---burst.nlogo

NETLOGO

HOW IT WORKS
------------
Uses some of the basic ideas of the enzyme kinetics module in the library. More details are commented in the procedures page.


HOW TO USE IT
-------------
By default the model starts with p-nitrophenyl acetate (pNPA) as the substrate and the number of enzyme molecules to be added set to fifty. These can be changed by using the chooser button and the slider. I suggest that you leave at the default setting to start with. The output box, to the right of the screen lists some basic information about the chosen substrate, which will be changed, if you alter the substrate, after you press the Setup button. 

Press the setup button. This will add 500 substrate molecules to the model. They'll appear as cyan coloured double blobs. You can hide them using the hide-substrate? switch, but this will not come into effect until you press the Go button.

Press Go. Nothing much will happen as there is no enzyme present. If you look carefully at the graph window you'll see the line moving along the bottom of the graph. Press the Add enzyme button. This immediately adds the requested number of enzyme molecules to the reaction mixture. Look at the graph. The red line, which represents the amount of enzyme mixture, rises immediately at the point of addition and then stays unchanged. The green line, the amount of product 1, almost immediately rises to the same level as the enzyme graph (the initial burst) and then continues rising more slowly ( the rate of deacylation. The size of the burst will be printed at the bottom of the output window. Compare this to the amount of enzyme used.

If you look at the graphics window you'll be able to see the enzyme's (red squares), product 1 molecules (small yellow circles) and product 2 molecules (small blue squares). You can slow the reaction down using the slider at the top left of the graphics window, and hide the substrate, if it's too obtrusive, using the hide button.

Change to the other substrate (a generic peptide), press Setup and repeat the above excersize. Compare the results with the different substrates.

THINGS TO NOTICE
----------------



THINGS TO TRY
-------------
Try varying the amount of enzyme added and look at the size of the burst.

Try using only one enzyme molecule so that you can concentrate on it. Run the graphic fairly slowly, using the slider, and hide the substrates. You'll be able to see the speed of binding to and release from, the enzyme of the substrate and the two products. Substrate bound to the enzyme is visible even when the hide-substrate button is on. Compare these binding/release activities using the different substrates. 

EXTENDING THE MODEL
-------------------
It would be easy to add more substrate variations with differing Ka/Kd values or perhaps introduce slider to let the user vary Ka/Kd values themselves.

You could set up a calculation of the rate of product 1 generation and compare these with Ka/Kd values.

NETLOGO FEATURES
----------------


RELATED MODELS
--------------
Enzyme Kinetics in the modules library


CREDITS AND REFERENCES
----------------------
Copyright: Dr. P. L. Birch - University of Paisley

Permission is granted to copy, distribute and adapt this model for any non-comercial use as long as this copyright notice is maintained.

A Web version is available at:

http://www-biol.paisley.ac.uk/courses/mechenz/serprot/burst.html
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NetLogo 2.1.0
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