created with NetLogo
view/download model file: Enzyme_modified.nlogo
This model demonstrates the kinetics of single-substrate enzyme-catalysis. The interactions between enzymes and substrates are often difficult to understand and the model allows users to visualize the complex reaction.
The standard equation for this reaction is shown below.
E + S <=======> E-S ------> E + P
Here E represents Enzyme, S Substrate, E-S Enzyme-Substrate complex, and P product. The rate constants are K1 for complex formation, K2 for complex dissociation, Kcat for catalysis. The first step in catalysis is the formation of the E-S complex. This can consist of either covalent or non-covalent bonding. The rates of complex formation and dissociation are very fast because they are determined by collision and separation of the molecules. The next step is for the enzyme to catalyze the conversion of substrate to product. This rate is much slower because the energy required for catalysis is much higher than that required for collision or separation.
Choose the values of K1, K2, and Kcat with appropriate sliders:
- K1 controls the rate at which substrates (green) and enzymes (red) stick together so that catalysis can occur
- K2 controls the rate at which they come unstuck
- Kcat controls the rate of the forward reaction by which an enzyme (red) converts a substrate (green) to a product (blue)
Having chosen appropriate values of the constants, press SETUP to clear the world and create a constant initial number of enzyme (red) molecules. Play with several different values to observe variable effects on complex formation and catalysis.
Press GO to start the simulation. A constant amount of enzyme (red) will be generated. The concentrations of substrate, complex, and product are plotted in the CONCENTRATIONS window.
Note that when complexes form they stop moving. This isn't intended to be physically realistic; it just makes the formation of complexes easier to see. (This shouldn't affect the overall behavior of the model.)
It is a little difficult to ensure that a reactant never participates in two reactions simultaneously. In the future, a primitive called GRAB may be added to NetLogo; then the code in the FORM-COMPLEX procedure wouldn't need to be quite so tricky.
modified version - go to Enzyme in the models library to see the original version
Thanks to Mike Stieff for his work on this model.
To refer to this model in academic publications, please use: Wilensky, U. (2001). NetLogo Enzyme Kinetics model. http://ccl.northwestern.edu/netlogo/models/EnzymeKinetics. Center for Connected Learning and Computer-Based Modeling, Northwestern University, Evanston, IL.