Protein Translocation

Information about the model

ProteinTranslocation model represents the translocation of each protein monomer species into and through the cell membrane (See also model summary).

Species

1. Small molecules: involved in ATP hydrolysis

• ATP
• ADP
• water
• PI
• H+

2. Protein monomers: Includes both cytosolic and membrane/extracellular compartmentalizations for each translocated protein
3. Enzymes:
   • Sec translocase pore: MG_055_170_277_464_476_20MER
   • SecA translocase: MG_072_DIMER

Reactions

1. Stoichiometry:
2. Catalysis: SecA translocase (MG_072_DIMER), Sec translocase pore (MG_055_170_277_464_476_20MER)
3. Kinetics: first order in the monomers and SecA concentrations

Files and folders

• *.txt files are antimony versions of the model
• *.xml files are sbml l2v4 versions of the model

ProteinTranslocation.xml from the root folder whole-cell-reduced\ProteinTranslocation is the most recent version of the model.

• old_versions folder contains old versions of the model
• src folder contains script for antimony version of the model generating using .csv files from the src/resources folder. These files species.csv and reactions.csv contains data (separated by ;) about species and reactions respectively from the Jonathan's table (also can be found on the Google Drive)

Building the model (how script works)

1. Go to src folder
2. Run javac *.java to compile script (if one of these files is changed it might be compiled again)
3. Run java -classpath . AntimonyBuilder [resultFilePath] [modelName] [pathToFileWithAllowableNames]. Script will write Antimony model named as modelName parameter (optional) or ProteinTranslocation (by default) in the file specified by the resultFilePath parameter (optional). By default antimony file will be saved in the root folder whole-cell-reduced\ProteinTranslocation with name ProteinTranslocation.txt. Also there is a possibility to create model with given subset of species presented. To set path to the file with species names subset the 3rd parameter pathToFileWithAllowableNames (optional) should be set.
   Note: if you want to use, e.g., modelName parameter, resultFilePath parameter must be set. To use pathToFileWithAllowableNames parameter one must set both modelName and resultFilePath parameters.
4. Use something to generate SBML file from the created Antimony. I use BioUML to do it.