An integrative simulation model linking major biochemical reactions of actin-polymerization to structural properties of actin filaments.
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.
Halavatyi
Aliaksandr A
AA
Department of Systems Analysis, Belarusian State University, 4, Nezavisimosti Ave, 220030 Minsk, Belarus.
Nazarov
Petr V
PV
Medves
Sandrine
S
van Troys
Marleen
M
Ampe
Christophe
C
Yatskou
Mikalai
M
Friederich
Evelyne
E
D051344:Actin Capping Proteins / Q000737:chemistry / Q000378:metabolism; D008841:Actin Cytoskeleton / Q000737:chemistry* / Q000378:metabolism*; D000199:Actins / Q000737:chemistry* / Q000378:metabolism*; D000255:Adenosine Triphosphate / Q000737:chemistry / Q000378:metabolism; D000818:Animals; D003198:Computer Simulation; D004926:Escherichia coli / Q000235:genetics; D005326:Fetal Proteins / Q000737:chemistry / Q000378:metabolism; D000080865:Formins; D008840:Microfilament Proteins / Q000737:chemistry / Q000378:metabolism; D009010:Monte Carlo Method; D009687:Nuclear Proteins / Q000737:chemistry / Q000378:metabolism; D011817:Rabbits; D012984:Software
D051344:Actin Capping Proteins; D000199:Actins; D005326:Fetal Proteins; D000080865:Formins; D008840:Microfilament Proteins; D009687:Nuclear Proteins; D000255:Adenosine Triphosphate