A systems model of Parkinson’s disease using biochemical systems theory (Sasidharakurup et al. 2017)

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Accession:237466
Major pathways involving in Parkinson's disease (PD) such as alphasynuclein aggregation, dopamine synthesis, lewy body formation, tau phosphorylation, parkin, and apoptosis were modeled using stochastic differential equations. Pathways were modeled and simulated using the biochemical pathway visualization program CellDesigner, a modeling tool for gene-regulatory and biochemical networks that support graphical notation and listing of symbols. The model allows a qualitative analysis of PD and a key signalling pathways for evaluating PD treatment conditions relating pathophysiology to molecular concentration changes recorded in experiments.
Reference:
1 . Sasidharakurup H, Melethadathil N, Nair B, Diwakar S (2017) A Systems Model of Parkinson's Disease Using Biochemical Systems Theory. OMICS 21:454-464 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Molecular Network;
Brain Region(s)/Organism: Generic;
Cell Type(s):
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s): Dopamine;
Simulation Environment: CellDesigner;
Model Concept(s): Signaling pathways; Pathophysiology; Parkinson's;
Implementer(s): Sasidharakurup, Hemalatha [hemalathas at am.amrita.edu]; Diwakar, Shyam [shyam at amrita.edu];
Search NeuronDB for information about:  Dopamine;
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Sasidharakurup_PD_BST_code
README.txt
BST_CellDesigner_XMLCode.xml
                            
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<!-- This model have been published in the following paper: 

Sasidharakurup H, Melethadathil N, Nair B, Diwakar S. "A Systems Model of Parkinson's Disease Using Biochemical Systems Theory", OMICS:A Journal of Integrative Biology 2017 21 8,454 -464.
Available at: http://online.liebertpub.com/doi/full/10.1089/omi.2017.0056 -->


<!-- Major pathways involving in Parkinson's disease such as alphasynuclein aggregation, dopamine synthesis, Lewy body formation, tau phosphorylation, parkin, and apoptosis were modeled 
using stochastic differential equations. Pathways were modeled and simulated using the biochemical pathway visualization program CellDesigner, a modeling tool for gene-regulatory and biochemical networks that support graphical notation and listing of symbols. -->

<!-- Last updated 10-January-2018
Developed by : Hemalatha Sasidharakurup & Dr. Shyam Diwakar    
Computational Neuroscience & Neurophysiology Lab, School of Biotechnology, Amrita University, India.
Email: shyam@amrita.edu, hemalathas@am.amrita.edu
www.amrita.edu/compneuro -->

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<species metaid="s97" id="s97" name="Tau P inhibition complex" compartment="default" initialAmount="0">
<annotation/>
</species>
<species metaid="s118" id="s118" name="insulin receptor complex" compartment="default" initialAmount="0">
<annotation/>
</species>
<species metaid="s138" id="s138" name="dopamine to dopamine reuptake transporter complex" compartment="default" initialAmount="0">
<annotation/>
</species>
<species metaid="s139" id="s139" name="dopamine reuptake complex" compartment="default" initialAmount="0">
<annotation/>
</species>
<species metaid="s223" id="s223" name="VDAC Complex" compartment="default" initialAmount="0">
<annotation/>
</species>
<species metaid="s241" id="s241" name="Pael-R degradation complex" compartment="default" initialAmount="0">
<annotation/>
</species>
<species metaid="s243" id="s243" name="Parkin degradation complex formation" compartment="default" initialAmount="0">
<annotation/>
</species>
<species metaid="s244" id="s244" name="PARIS degradation Complex" compartment="default" initialAmount="0">
<annotation/>
</species>
<species metaid="s296" id="s296" name="Caspase 9 inhibition complex" compartment="default" initialAmount="0">
<annotation/>
</species>
<species metaid="s307" id="s307" name="IAP inhibition complex" compartment="default" initialAmount="0">
<annotation/>
</species>
<species metaid="s310" id="s310" name="Caspase 3 inhibition complex" compartment="default" initialAmount="0">
<annotation/>
</species>
<species metaid="s316" id="s316" name="Cyt c Inhibition Complex" compartment="default" initialAmount="0">
<annotation/>
</species>
<species metaid="s220" id="s220" name="Hsp70 APAF inhibition complex" compartment="default" initialAmount="0">
<annotation/>
</species>
<species metaid="s222" id="s222" name="AIF inhibition complex" compartment="default" initialAmount="0">
<annotation/>
</species>
<species metaid="s202" id="s202" name="JNK inhibition complex" compartment="default" initialAmount="0">
<annotation/>
</species>

</listOfSpecies>


<listOfReactions>

<reaction metaid="re61" id="re2" name="re2" reversible="false">
<annotation/>
<listOfReactants>
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<reaction metaid="re7" id="re3" name="re3" reversible="false">
<annotation/>
<listOfReactants>
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<speciesReference metaid="CDMT00009" species="s8"/>
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<listOfProducts>
<speciesReference metaid="CDMT00010" species="s6"/>
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</reaction>
<reaction metaid="re8" id="re4" name="re4" reversible="false">
<annotation/>
<listOfReactants>
<speciesReference metaid="CDMT00011" species="s9"/>
<speciesReference metaid="CDMT00012" species="s10"/>
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<listOfProducts>
<speciesReference metaid="CDMT00013" species="s6"/>
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</reaction>
<reaction metaid="re23" id="re7" name="re7" reversible="false">
<annotation/>
<listOfReactants>
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<listOfProducts>
<speciesReference metaid="CDMT00022" species="s44"/>
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</reaction>
<reaction metaid="re24" id="re8" name="re8" reversible="false">
<annotation/>
<listOfReactants>
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</listOfReactants>
<listOfProducts>
<speciesReference metaid="CDMT00024" species="s21"/>
</listOfProducts>
</reaction>
<reaction metaid="CDMT00057" id="re9" name="re9" reversible="false">
<annotation/>
<listOfReactants>
<speciesReference metaid="CDMT00025" species="s45"/>
<speciesReference metaid="CDMT00026" species="s46"/>
<speciesReference metaid="CDMT00027" species="s21"/>
</listOfReactants>
<listOfProducts>
<speciesReference metaid="CDMT00028" species="s47"/>
</listOfProducts>
</reaction>
<reaction metaid="re27" id="re10" name="re10" reversible="false">
<annotation/>
<listOfReactants>
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<listOfProducts>
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</reaction>
<reaction metaid="re28" id="re11" name="re11" reversible="false">
<annotation/>
<listOfReactants>
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<listOfProducts>
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</reaction>
<reaction metaid="re29" id="re12" name="re12" reversible="false">
<annotation/>
<listOfReactants>
<speciesReference metaid="CDMT00035" species="s51"/>
<speciesReference metaid="CDMT00036" species="s52"/>
</listOfReactants>
<listOfProducts>
<speciesReference metaid="CDMT00037" species="s50"/>
</listOfProducts>
</reaction>
<reaction metaid="re31" id="re13" name="re13" reversible="false">
<annotation/>
<listOfReactants>
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<listOfProducts>
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</reaction>
<reaction metaid="re32" id="re14" name="re14" reversible="false">
<annotation/>
<listOfReactants>
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<listOfProducts>
<speciesReference metaid="CDMT00043" species="s55"/>
</listOfProducts>
</reaction>
<reaction metaid="re36" id="re15" name="re15" reversible="false">
<annotation/>
<listOfReactants>
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</listOfReactants>
<listOfProducts>
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</listOfProducts>
</reaction>
<reaction metaid="re37" id="re16" name="re16" reversible="false">
<annotation/>
<listOfReactants>
<speciesReference metaid="CDMT00046" species="s60"/>
</listOfReactants>
<listOfProducts>
<speciesReference metaid="CDMT00047" species="s54"/>
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</reaction>
<reaction metaid="re39" id="re17" name="re17" reversible="false">
<annotation/>
<listOfReactants>
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<listOfProducts>
<speciesReference metaid="CDMT00049" species="s54"/>
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</reaction>
<reaction metaid="re40" id="re18" name="re18" reversible="false">
<annotation/>
<listOfReactants>
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<listOfProducts>
<speciesReference metaid="CDMT00052" species="s66"/>
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</reaction>
<reaction metaid="re41" id="re19" name="re19" reversible="false">
<annotation/>
<listOfReactants>
<speciesReference metaid="CDMT00053" species="s64"/>
<speciesReference metaid="CDMT00054" species="s65"/>
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<listOfProducts>
<speciesReference metaid="CDMT00055" species="s60"/>
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</reaction>
<reaction metaid="re42" id="re20" name="re20" reversible="false">
<annotation/>
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</reaction>
<reaction metaid="re43" id="re21" name="re21" reversible="false">
<annotation/>
<listOfReactants>
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<listOfProducts>
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</reaction>
<reaction metaid="re44" id="re22" name="re22" reversible="false">
<annotation/>
<listOfReactants>
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<listOfProducts>
<speciesReference metaid="CDMT00063" species="s54"/>
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</reaction>
<reaction metaid="re45" id="re23" name="re23" reversible="false">
<annotation/>
<listOfReactants>
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<listOfProducts>
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</reaction>
<reaction metaid="re38" id="re24" name="re24" reversible="false">
<annotation/>
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<listOfProducts>
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</reaction>
<reaction metaid="re48" id="re25" name="re25" reversible="false">
<annotation/>
<listOfReactants>
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<speciesReference metaid="CDMT00075" species="s83"/>
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</reaction>
<reaction metaid="re51" id="re26" name="re26" reversible="false">
<annotation/>
<listOfReactants>
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<listOfProducts>
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</reaction>
<reaction metaid="re52" id="re27" name="re27" reversible="false">
<annotation/>
<listOfReactants>
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</listOfReactants>
<listOfProducts>
<speciesReference metaid="CDMT00088" species="s87"/>
</listOfProducts>
</reaction>
<reaction metaid="re56" id="re28" name="re28" reversible="false">
<annotation/>
<listOfReactants>
<speciesReference metaid="CDMT00089" species="s86"/>
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</listOfReactants>
<listOfProducts>
<speciesReference metaid="CDMT00091" species="s87"/>
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</reaction>
<reaction metaid="re57" id="re29" name="re29" reversible="false">
<annotation/>
<listOfReactants>
<speciesReference metaid="CDMT00092" species="s90"/>
</listOfReactants>
<listOfProducts>
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</listOfProducts>
</reaction>
<reaction metaid="re58" id="re30" name="re30" reversible="false">
<annotation/>
<listOfReactants>
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</listOfReactants>
<listOfProducts>
<speciesReference metaid="CDMT00096" species="s92"/>
</listOfProducts>
</reaction>
<reaction metaid="re59" id="re31" name="re31" reversible="false">
<annotation/>
<listOfReactants>
<speciesReference metaid="CDMT00097" species="s93"/>
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<listOfProducts>
<speciesReference metaid="CDMT00098" species="s87"/>
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</reaction>
<reaction metaid="re60" id="re32" name="re32" reversible="false">
<annotation/>
<listOfReactants>
<speciesReference metaid="CDMT00099" species="s94"/>
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<listOfProducts>
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</reaction>
<reaction metaid="re33" id="re33" name="re33" reversible="false">
<annotation/>
<listOfReactants>
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</listOfReactants>
<listOfProducts>
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</reaction>
<reaction metaid="re62" id="re34" name="re34" reversible="false">
<annotation/>
<listOfReactants>
<speciesReference metaid="CDMT00104" species="s86"/>
<speciesReference metaid="CDMT00105" species="s88"/>
</listOfReactants>
<listOfProducts>
<speciesReference metaid="CDMT00106" species="s93"/>
</listOfProducts>
</reaction>
<reaction metaid="re63" id="re35" name="re35" reversible="false">
<annotation/>
<listOfReactants>
<speciesReference metaid="CDMT00107" species="s86"/>
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<listOfProducts>
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</reaction>
<reaction metaid="re64" id="re36" name="re36" reversible="false">
<annotation/>
<listOfReactants>
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<listOfProducts>
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</reaction>
<reaction metaid="re65" id="re37" name="re37" reversible="false">
<annotation/>
<listOfReactants>
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<listOfProducts>
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</reaction>
<reaction metaid="re67" id="re38" name="re38" reversible="false">
<annotation/>
<listOfReactants>
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<listOfProducts>
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</reaction>
<reaction metaid="re68" id="re39" name="re39" reversible="false">
<annotation/>
<listOfReactants>
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</reaction>
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<annotation/>
<listOfReactants>
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<listOfProducts>
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</reaction>
<reaction metaid="re72" id="re41" name="re41" reversible="false">
<annotation/>
<listOfReactants>
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<listOfProducts>
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</reaction>
<reaction metaid="re73" id="re42" name="re42" reversible="false">
<annotation/>
<listOfReactants>
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<listOfProducts>
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</reaction>
<reaction metaid="re74" id="re43" name="re43" reversible="false">
<annotation/>
<listOfReactants>
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<listOfProducts>
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</reaction>
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<annotation/>
<listOfReactants>
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<listOfProducts>
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</reaction>
<reaction metaid="re86" id="re53" name="re53" reversible="false">
<annotation/>
<listOfReactants>
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<listOfProducts>
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</reaction>
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<annotation/>
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</reaction>
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<annotation/>
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</reaction>
<reaction metaid="re89" id="re56" name="re56" reversible="false">
<annotation/>
<listOfReactants>
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<listOfProducts>
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</reaction>
<reaction metaid="re90" id="re57" name="re57" reversible="false">
<annotation/>
<listOfReactants>
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<listOfProducts>
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</reaction>
<reaction metaid="re99" id="re66" name="re66" reversible="false">
<annotation/>
<listOfReactants>
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<listOfProducts>
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</reaction>
<reaction metaid="re101" id="re67" name="re67" reversible="false">
<annotation/>
<listOfReactants>
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</listOfReactants>
<listOfProducts>
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</reaction>
<reaction metaid="re102" id="re68" name="re68" reversible="false">
<annotation/>
<listOfReactants>
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<listOfProducts>
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</reaction>
<reaction metaid="re104" id="re69" name="re69" reversible="false">
<annotation/>
<listOfReactants>
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</reaction>
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<annotation/>
<listOfReactants>
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</reaction>
<reaction metaid="re114" id="re78" name="re78" reversible="false">
<annotation/>
<listOfReactants>
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</reaction>
<reaction metaid="re115" id="re79" name="re79" reversible="false">
<annotation/>
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</reaction>
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<annotation/>
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</reaction>
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<annotation/>
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</reaction>
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<annotation/>
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<annotation/>
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<annotation/>
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</model>
</sbml>

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