Registry of Standard Biological Models/Basic Component Models/Ribosome binding site (RBS)

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ID: Ribosome Binding Site (RBS)

  • Description: RBS promoting translation rate
  • Hypothesis:
    • Continuous and constant translation rate
    • Unlimited resource for translation (ribosome, tRNA ...)
  • Inputs:
    • [mRNA]
  • Outputs:
    • protein-synthesis-rate
  • Characteristic parameters:
    • translation-rate-per-mRNA
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RBS Brick Architecture

CellML structure (CellML 1.1 spec)

  • Component: RBS
  • Units:
    • Imported from Environment component
  • Variables:
    • mRNA (public interface= in )
    • translationRatePermRNA (public interface = none / init value = XXX)
    • protein-synthesis-rate (public interface = out / init value = XXX)
  • MathML
    • <amsmath> proteinSynthesisRate = translationRatePermRNA*[mRNA]</amsmath>

CellML File

<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/RBS.cml"
      cmeta:id="RBS"
      name="RBS">

<component name="RBS">

<variable name="proteinSynthesisRate" initial_value="" public_interface="out" units="moles_per_second"/> <variable name="nb_mRNA" initial_value="" public_interface="in" units="mole"/> <variable name="proteinSynthesisRatePermRNA" initial_value="1" public_interface="none" units="per_second"/>

[math]\displaystyle{ \lt apply id="proteinSynthesisRate"\gt \lt eq/\gt \lt ci\gt proteinSynthesisRate\lt /ci\gt \lt apply\gt \lt times/\gt \lt ci\gt proteinSynthesisRatePermRNA\lt /ci\gt \lt ci\gt nb_mRNA\lt /ci\gt \lt /apply\gt \lt /apply\gt }[/math]

</component>




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

       xlink:href="file://C:\CellML_models\units.cml">

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

</import>




</model> </syntax>


Comments

  • this component provides the synthesis rate of downstream proteins based on [mRNA] and RBS translation rate.
  • don't know if it is possible to characterize experimentally the translationRatePermRNA?
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