Table 2 List of reactions and parameter values for the ubiquitin-proteasome system

Protein synthesis

k ₁

NatP

k ₁

0.01 mol s^-1

Misfolding

k₂<#NatP><#ROS>

NatP, ROS

MisP, ROS

k ₂

2.0E-6 mol^-1 s^-1

Refolding

k₃ <#MisP>

MisP

NatP

k ₃

4.0E-6 s^-1

MisP/E3 binding

k₆₁ <#E3><#MisP>

E3, MisP

E3_MisP

k ₆₁

1.7E-5 mol^-1 s^-1

MisPE3 release

k_61r<#E3_MisP>

E3_MisP

E3, MisP

k _61r

2.0E-4 s^-1

E1/Ub binding

k₆₂ <#E1><#Ub><#ATP>/(5000+<#ATP>)

E1, Ub, ATP

E1_Ub, AMP

k ₆₂

2.0E-4 mol^-1 s^-1

E2/Ub binding

k₆₃ <#E2><#E1_Ub>

E2, E1_Ub

E1, E2_Ub

k ₆₃

1.0E-3 mol^-1 s^-1

Monoubiquitination

k₆₄ <#E2_Ub><#E3_MisP>

E2_Ub, E3_MisP

E2, E3, MisP_Ub

k ₆₄

1.0E-3 mol^-1 s^-1

Polyubiquitination1

k₆₅ <#E2_Ub><#MisP_Ub>

E2_Ub, MisP_Ub

MisP_Ub2

k ₆₅

1.0E-2 mol^-1 s^-1

Polyubiquitination2

k₆₅ <#E2_Ub><#MisP_Ub2>

E2_Ub, MisP_Ub2

MisP_Ub3

k ₆₅

1.0E-2 mol^-1 s^-1

⋮

⋮

⋮

⋮

⋮

⋮

Polyubiquitination7

k₆₅ <#E2_Ub><#MisP_Ub8>

E2_Ub, MisP_Ub7

MisP_Ub8

k ₆₅

1.0E-2 mol^-1 s^-1

De-ubiquitination1

k₆₆ <#DUB><#MisP_Ub8>

DUB, MisP_Ub8

DUB, MisP_Ub7, Ub

k ₆₆

1.0E-5 mol^-1 s^-1

⋮

⋮

⋮

⋮

⋮

⋮

De-ubiquitination8

k₆₆ <#DUB><#MisP_Ub>

DUB, MisP_Ub

DUB, MisP, Ub

k ₆₆

1.0E-5 mol^-1 s^-1

Proteasome binding1

k₆₇ <#MisP_Ub4><#Proteasome>

MisP_Ub4, Proteasome

MisP_Ub4_ Proteasome

k ₆₇

1.0E-5 mol^-1 s^-1

⋮

⋮

⋮

⋮

⋮

⋮

Proteasome binding5

k₆₇ <#MisP_Ub8><#Proteasome>

MisP_Ub8, Proteasome

MisP_Ub8_ Proteasome

k ₆₇

1.0E-5 mol^-1 s^-1

De-ubiquitinationBoundMisP1

k₆₈ <#DUB><#MisP_Ub4_Proteasome>

DUB, MisP_Ub4_Proteasome

DUB, MisP_Ub3, Ub, Proteasome

k ₆₈

1.0E-5 mol^-1 s^-1

De-ubiquitinationBoundMisP2

k₆₈ <#DUB><#MisP_Ub5_Proteasome>

DUB, MisP_Ub5_Proteasome

DUB, Ub, MisP_Ub4_Proteasome

k ₆₈

1.0E-5 mol^-1 s^-1

⋮

⋮

⋮

⋮

⋮

⋮

De-ubiquitinationBoundMisP5

k₆₈ <#DUB><#MisP_Ub8_Proteasome>

DUB, MisP_Ub8_Proteasome

DUB, Ub, MisP_Ub7_Proteasome

k ₆₈

1.0E-5 mol^-1 s^-1

ProteasomeActivity1

k₆₉ <#MisP_Ub4_Proteasome><#ATP>/(5000+<#ATP>)

ATP, MisP_Ub4_ Proteasome

ADP, Proteasome, 4Ub,

k ₆₉

1.0E-3 s^-1

⋮

⋮

⋮

⋮

⋮

⋮

ProteasomeActivity 5

k₆₉ <#MisP_Ub8_Proteasome><#ATP>/(5000+<#ATP>)

ATP, MisP_Ub8_ Proteasome

ADP, Proteasome, 8Ub,

k ₆₉

1.0E-3 s^-1