Spine |
Spatial dimensions: 3.0 Compartment size: 1.0E-15 |
Annotations: |
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GaiGTP |
Compartment: Spine
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Initial concentration: 2.3562470443292 |
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Annotations: |
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GaolfGDP |
Compartment: Spine
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Initial concentration: 0.00514744794169027 |
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Annotations: |
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Gbgolf |
Compartment: Spine
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Initial concentration: 107.875380092904 |
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Annotations: |
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Notes:
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The Gs protein is thought to be homologous to the Golf protein complex. Beta1 is listed because no information was provided on the specific beta subunit used.
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GaolfGTP |
Compartment: Spine
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Initial concentration: 1.13940415390363 |
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Annotations: |
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D1RDAGolf |
Compartment: Spine
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Initial concentration: 3.70188602073145 |
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Annotations: |
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Notes:
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The Golf is made up of the alpha, beta, and gamma subunits. The beta and gamma subunits of the Gs protein are used because Gs is homologous to the Golf protein, and Gbolf anf Ggolf could not be found.
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Golf |
Compartment: Spine
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Initial concentration: 1102.52804493589 |
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Annotations: |
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Notes:
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The Golf is made up of the alpha, beta, and gamma subunits. The beta and gamma subunits of the Gs protein are used because Gs is homologous to the Golf protein, and Gbolf and Ggolf could not be found.
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D1RGolf |
Compartment: Spine
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Initial concentration: 785.894688950477 |
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Annotations: |
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Notes:
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The Golf is made up of the alpha, beta, and gamma subunits. The beta and gamma subunits of the Gs protein are used because Gs is homologous to the Golf protein, and Gbolf and Ggolf could not be found.
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D1RDA |
Compartment: Spine
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Initial concentration: 16.100094198358 |
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Annotations: |
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D1R |
Compartment: Spine
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Initial concentration: 1194.30333083043 |
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Annotations: |
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cAMP |
Compartment: Spine
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Initial concentration: 91.6467576551524 |
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Annotations: |
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Ca |
Compartment: Spine
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Initial concentration: 60.0 |
Constant
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Annotations: |
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AC5 |
Compartment: Spine
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Initial concentration: 0.507493613791483 |
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Annotations: |
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AC5GaolfGTP |
Compartment: Spine
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Initial concentration: 0.397626017086897 |
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Annotations: |
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CaM |
Compartment: Spine
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Initial concentration: 7686.15789228991 |
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Annotations: |
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CaMCa2 |
Compartment: Spine
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Initial concentration: 316.776054644554 |
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Annotations: |
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CaMCa4 |
Compartment: Spine
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Initial concentration: 2.47080976475754 |
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Annotations: |
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PDE4 |
Compartment: Spine
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Initial concentration: 1531.9927671361 |
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Annotations: |
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PKA |
Compartment: Spine
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Initial concentration: 1100.85005741739 |
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Annotations: |
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PKAcAMP2 |
Compartment: Spine
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Initial concentration: 26.2312279909643 |
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Annotations: |
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PKAcAMP4 |
Compartment: Spine
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Initial concentration: 0.831786420159049 |
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Annotations: |
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PKAreg |
Compartment: Spine
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Initial concentration: 72.0869281714876 |
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Annotations: |
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PKAc |
Compartment: Spine
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Initial concentration: 11.5386581348021 |
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Annotations: |
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PP2B |
Compartment: Spine
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Initial concentration: 5.40475669921873 |
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Annotations: |
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Notes:
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Protein phosphatase 2B is also known as calcineurin.
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PP2Bc |
Compartment: Spine
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Initial concentration: 194.502520839594 |
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Annotations: |
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Notes:
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Assuming PP2Bc refers to entire catalytic part and not just the gamma catalytic subunit.
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PP2BCaM |
Compartment: Spine
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Initial concentration: 1380.87227011886 |
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Annotations: |
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PP2BCaMCa2 |
Compartment: Spine
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Initial concentration: 419.196440881025 |
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Annotations: |
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DARPP32 |
Compartment: Spine
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Initial concentration: 37271.6543135964 |
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Annotations: |
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PKAc*D32 |
Compartment: Spine
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Initial concentration: 7.16774795405187 |
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Annotations: |
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Notes:
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D32 appears to be a shortened name for DARPP32 and is used instead of writing it out.
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D32p34 |
Compartment: Spine
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Initial concentration: 0.678978545756906 |
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Annotations: |
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Notes:
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This appears to be a phosphorylated verison of D32, which is the shortened name for DARPP32 used in this model.
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B72PP2A |
Compartment: Spine
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Initial concentration: 860.232017549719 |
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Annotations: |
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Notes:
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This was assumed to be a modified version of PP2A. The three subunits of PP2A (alpha isoforms) are included.
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PKAc*B56PP2A |
Compartment: Spine
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Initial concentration: 16.40971542072 |
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Annotations: |
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B56PP2Ap |
Compartment: Spine
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Initial concentration: 410.242885172213 |
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Annotations: |
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Notes:
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The B56 and p are assumed to be modifications of PP2A. hasPart is used instead of isVersionOf, since PP2A consists of multiple subunits.
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CDK5 |
Compartment: Spine
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Initial concentration: 233.496415726183 |
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Annotations: |
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PP1 |
Compartment: Spine
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Initial concentration: 1493.10639547125 |
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Annotations: |
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Notes:
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PP1 consists of one catalytic and one regulatory subunit. The alpha catalytic subunit and regulatory subunit A were used here.
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CDK5*D32 |
Compartment: Spine
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Initial concentration: 1566.50358427382 |
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Annotations: |
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D32p75 |
Compartment: Spine
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Initial concentration: 8659.68104422894 |
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Annotations: |
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PKAcD32p75 |
Compartment: Spine
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Initial concentration: 36.9708066619157 |
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Annotations: |
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B72PPA2Ca |
Compartment: Spine
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Initial concentration: 51.6139210529853 |
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Annotations: |
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B56PP2Ap*D32p75 |
Compartment: Spine
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Initial concentration: 296.047711354635 |
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Annotations: |
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B72PP2A*D32p75 |
Compartment: Spine
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Initial concentration: 805.333502271791 |
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Annotations: |
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B72PP2ACa*D32p75 |
Compartment: Spine
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Initial concentration: 44.6960093760864 |
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Annotations: |
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PP1D32p34 |
Compartment: Spine
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Initial concentration: 506.893604528755 |
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Annotations: |
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PP2Bc*D32p34 |
Compartment: Spine
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Initial concentration: 0.0240114612997978 |
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Annotations: |
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B72PP2A*D32p34 |
Compartment: Spine
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Initial concentration: 224.645801649792 |
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Annotations: |
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DA |
Compartment: Spine
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Initial concentration: 10.0 |
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Annotations: |
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AMP |
Compartment: Spine
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Initial concentration: 0.0 |
Constant
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Annotations: |
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AC5Ca |
Compartment: Spine
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Initial concentration: 0.0338357229453947 |
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Annotations: |
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AC5CaGaolfGTP |
Compartment: Spine
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Initial concentration: 0.0265277448296902 |
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Annotations: |
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AC5GaiGTP |
Compartment: Spine
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Initial concentration: 1.70785338199615 |
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Annotations: |
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AC5CaGaiGTP |
Compartment: Spine
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Initial concentration: 0.113888299015711 |
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Annotations: |
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B56PP2A |
Compartment: Spine
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Initial concentration: 711.07555205532 |
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Annotations: |
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B56PP2A*D32p75 |
Compartment: Spine
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Initial concentration: 566.224135997113 |
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Annotations: |
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B72PP2ACa*D32p34 |
Compartment: Spine
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Initial concentration: 13.4787480996268 |
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Annotations: |
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PDE4*cAMP |
Compartment: Spine
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Initial concentration: 468.007232863897 |
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Annotations: |
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AC5GaolfGTPGaiGTP |
Compartment: Spine
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Initial concentration: 4.39135728748305E-4 |
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Annotations: |
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AC5CaGaolfGTPGaiGTP |
Compartment: Spine
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Initial concentration: 2.92811632030252E-5 |
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Annotations: |
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M4R |
Compartment: Spine
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Initial concentration: 1529.69994816436 |
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Annotations: |
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M4RACh |
Compartment: Spine
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Initial concentration: 25.650119219421 |
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Annotations: |
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M4RGi |
Compartment: Spine
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Initial concentration: 214.722656407666 |
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Annotations: |
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Gi |
Compartment: Spine
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Initial concentration: 1095.19571044122 |
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Annotations: |
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Notes:
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The Gi protein consists of three subunits: alpha, beta, and gamma. Alpha-1, beta-1, and gamma-2 were used because they are lowest numbers found on uniprot, although many different versions of the subunits exist.
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M4RAChGi |
Compartment: Spine
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Initial concentration: 229.927276208549 |
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Annotations: |
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Gbgi |
Compartment: Spine
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Initial concentration: 460.154356942568 |
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Annotations: |
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GaiGDP |
Compartment: Spine
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Initial concentration: 0.299804540897635 |
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Annotations: |
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ACh |
Compartment: Spine
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Initial concentration: 100.0 |
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Annotations: |
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Notes:
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The units of Acetyl-Choline (ACh) are in surface density instead (molecule/um^2) of volume density (mole/L) because there is a conflict for the second order binding to the receptor even when the original value of the rate constant is in volume units. The error is displayed as entities of different unitis cant be added. The solution was to express both the rate constant and the neurotransmitter in the same surface density units than the receptor. As Avogadro number is 6x10^23 and the conversion factor from L to um^3 is 10^15, 1mole/L equals 6x10^8 molecules/um^3.
The original values of [ACh] and the second order rate are (Falkenburger, 2010),
[ACh] = 100uM
k = 2.8 (uM^-1)*(s^-1)
k*[ACh] = 280 s^-1
which converted with the factor 1mole/L = 6x10^8 molecules/um^3
[ACh] = 100uM = 6x10^4 molecules/um^3
k = 2.8 (uM^-1)*(s^-1) = 2.8 x10^6 (M^-1)*(s^-1) = 4.7x10^-3 (um^3/molecules)*(s^-1)
k*[ACh] = 280 s^-1
which, for the sake of unit congruency (stupid program!) can be arbitrarily reduced to a surface density like,
[ACh] = 6x10^4 molecules/um^2
k = 4.7x10^-3 (um^2/molecules)*(s^-1)
k*[ACh] = 280 s^-1
As the ACh is a boundary element, i.e. its concentration wont be perturbed by the interaction with the system, the product k*[ACh] is a determined by the boundary function of ACh. Thus, while the conversions made above make the concentration and the rate constant meaninful when read, even after the second one (an imaginary 1um think extracellular layer of ACh at 100uM) for numeric purposes they are just a pain in the ass and make no differences. It is easier to trick the program by stating,
[ACh] = 100 molecule/micrometer^2
k = 2.8 (micrometer^2/molecule)*(s^-1)
Even when these numbers have cant be read straightforward.
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PDE10c |
Compartment: Spine
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Initial concentration: 0.230445425050315 |
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Annotations: |
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Notes:
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PDE10c appears to be a modification of PDE10 and does not appear to be a different subunit or molecule. Thus, both are written as a version of PDE10a.
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PDE10 |
Compartment: Spine
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Initial concentration: 246.931440841991 |
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Annotations: |
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Notes:
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PDE10c appears to be a modification of PDE10 and does not appear to be a different subunit or molecule. Thus, both are written as a version of PDE10a.
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PDE10*cAMP |
Compartment: Spine
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Initial concentration: 452.609318325671 |
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Annotations: |
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Notes:
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PDE10c appears to be a modification of PDE10 and does not appear to be a different subunit or molecule. Thus, both are written as a version of PDE10a.
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PDE10c*cAMP |
Compartment: Spine
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Initial concentration: 0.228795407287519 |
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Annotations: |
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Notes:
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PDE10c appears to be a modification of PDE10 and does not appear to be a different subunit or molecule. Thus, both are written as a version of PDE10a.
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ATP |
Compartment: Spine
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Initial concentration: 5000000.0 |
Constant
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Annotations: |
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AC5GaolfGTPGaiGTP*ATP |
Compartment: Spine
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Initial concentration: 0.109825804214832 |
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Annotations: |
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AC5GaiGTP*ATP |
Compartment: Spine
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Initial concentration: 427.086542949603 |
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Annotations: |
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AC5GaolfGTP*ATP |
Compartment: Spine
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Initial concentration: 99.5522607546951 |
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Annotations: |
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AC5*ATP |
Compartment: Spine
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Initial concentration: 126.887958343277 |
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Annotations: |
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AC5CaGaolfGTP*ATP |
Compartment: Spine
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Initial concentration: 6.63679803850652 |
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Annotations: |
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AC5CaGaiGTP*ATP |
Compartment: Spine
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Initial concentration: 28.4724047907866 |
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Annotations: |
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AC5CaGaolfGTPGaiGTP*ATP |
Compartment: Spine
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Initial concentration: 0.00732171483303589 |
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Annotations: |
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AC5Ca*ATP |
Compartment: Spine
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Initial concentration: 8.459194407526 |
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Annotations: |
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PP1*AKAR3p |
Compartment: Spine
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Initial concentration: 0.0 |
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Annotations: |
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Notes:
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AKAR3 is a FRET-based A-kinase activity reporter, or a biosensor, developed by Allen and Zhang (2006). It was applied in Castro et al (2013) to measure PKA dynamics. In this model it is used to measure PKA dynamics in the D1+MSN model. AKAR3p is assumed to be the phosphorylated version of AKAR3.
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PKAc*AKAR3 |
Compartment: Spine
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Initial concentration: 0.0 |
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Annotations: |
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Notes:
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AKAR3 is a FRET-based A-kinase activity reporter, or a biosensor, developed by Allen and Zhang (2006). It was applied in Castro et al (2013) to measure PKA dynamics. In this model it is used to measure PKA dynamics in the D1+MSN model. AKAR3p is assumed to be the phosphorylated version of AKAR3.
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Initial concentration: 35.1161215095719 |
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Annotations: |
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