential for the dissipative assembly-disassembly cycles: (i) There is a pool of free ATP(GTP) resulting in a continuous supply of the ATP(GTP) species [1]; (ii) hydrolysis takes place at random subunits within the filaments [11,12]; and (iii) hydrolysis results in an increased dissociation rate [1]. A simple stochastic process incorporates these features and has been used before to model cytoskeletal filaments [11,[13][14][15][16][17][18][19][20][21].…”

Section: Introductionmentioning

confidence: 99%

Association-dissociation process with aging subunits: Recursive solution

Niedermayer

Lipowsky

2015

Phys. Rev. E

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The coupling of stochastic growth and shrinkage of one-dimensional structures to random aging of the constituting subunits defines the simple association-dissociation-aging process which captures the essential features of the nonequilibrium assembly of cytoskeletal filaments. Because of correlations, previously employed mean-field methods fail to correctly describe filament growth. We study an alternative formulation of the full master equation of the stochastic process. An ansatz for the steady-state solution leads to a recursion relation which allows for the calculation of all emergent quantities with increasing accuracy and in excellent agreement with stochastic simulations.

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A New Theoretical Approach to Analyze Complex Processes in Cytoskeleton Proteins

Cited by 4 publications

References 30 publications

The Role of Multifilament Structures and Lateral Interactions in Dynamics of Cytoskeleton Proteins and Assemblies

The Role of Multifilament Structures and Lateral Interactions in Dynamics of Cytoskeleton Proteins and Assemblies

Theoretical Analysis of Microtubule Dynamics at All Times

Association-dissociation process with aging subunits: Recursive solution

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