Biology Reference
In-Depth Information
Fig. 1. Classification of concepts about the
process of signaling
.
I name the catalytic reaction catalytic reaction in complex, where the catalyst is used only once without
being recycled any more. The Petri net unit accounting for catalytic reaction in complex includes no
backward arc from a transition to a
place
associated with the catalyst. The steric hindrance effect has not
been taken into account properly in any representation of signaling pathways so far. Petri net modeling
is in need of careful involvement of the steric hindrance effect so as to represent physical quantity of
reactants correctly.
Complex formation is divided into two groups: complex formation for allosteric effect and complex
formation for transportation. Although both the units have the same topological connections of the nodes,
focused reactants are opposite. It is a state of a component that is focused in complex formation for
allosteric effect. In contrast, it is a state of a complex as a whole that is focused in complex formation for
transportation, because the complex as a whole is recognized by a transporter in a succeeding reaction.
Catalytic reaction is also divided into two groups: catalytic reaction in solution and catalytic reaction
in transient complex. The two groups are divided according to involvement of
molecular recognition
in the reactions. Catalytic reaction in solution involves only molecular recognition at a catalytic site,
whereas catalytic reaction in transient complex involves its particular
molecular recognition
in addition
to
molecular recognition
at a catalytic site. However, both the reactions have no difference in their
productivity, so that both the reactions are associated with the same Petri net units.
Accordingly all the units consist with units of 'the transmission of
activity
through
molecular recog-
nition
'. Because the units are disjoint and cover all the signaling reactions, one can construct Petri net
models without ambiguity based on the units.
