TY - JOUR
T1 - An integrative simulation model linking major biochemical reactions of actin-polymerization to structural properties of actin filaments
AU - Halavatyi, Aliaksandr A.
AU - Nazarov, Petr V.
AU - Medves, Sandrine
AU - van Troys, Marleen
AU - Ampe, Christophe
AU - Yatskou, Mikalai
AU - Friederich, Evelyne
N1 - Funding Information:
This work was supported by Fonds National de la Recherche , Luxembourg (grant nr FNR/05/MA6/17), Human Frontier Science Program (grant nr RGP0058/2005) and the FWO-Vlaanderen to MVT and CA (grant nr G.0157.05), CNRS. AAH was a recipient of an ESF Exchange Visit Grant.
PY - 2009/3
Y1 - 2009/3
N2 - 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.
AB - 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.
KW - Actin
KW - Filament
KW - Model
KW - Monte Carlo simulation
KW - Polymerization
KW - Software
UR - http://www.scopus.com/inward/record.url?scp=58749086550&partnerID=8YFLogxK
U2 - 10.1016/j.bpc.2008.11.006
DO - 10.1016/j.bpc.2008.11.006
M3 - Article
C2 - 19101066
AN - SCOPUS:58749086550
SN - 0301-4622
VL - 140
SP - 24
EP - 34
JO - Biophysical Chemistry
JF - Biophysical Chemistry
IS - 1-3
ER -