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 -cp . AntimonyBuilder. Following optional parameters are available:

• --filePath=<pathToResultFile> defines path to the output antimony file with results. Default value: ..\ProteinTranslocation.txt, i.e. by default file will be saved in the root folder whole-cell-reduced\ProteinTranslocation with name ProteinTranslocation.txt.
• --modelName=<modelName> defines antimony model name. Default value: ProteinTranslocation.
• --subset=<pathToFileWithAllowableSpeciesNames> defines path to the file with subset of allowable species names (comma separated). If just part of the model should be generated.

4. Use any tool you want to generate SBML file from the created Antimony. I use BioUML to do it.