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Molecule Parameter List for AA

The statistics table lists the distribution of a molecule acting either as a substrate, product, enzyme or as a molecule within the network.
The text color of a molecule is highlighted by color.
Statistics
AA participated asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1000540

Accession and Pathway Details
Accession NameAccession No.Accession TypePathway Link
  • Synaptic_
    Network
  • 16Network
    Shared_Object_Synaptic_Network PKC PLA2 
    PLCbeta Gq MAPK 
    Ras EGFR Sos 
    PLC_g CaMKII CaM 
    PP1 PP2B PKA 
    AC CaRegulation 
    This model is an annotated version of the synaptic signaling network.
    The primary reference is Bhalla US and Iyengar R. Science (1999) 283(5400):381-7 but several of the model pathways have been updated.
    Bhalla US Biophys J. 2002 Aug;83(2):740-52
    Bhalla US J Comput Neurosci. 2002 Jul-Aug;13(1):49-62

    AA acting as a Molecule in  
    Synaptic_Network Network
    NameAccession NamePathway NameInitial Conc.
    (uM)
    Volume
    (fL)
    Buffered
    AA
  • Synaptic_
    Network

    Accession No. : 16
  • Shared_Object_
    Synaptic_
    Network

    Pathway No. : 70
  • 01000No
    Arachidonic Acid. This messenger diffuses through membranes as well as cytosolically, has been suggested as a possible retrograde messenger at synapses.

    AA acting as a Product of an Enzyme in  
    Synaptic_Network Network
     Enzyme Molecule /
    Enzyme Activity
    Accession NamePathway NameKm (uM)kcat (s^-1)RatioEnzyme TypeReagents
    1PLA2-Ca*  /
    kenz
  • Synaptic_
    Network

    Accession No. : 16
  • PLA2
    Pathway No. : 72
    205.44explicit E-S complexSubstrate
    APC

    Product
    AA
        Based on Leslie and Channon 1990 BBA 1045:261, in relation to the other PLA2 inputs (not including MAPK). Ca alone is rather a weak input.
    2PIP2-PLA2*  /
    kenz
  • Synaptic_
    Network

    Accession No. : 16
  • PLA2
    Pathway No. : 72
    2011.044explicit E-S complexSubstrate
    APC

    Product
    AA
        Based on Leslie and Channon 1990 BBA 1045:261.
    3PIP2-Ca-PLA2*  /
    kenz
  • Synaptic_
    Network

    Accession No. : 16
  • PLA2
    Pathway No. : 72
    20364explicit E-S complexSubstrate
    APC

    Product
    AA
        Based on AA generation by different stimuli according to Leslie and Channon 1990 BBA 1045:261
    4DAG-Ca-PLA2*  /
    kenz
  • Synaptic_
    Network

    Accession No. : 16
  • PLA2
    Pathway No. : 72
    20604explicit E-S complexSubstrate
    APC

    Product
    AA
        Based on Leslie and Channon 1990 BBA 1045:261.
    5PLA2*-Ca  /
    kenz
  • Synaptic_
    Network

    Accession No. : 16
  • PLA2
    Pathway No. : 72
    201204explicit E-S complexSubstrate
    APC

    Product
    AA
        This form should be 3 to 6 times as fast as the Ca-only form, from Lin et al 1993 Cell 269-278 Nemenoff et al 1993 JBC 268:1960 Several forms contribute to the Ca-stimulated form, so this rate has to be a factor larger than their total contribution. I assign Vmax as the scale factor here because there is lots of APC substrate, so all the PLA2 complex enzymes are limited primarily by Vmax.

    AA acting as a Substrate in a reaction in  
    Synaptic_Network Network
    Kd is calculated only for second order reactions, like nA+nB <->nC or nA<->nC+nD, where n is number and A,B,C,D are molecules, where as for first order reactions Keq is calculated. Kd for higher order reaction are not consider.
     NameAccession NamePathway NameKfKbKdtauReagents
    1
  • PKC-act-by-Ca-AA
  • Synaptic_
    Network

    Accession No. : 16
  • PKC
    Pathway No. : 71
    0.0012
    (uM^-1 s^-1)
    0.1
    (s^-1)
    Kd(bf) = 83.3333(uM)-Substrate
    AA
    PKC-Ca

    Product
    PKC-Ca-AA*
      Ca-dependent AA activation of PKC. Note that this step combines the AA activation and also the membrane translocation. From Schaechter and Benowitz 1993 J Neurosci 13(10):4361
    2PKC-act-by-AA
  • Synaptic_
    Network

    Accession No. : 16
  • PKC
    Pathway No. : 71
    0.0001
    (uM^-1 s^-1)
    0.1
    (s^-1)
    Kd(bf) = 833.3333(uM)-Substrate
    AA
    PKC-cytosolic

    Product
    PKC-AA*
      AA stimulates PKC activity even at rather low Ca. Schaechter and Benowitz 1993 J Neurosci 13(10):4361 Note that this one reaction combines the initial interaction and also membrane translocation.
    3PKC-n-DAG-AA
  • Synaptic_
    Network

    Accession No. : 16
  • PKC
    Pathway No. : 71
    0.018
    (uM^-1 s^-1)
    2
    (s^-1)
    Kd(bf) = 111.1111(uM)-Substrate
    AA
    PKC-DAG

    Product
    PKC-DAG-AA
      This is one of the more interesting steps. Mechanistically it does not seem necessary at first glance. Turns out that one needs this step to quantitatively match the curves in Schaechter and Benowitz 1993 J Neurosci 13(10):4361 and Shinomura et al 1991 PNAS 88:5149-5153. There is a synergy between DAG and AA activation even at low Ca levels, which is most simply represented by this reaction. Tau is assumed to be fast. Kd comes from matching the experimental curves.
    4Degrade-AA
  • Synaptic_
    Network

    Accession No. : 16
  • PLA2
    Pathway No. : 72
    0.4
    (s^-1)
    0
    (s^-1)
    --Substrate
    AA

    Product
    APC
      Degradation pathway for AA. APC is a convenient buffered pool to dump it back into, though the actual metabolism is probably far more complex. For the purposes of the full model we use a rate of degradation of 0.4/sec to give a dynamic range of AA comparable to what is seen experimentally. Wijkander and Sundler 1991 Eur J Biochem 202:873 Leslie and Channon 1990 BBA 1045:261



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