Software update: biochemical kinetics & equilibria
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).
'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:
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.
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
>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-
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
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
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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