Free software for complex kinetics and equilibria

Petr Kuzmic pkuzmic at biokin.com
Wed Sep 17 07:43:21 EST 1997


Program  D Y N A F I T    U P D A T E
==========================================================

Public domain program DynaFit for the analysis and simula-
tion of enzyme kinetic and receptor binding data was upda-
ted to version 2.17.5 (09/16/97).  

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                       'RAPID-EQUILIBRIUM' ENZYME KINETICS 

The notation for  enzyme  mechanisms  analyzed  under  the
'rapid-equilibrium approximation' was simplified.   We  no
longer have to specify both dissociation  and  association
rate constants for each reaction step.  Instead, the newly
introduced keywords ASSOC and DISSOC allow the  definition
of association and dissociation equilibrium constants.  An
example problem is based on the initial velocities for ami-
nopeptidase B (from the laboratory of Prof. D.H. Rich).The
most plausible inhibition mechanism  (partial, noncompeti-
tive, double-site) is notated as follows:

 [mechanism]    
                                        
     E + S <==> ES   :  Ks       dissoc.
     ES ---> E + P   :  kcat          
     E + I <==> EI   :  Ki       dissoc.
     ES + I <==> ESI :  Kis      dissoc.
     ESI ---> EI + P :  kcat'      
     EI + I <==> EI2 :  Ki2      dissoc.

It is important that the inhibitor can be 'tight-binding'.
See directory ./TEST/AMIPEP-B in the test problem archive.

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                                  INTERESTING APPLICATIONS

The usefulness of the program DynaFit for enzyme and recep-
tor studies is obvious, but the following applications are
interesting in that they come from neighboring disciplines.

** CYTOFLUORIMETRY: DYNAMICS OF FLUORESCENT PHOTOBLEACHING

A zoologist working at an Italian university wrote:

"I wish to express to you my gratitude for making available
your program Dynafit. I think it works really great! I  am 
using it to study the bleaching kinetics of fluorophores 
in cytofluorimetry, which appears to involve several concom-
itant and successive  reversible  and  irreveversible  reac-
tions.  Indeed, solving analytically the underlying system 
of differential equations would be extremely complicated."  

** INDUSTRIAL REACTOR KINETICS: IMMOBILIZED ENZYMES




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