Biology Reference
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Table 9.4 Examples of equilibrial and dissipative nodes and edges in bionetworks
Equilibrial
Dissipative
Nodes
Proteins, RNAs, DNAs
(a) ATP hydrolysis, NADH oxidation
(b) Activated G protein
(c) Supercoiled circular DNA
Edges
Protein-protein, protein-RNA,
protein-DNA interactions, etc.
(see Table 9.5 )
(a) Proton-motive force (the
chemiosmotic theory), conformational
energy (the conformon theory)
(b) Binding to adenylate cyclase
(c) Activation of select gene expressions
Table 9.5 The nine classes of interactomes in living cells predicted on the
basis of the three classes of nodes
Protein (p)
RNA (r)
DNA (d)
Protein (p)
p-p
p-r
p-d
RNA (r)
r-p
r-r
r-d
DNA (d)
d-p
d-r
d-d
sizes. The size (or geometry in general) of a network is related to kinematics and the
energy dissipatiZon by networks is related to dynamics , thus providing yet another
example illustrating the operation of the principle of the kinematics-dynamics
complementarity in biology. Thus, we can divide bionetworks into equilibrons
and dissipatons , depending on whether or not free energy dissipation is needed
to maintain their existence. In other words, we can recognize two classes of
bionetworks - “equilibrium bionetworks” and “dissipative bionetworks”. The
nodes and edges of equilibrium bionetworks do not dissipate free energy but those
of dissipative bionetworks do (or are dissipation-dependent) (Table 9.4 ). That is,
the nodes and edges of equilibrium bionetworks remain intact while the nodes and
edges of dissipative bionetworks disappear when free energy supply is interrupted.
Another way of characterizing bionetworks or interactomes is in terms of the
three fundamental building blocks of living cells, namely, proteins (p), RNA (r),
and DNA (d), leading to a 3
3 table shown in Table 9.5 . In the absence of clear
evidence suggesting otherwise, it is here assumed that the interactions appearing
in Table 9.5 are “directional” in the sense that, for example, the interaction, p-r,
is not the same as the interaction r-p. In other words, Table 9.5 is asymmetric
with respect to the diagonal.
Applying Prigogine's classification scheme of structures into equilibrium and
dissipative structures (Sect. 3.1 ) to Table 9.5 , we can generate a system of 18
classes of interactions as shown in Table 9.6 . The examples shown in Table 9.6 for
each of these 18 classes of interactions reflect my limited knowledge and may need
to be replaced with better ones in the future but the structure of the table itself may
remain valid, reminiscent of the periodic table in chemistry. Hence, we may refer to
Table 9.6 as the periodic table of interactomes . A similar table was suggested for
molecular machines in Sect. 11.4.4 . It is interesting to note that both these tables
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