Reference : An integrative simulation model linking major biochemical reactions of actin-polymeri...

	Document type :	Scientific journals : Article
	Discipline(s) :	Life sciences : Biochemistry, biophysics & molecular biology
	To cite this reference:	http://hdl.handle.net/10993/7446

Title :	An integrative simulation model linking major biochemical reactions of actin-polymerization to structural properties of actin filaments
Language :	English
Author, co-author :	Halavatyi, A. A. [Department of Systems Analysis, Belarusian State University, 4, Nezavisimosti Ave, 220030 Minsk, Belarus, Faculty of Sciences, Technology and Communication, Life Sciences Research Unit, 162 A, avenue de la Faïencerie, L-1511 Luxembourg, Luxembourg]
	Nazarov, P. V. [Department of Systems Analysis, Belarusian State University, 4, Nezavisimosti Ave, 220030 Minsk, Belarus, Centre de Recherche Public Santé, 84, Rue Val Fleuri, L-1526 Luxembourg, Luxembourg]
	Medves, S. [Faculty of Sciences, Technology and Communication, Life Sciences Research Unit, 162 A, avenue de la Faïencerie, L-1511 Luxembourg, Luxembourg]
	van Troys, M. [VIB Department for Molecular Biomedical Research, UGent, VIB, A. Baertsoenkaai 3, Gent, Belgium, Department of Biochemistry, Faculty of Medicine and Health Sciences, UGent, A. Baertsoenkaai 3, Gent, Belgium]
	Ampe, C. [VIB Department for Molecular Biomedical Research, UGent, VIB, A. Baertsoenkaai 3, Gent, Belgium, Department of Biochemistry, Faculty of Medicine and Health Sciences, UGent, A. Baertsoenkaai 3, Gent, Belgium]
	Yatskou, M. [Faculty of Sciences, Technology and Communication, Life Sciences Research Unit, 162 A, avenue de la Faïencerie, L-1511 Luxembourg, Luxembourg, Centre de Recherche Public Santé, 84, Rue Val Fleuri, L-1526 Luxembourg, Luxembourg]
	Friederich, Evelyne [University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Life Science Research Unit >]
Publication date :	2009
Journal title :	Biophysical Chemistry
Publisher :	Elsevier Science
Volume :	140
Issue/season :	1-3
Pages :	24-34
Peer reviewed :	Yes (verified by ORBilu)
Audience :	International
ISSN :	0301-4622
City :	Amsterdam
Country :	The Netherlands
Keywords :	[en] Actin ; Filament ; Model ; Monte Carlo simulation ; Polymerization ; Software ; Monte Carlo method ; Actin Capping Proteins ; Actins ; Adenosine Triphosphate ; Animals ; Computer Simulation ; Escherichia coli ; Fetal Proteins ; Microfilament Proteins ; Microfilaments ; Monte Carlo Method ; Nuclear Proteins ; Rabbits
Abstract :	[en] 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. © 2008 Elsevier B.V. All rights reserved.
Permalink :	http://hdl.handle.net/10993/7446
DOI :	10.1016/j.bpc.2008.11.006

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