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Molecule Parameter List for Autonomous

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
Autonomous participated asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1101022

Accession and Pathway Details
Accession NameAccession No.Accession TypePathway Link
CaMKII33Network
Shared_Object_CaMKII CaM CaMKII 
CaN 
This is a deterministic, point kinetics approximation to the dendritic spine CaMKII model described in William R. Holmes J Comput Neurosci. (2000) 8(1):65-85. Rates are the same but the responses differ somewhat because this model does not include the stochastic and diffusive calculations of the original.

Autonomous acting as a Molecule in  
CaMKII Network
NameAccession NamePathway NameInitial Conc.
(uM)
Volume
(fL)
Buffered
AutonomousCaMKII
Accession No. : 33
CaMKII
Pathway No. : 174
00.1309No

Autonomous acting as a Summed Molecule in  
CaMKII Network
Accession NamePathway NameTargetInput
CaMKII
Accession No. : 33
CaMKII
Pathway No. : 174
Tot-active-CaMKIICaMKII-CaMCa4
Trapped-T286
Capped
Autonomous

Autonomous acting as a Substrate for an Enzyme in  
CaMKII Network
Enzyme Molecule /
Enzyme Activity
Accession NamePathway NameKm (uM)kcat (s^-1)RatioEnzyme TypeReagents
  • Tot-active-CaMKI
    I
      /
    phosph_T305
  • CaMKII
    Accession No. : 33
    CaMKII
    Pathway No. : 174
    1.27325100explicit E-S complexSubstrate
    Autonomous

    Product
    Capped
    This enzyme also represents an intra-holoenzyme reaction. So it is not really treated as an enzyme in Holme's model, more like a probability of reaction that scales according to the number of active CaMKII neighboring subunits. Here we approximate it as an enzyme rate limited by the k1=0.1 step, no back reaction, and with a scaling from Total_CaMKII such that the effective forward rate will simply be the fraction of CaMKII that are active, times 1/10 for nearest neigbors, times k1.

    Autonomous acting as a Substrate in a reaction in  
    CaMKII 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
    1dephosph_T286CaMKII
    Accession No. : 33
    CaMKII
    Pathway No. : 174
    0.003
    (s^-1)
    0
    (s^-1)
    --Substrate
    Autonomous

    Product
    CaMKII
    2
  • Autonomous-bind-
    CaMCa4
  • CaMKII
    Accession No. : 33
    CaMKII
    Pathway No. : 174
    33.2998
    (uM^-1 s^-1)
    0
    (s^-1)
    --Substrate
    Autonomous
    CaMCa4

    Product
    Trapped-T286

    Autonomous acting as a Product in a reaction in  
    CaMKII 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
  • Autonomous_
    lose_CaMCa4
  • CaMKII
    Accession No. : 33
    CaMKII
    Pathway No. : 174
    0.02
    (s^-1)
    0
    (uM^-1 s^-1)
    --Substrate
    Trapped-T286

    Product
    Autonomous
    CaMCa4
      Holmes says that this rate is variable, and depends on Ca conc. It is 0.1 when [Ca] = 10 nM, and 0.00355/sec when [Ca] is 1.0 For our purposes, we assume a good steady approx to this rate is 0.02.
    2dephosph_T305CaMKII
    Accession No. : 33
    CaMKII
    Pathway No. : 174
    0.01
    (s^-1)
    0
    (s^-1)
    --Substrate
    Capped

    Product
    Autonomous
      This is treated as a separate reaction because it is independent of the CaMKII concentration or activation state, unlike the forward reaction in the Holmes paper. Holmes tries a range of rates for this step, and says it doesn't matter much.



    Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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