Biology Reference
In-Depth Information
Table 1
Petri net units for signaling pathways
Type of signaling
reaction
Productive reaction
Regulatory reaction
Subtype of signaling
reaction
(Any)
Catalytic reaction
in complex
Petri net unit
Type of signaling
reaction
Regulatory reaction
Regulatory reaction
Subtype of signaling
reaction
Complex formation
for allosteric effect
Complex formation
for transportation
Petri net unit
Petri nets are Condition Event nets and tokens are positioned to be ready for firing the
places
. See Denotation of molecules in
signaling pathways for legends of labels of
places
. See Fig. 1(A) for types and subtypes of signaling reactions. Cofactors are
omitted from the representation because cofactors are considered to be represented with no ambiguity in existing models [3-5].
Table 1 illustrates each unit with a reaction holding two input
places
and one output
place
. There can be more than two input
places
as well as more than one output
place
, according to the number of focused species carrying activity and molecular
recognition.
Productive reaction: Reactant Y changes a state of reactant X to a certain state X(*) reiteratively, inducing activation or
inactivation of the reactant X (*: one of the external states indicated in Fig. 1B).
Complex formation for allosteric effect: Complex formation between X and Y changes a state of a focused component X to
a bound state X(B), inducing activation or inactivation of the component X, with the consequence that a complex [
X
:
Y
]is
formed.
Complex formation of transportation: Complex formation between X and Y produces a complex [
X
:
Y
], which is recognized
as a whole in a succeeding transportation reaction.
Catalytic reaction in complex: Reactant X and reactant Y forms a complex in advance (X[
X
:
Y
], Y[
X
,
Y
]) and reactant Y
changes a state of reactant X to a certain state X(*) only once, inducing activation or inactivation of the reactant X (*: one of
the external states indicated in Fig. 1B).
A: Is-a conceptual hierarchy of signaling reactions, which are used in labels of
transitions
. A symbol
'
+
' indicates an is-a relation between an upper concept and a lower concept.
B: A list of external states of reactants and symbols standing for the external states, which are used in
labels of
places
.
Productive reaction includes catalytic reaction in solution, catalytic reaction in transient complex,
transportation, and gene expression, while regulatory reaction includes complex formation and catalytic
reaction in complex. A catalytic reaction that occurs in a complex does not belong to productive reaction
but to regulatory reaction, because the catalytic reaction occurs only once owing to the steric hindrance.
