1. An Automated Integrative Computer Simulation Approach for Stochastic Modelling of Actin Polymerization
Mikalai Yatskou, Aliaxander Halavatyi, Peter Nazarov, Sandrine Medves, Evelyne Friederich
Cytoskeleton and Cell Plasticity Laboratory, Life Sciences Research Unit, Faculty of Sciences, Technology and Communication, University of Luxembourg, Luxembourg Tel/ Fax: (0) ,
Marleen van Troys, Christophe Ampe
Department of Biochemistry, Faculty of Medicine and Health Sciences, University of Gent, Gent, Belgium
Introduction
Deterministic biochemical models cannot describe adequately many actin-polymerization processes, such as spontaneous/stimulated actin nucleation, branching, severing, annealing, complete depolymerization, (un)capping, two-step hydrolysis1.
Therefore, the stochastic models have to be used drastically2,3.
However, so far, no comprehensive universal stochastic model with a broad application panel and software for biochemical actin-polymerization processes are available.
Results
Fig.6 The schematic diagram for optical processes in the tetramer
Goal: developing an automated integrative computer-simulation approach for stochastic modelling of actin-polymerization processes in life cells.
Formalization
Fig.6 The schematic diagram for optical processes in the tetramer
Fig.7 Results of simulation of the tetramer fluorescence anisotropy
Conclusions
Two different energy transfer processes within zinc porphyrin tetramer can be distinguished and determined by Monte Carlo simulation
The presented computer approach is demonstrated to be a new and powerful tool for simulation and analysis of energy transfer processes by the sample of a porphyrin tetramer. This approach may be easily translated to the analysis of energy transfer processes in other molecular systems
Software ActSimChem
The computer program has the facilities:
Fig.3 Fluorescence and its anisotropy decays
Simulation
Decay analysis
2D visualization
Error analysis
Import/Export data
Monte Carlo Simulation Analysis
Planned Development of professional universal software for simulation-based analysis of time-resolved fluorescence data
Fig.8 Typical window of the program
Authors thanks Prof. V.V. Apanasovich of Belarusian State University, Prof. of CRP-Sante for useful discussion.
Acknowledgement
References
2. Roland, J. et al ; Biophys. J
1. Brooks, F.J.;Carlsson, A.E. Biophys. J , pp. …
3. Fass, J. et al J. Theor Biol 2008, 242 (1996)
4. Kleima, F.J.; Hofmann, E.; Gobets, B.; van Stokkum, I.H.M.; van Grondelle, R.; Diederichs, K., van Amerongen, H.
Biophys. J. 78, (2000)