PURE system simulator
The PURE system simulator
The PURE system simulator is a deterministic model of mRNA-directed protein synthesis based on the components of an E. coli-based reconstituted in vitro translation system, the PURE system (ref 1). The computational model is constructed according to the generally understood molecular mechanisms of the E. coli protein translation process and a number of previous kinetic studies. Ordinary differential equations (ODE) are used to describe the rates of all of the reactions and the reactions are modeled as either first- or second-order reactions. The full model is implemented in Matlab (Mathworks, Natick, MA, USA) for the simulation. Currently, formyl-Met-Gly-Gly tripeptiide (fMGG) synthesis can be simulated. We here provide the model files and Matlab source codes for the simulation including explanations how to use these files.
Model files
Model construction is performed by constructing a kinetic model of the sub-systems that constitute the entire mRNA-directed protein translation system. They include translation initiation, elongation, termination and ribosome recycling, aminoacylation, the formylation of initiator tRNA, and energy regeneration. The sub-systems are further divided into several modules, which results in a total of 26 modules. The modules are described in SBML (Systems Biology Markup Language) format and they are merged into a single SBML model file. The files can be opened by using software CellDesigner, a modeling tool of biochemical networks.
You can download 26 SBML model files from here.
You can download the merged, single SBML model file from here.
Matlab source codes
The full model is implemented in Matlab (Mathworks, Natick, MA, USA) using ODE for the simulation of fMGG synthesis. The model includes 241 components, 27 of which are the initial components, and 968 reactions. To run a simulation, initial concentration of components and kinetic parameters for reactions should be provided. The default concentration values are used from the optimized PURE system (ref 2) and default kinetic parameter values are obtained primarily from a number of previous kinetic studies. They are set by separate csv files to manage the values.
You can download Matlab sample source codes with default initial concentration and parameter sets from here.
How to use Matlab source codes
Files below can be extracted from Simulate_fMGG_synthesis.zip.
Simulate_fMGG_synthesis/fMGG_synthesis.m : A source code describing ODE
Simulate_fMGG_synthesis/fMGG_synthesis_Sample.m : A sample source code to run a simulation
Simulate_fMGG_synthesis/dat/fMGG_synthesis_initial_values.csv :A resource file describing initial concentration values
Simulate_fMGG_synthesis/dat/fMGG_synthesis_parameters.csv :A resource file describing kinetic parameter values
Simulate_fMGG_synthesis/dat/fMGG_synthesis_reactions.csv :A file to explain what kind of reactions extracted from merged single SBML file (fMGG_synthesis.xml)
To run a simulation in Matlab, add a path to the Simulate_fMGG_synthesis directory and run fMGG_synthesis_sample.m file. If you'd like to change initial concentration values or kinetic parameter values, please edit two resource files.
Contact information
If you have any question regarding our simulator, please contact us (yshimizu [[at]] riken.jp or matsuura_tomoaki [[at]] bio.eng.osaka-u.ac.jp).