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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]