Object Type:
enz
Description:
Enzyme activity for a pre-existing pool. An enz does two
things: it handles the reactions in the Michaelis-Menten (MM)
scheme below, and it also acts as a pool to represent the
enzyme-substrate complex. It can only be
created on a pool, it is not an independent object.
The MM scheme is modeled as:
k1
k3
Substrate + Enzyme <-----> EnzComplex ----> Enz + Prd
k2
The enz is really a utility object, as it replaces
two reacs and a pool, but does not add anything extra.
Author:
U. S. Bhalla, National Centre for Biological Sciences,
Bangalore, India. (1993).
----------------------------------------------------------------------------ELEMENT PARAMETERS
DataStructure:
Size:
enz_type
[in src/kinetics/kin_struct.h]
bytes
Fields:
CoComplex
CoComplexInit
nComplex
nComplexInit
vol
sA
pA
eA
B
k1,k2,k3
Concentration of enz-substrate complex.
CoComplex = nComplex/vol
Initial concentration of enz-substrate
complex.
CoComplex gets set to this value on
RESET.
Number of molecules of complex.
Initial number of molecules of complex.
'nComplex'gets set to this value on
RESET.
Volume occupied by enzyme. Often
involves scale factor so as to have
direct conversion from 'n' to some
sensible units of Co, such as
micromolar.
A state variable to pass to substrate
in messages.
A state variable to pass to products
in messages.
A state variable to pass to parent
enzyme pool in messages.
B state variable to pass to substrate
and parent enzyme pool in messages
Michaelis-Menten parameters.
keepconc
usecomplex
Flag determining whether to change
concs or n when volume changes
Flag. Determines whether the enzyme
complex is used when the parent enzyme
is involved in other reactions.
Consider:
E + A <----> E.A
where E is a pool reacting with A.
Suppose E has an enzyme site. Then,
whenever some of the enzyme is complexed
with a substrate, the conc of E
decreases unless 'usecomplex' is true.
Internal variable. ksum = k2 + k3.
ksum
----------------------------------------------------------------------------SIMULATION PARAMETERS
Function:
EnzFunc
Classes:
segment
Actions:
PROCESS
RESET
SET
Messages:
ENZYME
[in src/kinetics/enz.c]
SUBSTRATE
n
[n is number of molecules of enzyme
pool to which this site is attached]
n
[Number of molecules of
substrate]
VOL
INTRAMOL
vol
[volume of enzyme pool]
n
[Total number of molecules in an
intramolecular reaction]
----------------------------------------------------------------------------Notes: See pool documentation for example of use.
-----------------------------------------------------------------------------