BioQUEST Metabolic Pathways/Enzyme Kinetics Simulation
The following pictures show some of the capabilities of the module "Metabolic Pathways". This is part of the BioQUEST Collection and can be ordered through the ePress Project at the University of Maryland (asdg@umdd.umd.edu).
This software was developed by Brian White.
Metabolic Pathways is a set of building blocks that run on the numerical simulation program Extend. They allow the user to construct model of uncatalyzed and catalyzed reactions and to model the flows of reactants and products over time.
The following is an example of the simplest possible model: the uncatalyzed equilibrium of compounds A and B. This pathway was created by pasting in the two rectangles representing the quantities of compounds A and B as well as the reaction A <--> B. The reactants and reaction are then connected by lines to indicate reaction flow and the kinetic and thermodynamic properties of the reaction can be set by the user.
Keq = the equilibrium constant for the reaction A <--> B
Kf = the rate constant for the forward reaction (A --> B).
The user can then set the initial concentrations of A and B.
If [A] initial = 1000 and [B] initial = 0, the following result
is obtained:
At equilibrium, B/A = 10.
The user can then demonstrate that the equilibrium is the same no matter what the initial concentrations. For example, if [A] initial = 0 and [B] initial = 1000, the following result is obtained:
The user can model more complex pathways. In the figure below, there are two sequential reactions:
(1) A <---> B Keq = 0.1
(2) B <---> C Keq = 10
In this case, the second reaction "pulls" the first reaction forward, leading to net synthesis of B.
The user can then change the Keq's to show that the process also works if the first reaction "pushes" the second.
(1) A <---> B Keq = 10
(2) B <---> C Keq = 0.1
This gives the following result:
Note that the results are the same in that [A] = [C] at equilibrium although in the second reaction, there is less of A and C because of the large build-up of B required in the second case.
These reactions are uncatalyzed, but other building-blocks allow construction of pathways with enzyme-catalyzed reactions as well as steady-state and pulsed concentration scenarios.
The user can also set up models where the enzymes' activities are regulated by compounds in the pathway. This is accomplished by connecting to the "terminal" on the enzyme building block labeled "-". A complex example is shown below:
