title: In silico modeling of the effects of alpha-synuclein oligomerization on dopaminergic neuronal homeostasis.
abstract: BACKGROUND
  Alpha-synuclein (ASYN) is central in Parkinson's disease (PD) pathogenesis. Converging pieces of evidence suggest that the levels of ASYN expression play a critical role in both familial and sporadic Parkinson's disease. ASYN fibrils are the main component of inclusions called Lewy Bodies (LBs) which are found mainly in the surviving neurons of the substantia nigra. Despite the accumulated knowledge regarding the involvement of ASYN in molecular mechanisms underlying the development of PD, there is much information missing which prevents understanding the causes of the disease and how to stop its progression.
  
  
  RESULTS
  Using a Systems Biology approach, we develop a biomolecular reactions model that describes the intracellular ASYN dynamics in relation to overexpression, post-translational modification, oligomerization and degradation of the protein. Especially for the proteolysis of ASYN, the model takes into account the biological knowledge regarding the contribution of Chaperone Mediated Autophagy (CMA), macro-autophagic and proteasome pathways in the protein's degradation. Importantly, inhibitory phenomena, caused by ASYN, concerning CMA (more specifically the lysosomal-associated membrane protein 2a, abbreviated as Lamp2a receptor, which is the rate limiting step of CMA) and the proteasome are carefully modeled. The model is validated by simulation studies of known experimental overexpression data from SH-SY5Y cells and the unknown model parameters are estimated either computationally or by experimental fitting. The calibrated model is then tested under three hypothetical intervention scenarios and in all cases predicts increased cell viability that agrees with experimental evidence. The biomodel has been annotated and is made available in SBML format.
  
  
  CONCLUSIONS
  The mathematical model presented here successfully simulates the dynamic phenomena of ASYN overexpression and oligomerization and predicts the biological system's behavior in a number of scenarios not used for model calibration. It allows, for the first time, to qualitatively estimate the protein levels that are capable of deregulating proteolytic homeostasis. In addition, it can help form new hypotheses for intervention that could be tested experimentally.
authors.forename: Eleftherios
authors.initials: E
authors.lastname: Ouzounoglou
authors.forename: Dimitrios
authors.initials: D
authors.lastname: Kalamatianos
authors.forename: Evangelia
authors.initials: E
authors.lastname: Emmanouilidou
authors.forename: Maria
authors.initials: M
authors.lastname: Xilouri
authors.forename: Leonidas
authors.initials: L
authors.lastname: Stefanis
authors.forename: Kostas
authors.initials: K
authors.lastname: Vekrellis
authors.affiliation: Department of Informatics and Telecommunications, Graduate Program "Information Technologies in Medicine and Biology", National and Kapodistrian University of Athens, Athens 15784, Greece. eliasm@di.uoa.gr.
authors.forename: Elias S
authors.initials: ES
authors.lastname: Manolakos
mesh_terms: D001343:Autophagy; D003198:Computer Simulation; D059290:Dopaminergic Neurons / Q000166:cytology / Q000378:metabolism*; D006706:Homeostasis; D008954:Models, Biological; D018832:Molecular Chaperones / Q000378:metabolism; D046988:Proteasome Endopeptidase Complex / Q000378:metabolism; D055503:Protein Multimerization; D020836:Protein Structure, Quaternary; D015203:Reproducibility of Results; D049490:Systems Biology / Q000379:methods*; D051844:alpha-Synuclein / Q000737:chemistry*
chemical_list: D018832:Molecular Chaperones; D051844:alpha-Synuclein; D046988:Proteasome Endopeptidase Complex