Protein-Small compounds Interaction Networks¶
Protein-small compound interaction networks have two columns. Similar to a PPI network, but the user should add the prefix “SMALL-” to encode a small compound that interacts with the protein or protein complex.
Examples:
SOURCE TARGET
PER-araF SMALL-PER-alpha-L-arabinofuranose
PER-araF SMALL-PER-beta-L-arabinofuranose
PER-araF SMALL-PER-alpha-L-arabinopyranose
PER-araF SMALL-PER-beta-L-arabinopyranose
[crp, crp] SMALL-CAMP
[crp, SMALL-CAMP, crp] SMALL-CAMP
[lacI, lacI] SMALL-ALLOLACTOSE
[lacI, SMALL-ALLOLACTOSE, lacI] SMALL-ALLOLACTOSE
[araG, araG] SMALL-ATP
araC SMALL-alpha-L-arabinopyranose
[araC, araC] SMALL-alpha-L-arabinopyranose
[araC, SMALL-alpha-L-arabinopyranose, araC] SMALL-alpha-L-arabinopyranose
Finally, execute the “Rules from protein-small compounds.ipynb” to obtain the Rules to model the defined interaction network. The complete rule-based model can be found in the arabinose folder from the Network Biology Lab GitHub repository here.
Rule('ProtMet_RuleAssembly_1',
prot(name = 'araF', loc = 'per', met = None, up = None, dw = None) +
met(name = 'alpha_L_arabinofuranose', loc = 'per', prot = None) |
prot(name = 'araF', loc = 'per', met = 1, up = None, dw = None) %
met(name = 'alpha_L_arabinofuranose', loc = 'per', prot = 1),
Parameter('fwd_ProtMet_RuleAssembly_1', 1),
Parameter('rvs_ProtMet_RuleAssembly_1', 1))
Rule('ProtMet_RuleAssembly_2',
prot(name = 'araF', loc = 'per', met = None, up = None, dw = None) +
met(name = 'beta_L_arabinofuranose', loc = 'per', prot = None) |
prot(name = 'araF', loc = 'per', met = 1, up = None, dw = None) %
met(name = 'beta_L_arabinofuranose', loc = 'per', prot = 1),
Parameter('fwd_ProtMet_RuleAssembly_2', 1),
Parameter('rvs_ProtMet_RuleAssembly_2', 1))
Rule('ProtMet_RuleAssembly_3',
prot(name = 'araF', loc = 'per', met = None, up = None, dw = None) +
met(name = 'alpha_L_arabinopyranose', loc = 'per', prot = None) |
prot(name = 'araF', loc = 'per', met = 1, up = None, dw = None) %
met(name = 'alpha_L_arabinopyranose', loc = 'per', prot = 1),
Parameter('fwd_ProtMet_RuleAssembly_3', 1),
Parameter('rvs_ProtMet_RuleAssembly_3', 1))
Rule('ProtMet_RuleAssembly_4',
prot(name = 'araF', loc = 'per', met = None, up = None, dw = None) +
met(name = 'beta_L_arabinopyranose', loc = 'per', prot = None) |
prot(name = 'araF', loc = 'per', met = 1, up = None, dw = None) %
met(name = 'beta_L_arabinopyranose', loc = 'per', prot = 1),
Parameter('fwd_ProtMet_RuleAssembly_4', 1),
Parameter('rvs_ProtMet_RuleAssembly_4', 1))
Rule('ProtMet_RuleAssembly_5',
prot(name = 'crp', loc = 'cyt', met = None, up = None, dw = 1) %
prot(name = 'crp', loc = 'cyt', met = None, up = 1, dw = None) +
met(name = 'CAMP', loc = 'cyt', prot = None) |
prot(name = 'crp', loc = 'cyt', met = None, up = None, dw = 1) %
prot(name = 'crp', loc = 'cyt', met = 2, up = 1, dw = None) %
met(name = 'CAMP', loc = 'cyt', prot = 2),
Parameter('fwd_ProtMet_RuleAssembly_5', 1),
Parameter('rvs_ProtMet_RuleAssembly_5', 1))
Rule('ProtMet_RuleAssembly_6',
prot(name = 'crp', loc = 'cyt', met = 2, up = None, dw = 1) %
met(name = 'CAMP', loc = 'cyt', prot = 2) %
prot(name = 'crp', loc = 'cyt', met = None, up = 1, dw = None) +
met(name = 'CAMP', loc = 'cyt', prot = None) |
prot(name = 'crp', loc = 'cyt', met = 2, up = None, dw = 1) %
met(name = 'CAMP', loc = 'cyt', prot = 2) %
prot(name = 'crp', loc = 'cyt', met = 3, up = 1, dw = None) %
met(name = 'CAMP', loc = 'cyt', prot = 3),
Parameter('fwd_ProtMet_RuleAssembly_6', 1),
Parameter('rvs_ProtMet_RuleAssembly_6', 1))
Rule('ProtMet_RuleAssembly_7',
prot(name = 'lacI', loc = 'cyt', met = None, up = None, dw = 1) %
prot(name = 'lacI', loc = 'cyt', met = None, up = 1, dw = None) +
met(name = 'ALLOLACTOSE', loc = 'cyt', prot = None) |
prot(name = 'lacI', loc = 'cyt', met = None, up = None, dw = 1) %
prot(name = 'lacI', loc = 'cyt', met = 2, up = 1, dw = None) %
met(name = 'ALLOLACTOSE', loc = 'cyt', prot = 2),
Parameter('fwd_ProtMet_RuleAssembly_7', 1),
Parameter('rvs_ProtMet_RuleAssembly_7', 1))
Rule('ProtMet_RuleAssembly_8',
prot(name = 'lacI', loc = 'cyt', met = 2, up = None, dw = 1) %
met(name = 'ALLOLACTOSE', loc = 'cyt', prot = 2) %
prot(name = 'lacI', loc = 'cyt', met = None, up = 1, dw = None) +
met(name = 'ALLOLACTOSE', loc = 'cyt', prot = None) |
prot(name = 'lacI', loc = 'cyt', met = 2, up = None, dw = 1) %
met(name = 'ALLOLACTOSE', loc = 'cyt', prot = 2) %
prot(name = 'lacI', loc = 'cyt', met = 3, up = 1, dw = None) %
met(name = 'ALLOLACTOSE', loc = 'cyt', prot = 3),
Parameter('fwd_ProtMet_RuleAssembly_8', 1),
Parameter('rvs_ProtMet_RuleAssembly_8', 1))
Rule('ProtMet_RuleAssembly_9',
prot(name = 'araG', loc = 'cyt', met = None, up = None, dw = 1) %
prot(name = 'araG', loc = 'cyt', met = None, up = 1, dw = None) +
met(name = 'ATP', loc = 'cyt', prot = None) |
prot(name = 'araG', loc = 'cyt', met = None, up = None, dw = 1) %
prot(name = 'araG', loc = 'cyt', met = 2, up = 1, dw = None) %
met(name = 'ATP', loc = 'cyt', prot = 2),
Parameter('fwd_ProtMet_RuleAssembly_9', 1),
Parameter('rvs_ProtMet_RuleAssembly_9', 1))
Rule('ProtMet_RuleAssembly_10',
prot(name = 'araC', loc = 'cyt', met = None, up = None, dw = 1) %
prot(name = 'araC', loc = 'cyt', met = None, up = 1, dw = None) +
met(name = 'alpha_L_arabinopyranose', loc = 'cyt', prot = None) |
prot(name = 'araC', loc = 'cyt', met = None, up = None, dw = 1) %
prot(name = 'araC', loc = 'cyt', met = 2, up = 1, dw = None) %
met(name = 'alpha_L_arabinopyranose', loc = 'cyt', prot = 2),
Parameter('fwd_ProtMet_RuleAssembly_10', 1),
Parameter('rvs_ProtMet_RuleAssembly_10', 1))
Rule('ProtMet_RuleAssembly_11',
prot(name = 'araC', loc = 'cyt', met = 2, up = None, dw = 1) %
met(name = 'alpha_L_arabinopyranose', loc = 'cyt', prot = 2) %
prot(name = 'araC', loc = 'cyt', met = None, up = 1, dw = None) +
met(name = 'alpha_L_arabinopyranose', loc = 'cyt', prot = None) |
prot(name = 'araC', loc = 'cyt', met = 2, up = None, dw = 1) %
met(name = 'alpha_L_arabinopyranose', loc = 'cyt', prot = 2) %
prot(name = 'araC', loc = 'cyt', met = 3, up = 1, dw = None) %
met(name = 'alpha_L_arabinopyranose', loc = 'cyt', prot = 3),
Parameter('fwd_ProtMet_RuleAssembly_11', 1),
Parameter('rvs_ProtMet_RuleAssembly_11', 1))
Note
Reversibility of Rules. Atlas writes reversible Rules for each
reaction declared in the network file. The Parameter('rvs_RuleName', 1))
must be set to zero to define an irreversible reaction.
Note
Uniqueness of Rule names. Atlas will write Rules with numbered names. Use only one file to model the many interactions the system has.
Note
Simulation. The model can be simulated only with the instantiation of
Monomers
and Initials
(More here).
Run Monomer+Initials+Observables from metabolic network.ipynb to obtain
automatically the necessary Monomers
and Initials
(including
proteins and enzymatic complexes). Manually add the necessary Monomers
and Initials
for non-enzymatic proteins.
Plotting. The model can be observed only with the instantation of
Observables
(More here).
Run Monomer+Initials+Observables from metabolic network.ipynb to obtain
automatically the all possible Observables
for enzymatic proteins. Other
observables for proteins should be added manually.