The complete set of thermodynamically
consistent sub-cyclic routes
that produce a net positive reaction flux in the dihydrofolate reductase
(DHFR) network is identified by a novel approach based on the theory
of graphs. The net positive flux cycles that yield the minimal set
of linearly independent rate equations (“mechanisms”)
are then selected. The steady-state flux (reaction rate) through these
constituent sub-cycles is quantified, and the sub-cycle that generates
the maximum flux is identified as the most probable mechanism of the
pathway. This analysis is performed for both wild-type and mutant Escherichia coli DHFR systems. The graph-theoretical
method of visualization of networks developed here should prove to
be a useful tool for elucidating the kinetic mechanism complex cyclic
reaction networks.