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

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

Reaction Kinetic rate law Reactants Products Parameter name Valuea
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 k61r<#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
  1. amol, number of molecules