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

Aliaksandr A. Halavatyi, Petr V. Nazarov, Sandrine Medves, Marleen van Troys, Christophe Ampe, Mikalai Yatskou, Evelyne Friederich*

*Corresponding author for this work

    Research output: Contribution to journalArticleResearchpeer-review

    10 Citations (Scopus)

    Abstract

    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 silico any specific actin-polymerization system.

    Original languageEnglish
    Pages (from-to)24-34
    Number of pages11
    JournalBiophysical Chemistry
    Volume140
    Issue number1-3
    DOIs
    Publication statusPublished - Mar 2009

    Keywords

    • Actin
    • Filament
    • Model
    • Monte Carlo simulation
    • Polymerization
    • Software

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