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Table 1 List of species with database terms and initial conditions

From: An in silico model of the ubiquitin-proteasome system that incorporates normal homeostasis and age-related decline

Species description Species Name Database term Initial Amount
Native protein NatP N/A 500
Misfolded protein MisP N/A 0
Ubiquitin Ub IPR000626 500
Ubiquitin activating enzyme E1 IPR000011 100
Ubiquitin conjugating enzyme E2 IPR000608 100
Ubiquitin ligase (HECT) E3 IPR000569 100
De-ubiquitinating enzyme DUB IPR001394 200
Proteasome Proteasome GO:0000502 100
Reactive oxygen species ROS CHEBI:26523 10
Adenosine triphosphate ATP CHEBI:15422 10000
Adenosine diphosphate ADP CHEBI:16761 1000
Adenosine monophosphate AMP CHEBI:22254 1000
Misfolded protein bound by E3 E3_MisP IPR000569 0
E1 bound by Ub E1_Ub IPR000011 0
E2 bound by Ub E2_Ub IPR000608 0
Monoubiquitinated misfolded protein MisP_Ub IPR000626 0
Polyubiquitinated misfolded protein MisP_Ub2, ... MisP_Ub8 IPR000626 0
Polyubiquitinated protein bound to proteasome MisP_Ub4_Proteasome ... MisP_Ub8_Proteasome IPR000626 GO:0000502 0
Aggregated protein AggP N/A 0
Sequestered aggregated protein SeqAggP N/A 0
Aggregated protein bound to proteasome AggP_Proteasome GO:0000502 0
Dummy species to track chain length of substrate at degradation degUb4, ..., degUb8 N/A 0
  1. IPR: InterPro [46]
  2. GO: Gene ontology [47]
  3. CHEBI: Chemical Entities of Biological Interest database [48]