Registry of Standard Biological Models/Basic Component Models/Protein

Protein model architecture

Description: Protein molecule module Hypothesis: Protein molecules are produced following the binding of a mRNA by a ribosome. Protein degradation follows an exponential decay law unlimited resources for translation (ribosomes, tRNA ...). Inputs: time RiPS-IN (RIbosomes Per Second IN) Outputs: [Protein] concentration Characteristic parameters: proteinDegradationRate (depends on degradation pathway or growth dilution due to division rate)

Protein Brick Architecture (to be updated)

CellML structure (CellML 1.1 spec)

• Component: protein-molecule
• Units:
  • Imported from Environment component
• Variables:
  • time (public interface = in)
  • RiPS-IN (public interface = in )
  • proteinDegradationRate (public interface = none / init value = (depends on the protein))
  • protein (public interface = out / init value = 0.0 - maybe init value should also be an input parameter-)
• MathML
  • [math]\displaystyle{ \frac{d[protein]}{dtime} = RiPS-IN - proteinDegradationRate*[protein] }[/math]

Examples

BioBricks from Registry	CellML file
<bbpart>BBa_E0040</bbpart> ==> GFP protein	Media:BBa_E0040_Model.xml
other part	other file

CellML File

CellMl Code

<syntax type = 'xml'>

<?xml version="1.0"?>

<model xmlns="http://www.cellml.org/cellml/1.0#"

      xmlns:cmeta="http://www.cellml.org/metadata/1.0#"
      xml:base="file:///C:/CellML_models/protein.cml"
      cmeta:id="protein"
      name="protein">
 

<component name="Protein">

     <variable name="proteinDegradationRate"     initial_value="0.01"   public_interface="none" units="per_second"/>
     <variable name="proteinConcentration"       initial_value="0"     public_interface="out"  units="mole"/>
     <variable name="RiPS-IN"                    initial_value="none"  public_interface="in"   units="moles_per_second"/>
     <variable name="time"                       initial_value="none"  public_interface="in"   units="second"/>

[math]\displaystyle{ \lt apply id="rate of change of protein"\gt \lt eq/\gt \lt apply\gt \lt diff/\gt \lt bvar\gt \lt ci\gt time\lt /ci\gt \lt /bvar\gt \lt ci\gt proteinConcentration\lt /ci\gt \lt /apply\gt \lt apply\gt \lt minus/\gt \lt ci\gt RiPS-IN\lt /ci\gt \lt apply\gt \lt times/\gt \lt ci\gt proteinDegradationRate\lt /ci\gt \lt ci\gt proteinConcentration\lt /ci\gt \lt /apply\gt \lt /apply\gt \lt /apply\gt }[/math]

</component>

<import xmlns:xlink="http://www.w3.org/1999/xlink"

             xlink:href="http://openwetware.org/index.php?title=Registry_of_Standard_Biological_Models/Basic_Component_Models/Units&action=raw">

     <units name="per_second"       units_ref="per_second"/>
     <units name="moles_per_second" units_ref="moles_per_second"/>

</import>

</model> </syntax>

Comments

• This component represents a Protein. It is characterized by the degradation rate of the protein.
• It requires a 'RiPS-IN' input signal, it is provided by a RBS component, or a Promoter+RBS component