Actin polymerization kinetics, cap structure, and fluctuations

Vavylonis, Dimitrios; Yang, Qingbo; O’Shaughnessy, Ben

doi:10.1073/pnas.0501435102

Cited by 119 publications

(202 citation statements)

References 55 publications

(130 reference statements)

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“…1. 15,21 The hydrolysis mechanism for the cytoskeleton filament is still under discussion, [21][22][23][24][25][26][27][28][29][30] and we assume here that all T-subunits on microtubules can be hydrolyzed with the same rate r as indicated in Fig.1. The hydrolyzed D-subunits can detach from the "plus" end of the microtubules with a rate W D (see Fig.…”

Section: Theoretical Methodsmentioning

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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Section: Theoretical Methodsmentioning

confidence: 99%

Theoretical Analysis of Microtubule Dynamics at All Times

Kolomeisky

2014

J. Phys. Chem. B

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“…(hydrolysis of ATP in filaments) with the overall rate constant 0.0007 s -1 , which is assumed to be a lowest limit for an approximative two-step hydrolysis rate constant (including phosphate release), and is a product of rate constants for hydrolysis 0.3 s -1 [42] and phosphate release 0.0026−0.004 s -1 [43,44].…”

Section: Strategy For Model Evaluation and Analysismentioning

confidence: 99%

An integrative simulation model linking major biochemical reactions of actin-polymerization to structural properties of actin filaments

Halavatyi

Nazarov

Medves

et al. 2009

Biophysical Chemistry

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We report on an advanced universal Monte Carlo simulation model of actin polymerization processes offering a broad application panel. The model integrates major actin-related reactions, such as assembly of actin nuclei, association/dissociation of monomers to filament ends, ATP-hydrolysis via ADP-Pi formation and ADP-ATP exchange, filament branching, fragmentation and annealing or the effects of regulatory proteins. Importantly, these reactions are linked to information on the nucleotide state of actin subunits in filaments (ATP hydrolysis) and the distribution of actin filament lengths. The developed stochastic simulation modelling schemes were validated on: i) synthetic theoretical data generated by a deterministic model and ii) sets of our and published experimental data obtained from fluorescence pyrene-actin experiments. Build on an open-architecture principle, the designed model can be extended for predictive evaluation of the activities of other actin-interacting proteins and can be applied for the analysis of experimental pyrene actin-based or fluorescence microscopy data. We provide a user-friendly, free software package ActinSimChem that integrates the implemented simulation algorithms and that is made available to the scientific community for modelling in silica any specific actin-polymerization system

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“…13,17,20 It gives a reasonable description of many features in actin filaments and microtubules, especially at high concentrations of free actin and tubulin monomers in the solution. However, current methods do not work well at biologically relevant conditions which correspond to small and intermediate concentrations near the critical concentration.…”

Section: ■ Introductionmentioning

confidence: 99%

A New Theoretical Approach to Analyze Complex Processes in Cytoskeleton Proteins

Kolomeisky

2014

J. Phys. Chem. B

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Cytoskeleton proteins are filament structures that support a large number of important biological processes. These dynamic biopolymers exist in nonequilibrium conditions stimulated by hydrolysis chemical reactions in their monomers. Current theoretical methods provide a comprehensive picture of biochemical and biophysical processes in cytoskeleton proteins. However, the description is only qualitative under biologically relevant conditions because utilized theoretical mean-field models neglect correlations. We develop a new theoretical method to describe dynamic processes in cytoskeleton proteins that takes into account spatial correlations in the chemical composition of these biopolymers. Our approach is based on analysis of probabilities of different clusters of subunits. It allows us to obtain exact analytical expressions for a variety of dynamic properties of cytoskeleton filaments. By comparing theoretical predictions with Monte Carlo computer simulations, it is shown that our method provides a fully quantitative description of complex dynamic phenomena in cytoskeleton proteins under all conditions.

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Actin polymerization kinetics, cap structure, and fluctuations

Abstract: ATP cap ͉ length diffusivity ͉ modeling ͉ critical concentration

Cited by 119 publications

References 55 publications

Theoretical Analysis of Microtubule Dynamics at All Times

Theoretical Analysis of Microtubule Dynamics at All Times

An integrative simulation model linking major biochemical reactions of actin-polymerization to structural properties of actin filaments

A New Theoretical Approach to Analyze Complex Processes in Cytoskeleton Proteins

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