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

Halavatyi, Aliaksandr; Nazarov, Petr V.; Medves, Sandrine; Troys, Marleen Van; Ampè, Christophe; Yatskou, Mikalai M.; Friederich, Evelyne

doi:10.1016/j.bpc.2008.11.006

Cited by 12 publications

(25 citation statements)

References 56 publications

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“…The polymerizationr eactiono fa ctin exhibits ah igh sensitivity for only some of the rate constants used to describe the polymerization process: k SNUC , k ASTB , k ASDB , k DIPB , k DIDB ,a nd k DITB . [35] These rate constantsdescribe the nucleation process and the association/dissociation processes of actin monomers at the barbed end of the filament, which exhibits faster elongation rates compared to the pointed end (see also Figure S1 in the Supporting Information, SI). [35] To quantify the effects of temperature, pressure, and co-solvents on the kinetics of the polymerization process, the rate constantsw ere varied to simulate the experimental datao btained.…”

Section: Resultsmentioning

confidence: 98%

“…[35] These rate constantsdescribe the nucleation process and the association/dissociation processes of actin monomers at the barbed end of the filament, which exhibits faster elongation rates compared to the pointed end (see also Figure S1 in the Supporting Information, SI). [35] To quantify the effects of temperature, pressure, and co-solvents on the kinetics of the polymerization process, the rate constantsw ere varied to simulate the experimental datao btained. We found that in case of the Mg 2 + -induced polymerization reaction, the rate constant of the initial polymerization reaction observed, k obs ,i sm ainly effected by the nucleation step, in good agreement with literature data (examples are given in Figure 3).…”

Section: Resultsmentioning

confidence: 98%

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Combined Effects of Temperature, Pressure, and Co‐Solvents on the Polymerization Kinetics of Actin

et al. 2015

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In vivo studies have shown that the cytoskeleton of cells is very sensitive to changes in temperature and pressure. In particular, actin filaments get depolymerized when pressure is increased up to several hundred bars, conditions that are easily encountered in the deep sea. We quantitatively evaluate the effects of temperature, pressure, and osmolytes on the kinetics of the polymerization reaction of actin by high-pressure stopped-flow experiments in combination with fluorescence detection and an integrative stochastic simulation of the polymerization process. We show that the compatible osmolyte trimethylamine-N-oxide is not only able to compensate for the strongly retarding effect of chaotropic agents, such as urea, on actin polymerization, it is also able to largely offset the deteriorating effect of pressure on actin polymerization, thereby allowing biological cells to better cope with extreme environmental conditions.

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Section: Resultsmentioning

confidence: 98%

Section: Resultsmentioning

confidence: 98%

Combined Effects of Temperature, Pressure, and Co‐Solvents on the Polymerization Kinetics of Actin

et al. 2015

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“…Images were acquired from at least two separate experiments. Graphing analysis and curve fitting was performed using Graphpad Prism and FRAPAnalyser (Halavatyi et al, 2009). …”

Section: Frap Imagingmentioning

confidence: 99%

Persistent nuclear actin filaments inhibit transcription by RNA polymerase II

Serebryannyy

Parilla

Annibale

et al. 2016

Journal of Cell Science

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Actin is abundant in the nucleus and it is clear that nuclear actin has important functions. However, mystery surrounds the absence of classical actin filaments in the nucleus. To address this question, we investigated how polymerizing nuclear actin into persistent nuclear actin filaments affected transcription by RNA polymerase II. Nuclear filaments impaired nuclear actin dynamics by polymerizing and sequestering nuclear actin. Polymerizing actin into stable nuclear filaments disrupted the interaction of actin with RNA polymerase II and correlated with impaired RNA polymerase II localization, dynamics, gene recruitment, and reduced global transcription and cell proliferation. Polymerizing and crosslinking nuclear actin in vitro similarly disrupted the actin-RNA-polymerase-II interaction and inhibited transcription. These data rationalize the general absence of stable actin filaments in mammalian somatic nuclei. They also suggest a dynamic pool of nuclear actin is required for the proper localization and activity of RNA polymerase II.

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“…This stochastic approach provides precise information on the dynamics of G-and F-actin, including the structural compositions of actin filaments (Halavatyi et al 2009). We adapted the SSA for the simulation of a FRAP experiment, considering bleached and unbleached actin subunits as independent molecular species.…”

Section: Stochastic Simulation Algorithmmentioning

confidence: 99%

A mathematical model of actin filament turnover for fitting FRAP data

Halavatyi

Nazarov²,

Tanoury

et al. 2009

Eur Biophys J

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A novel mathematical model of the actin dynamics in living cells under steady-state conditions has been developed for fluorescence recovery after photobleaching (FRAP) experiments. As opposed to other FRAP fitting models, which use the average lifetime of actins in filaments and the actin turnover rate as fitting parameters, our model operates with unbiased actin association/dissociation rate constants and accounts for the filament length. The mathematical formalism is based on a system of stochastic differential equations. The derived equations were validated on synthetic theoretical data generated by a stochastic simulation algorithm adapted for the simulation of FRAP experiments. Consistent with experimental findings, the results of this work showed that (1) fluorescence recovery is a function of the average filament length, (2) the F-actin turnover and the FRAP are accelerated in the presence of actin nucleating proteins, (3) the FRAP curves may exhibit both a linear and non-linear behaviour depending on the parameters of actin polymerisation, and (4) our model resulted in more accurate parameter estimations of actin dynamics as compared with other FRAP fitting models. Additionally, we provide a computational tool that integrates the model and that can be used for interpretation of FRAP data on actin cytoskeleton.

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

Cited by 12 publications

References 56 publications

Combined Effects of Temperature, Pressure, and Co‐Solvents on the Polymerization Kinetics of Actin

Combined Effects of Temperature, Pressure, and Co‐Solvents on the Polymerization Kinetics of Actin

Persistent nuclear actin filaments inhibit transcription by RNA polymerase II

A mathematical model of actin filament turnover for fitting FRAP data

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