DynaFit Scripting Manual

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Mechanism

The reaction mechanism for the given biochemical system is specified in the [mechanism] section of the script file. Some examples of valid reaction mechanisms translated into DynaFit notation follow.

Example 1a: Competitive inhibition of an enzyme

[mechanism]
   E + S <===> ES    :  k   ks
   ES ---> E + P     :  kr
   E + I <===> EI    :  k   ki

Example 1b: The same mechanisms under rapid-equilibrium approximation

[mechanism]
   E + S <===> ES    :  Ks  dissoc
   ES ---> E + P     :  kr
   E + I <===> EI    :  Ki  dissoc

Example 2: Two-site binding of a protein trimer to DNA

[mechanism]
   P + P + P <=> T          :   k  k1
   T + DNA <==> T.DNA       :   k  k2
   T + T + DNA <==> T2.DNA  :   k  k3

Example 3: An oscillatory metabolic cascade

[mechanism]
         S1 + E <===> S1.E        :    k      ks1
           S1.E  ---> E + S2      :    kr1
         S2 + E <===> S2.E        :    k      ks2
                 ---> S1          :    v1
              S2 --->             :    v2

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Petr Kuzmic | Jul 12 2005