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Software update: biochemical kinetics & equilibria

Petr Kuzmic pkuzmic at biokin.com
Wed Sep 17 17:36:42 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).  


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:

     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.

                                  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.


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."  


>From a graduate student at an Engineering Department:

"The title of my project is 'Hydrolysis of Penicillin G to
6-aminopenicillanic acid  in  Batch  Stirred-Tank  Reactor 
(BSTR) and Recirculated Packed Bed Batch Reactor  (RPBR)'. 
The scope involves:  (1) Comparison  of  effectiveness  of  
immobilised  penicillin amidase (IPA) in RPBR to BSTR. (2) 
Kinetic modelling using 3 kinetic models with different ki-
netic mechanisms."

The results from this study, involving a complex mechanism
of product inhibition, are a subject of a manuscript to be 
submitted to a biotechnological  or  chemical  engineering 
journal jointly with BioKin Ltd.

                      'EUROPEAN MIRROR SITE' AT OXFORD, UK

David Fell of Oxford Brookes  University  (UK)  graciously 
offered to host a mirror copy of DynaFit  distribution  in
the 'BMSDARWIN' archives. The mirror files are  likely  to 
remain a version or two behind, so use FTP to Oxford  only 
if you experience problems in downloading from the  BioKin 

                                                 NEW USERS

Recent additions to the list  of  registered  institutions
(total 414 registered users, up from 305 on August 29):

	* Cambridge University
	* Baylor College of Medicine
	* Harvard Medical School
	* NOVO Nordisk A/S
	* Abbott Labratories
	* Hoechst Marion Roussel
	* National Institutes of Health

                                            DOWNLOAD LINKS

http://www.biokin.com/dynafit/index.shtml  ...Madison site
ftp://bmsdarwin.brookes.ac.uk/pub/software/ ...Oxford site

Petr Kuzmic Ph.D. * BioKin Ltd. * Madison, WI 53708-8336, USA
pkuzmic at biokin.com * http://www.biokin.com * 608.256.1269 fax

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