Enzyme Kinetics Simulator
Equations in this simulation
| v | reaction rate | product made per second, in µM/s; the curve rises steeply at low [S] and levels off at Vmax | |
|---|---|---|---|
| [S] | substrate concentration (falls as it is used) | starts at Substrate concentration [S]₀ | |
| Km | Michaelis constant Km (mM) | the [S] at which the rate is half of Vmax; a low Km means the enzyme grabs its substrate even when there is little of it | |
| Vmax | maximum rate | reached when every enzyme is busy |
With the current values:
| kcat | Turnover number kcat (per second) | molecules of substrate one enzyme converts per second when saturated: about 100 for many enzymes, 10⁶ for catalase | |
|---|---|---|---|
| [E]₀ | Enzyme concentration [E]₀ (µM) | doubling the enzyme doubles Vmax but leaves Km alone |
With the current values:
| [I] | Inhibitor concentration [I] (mM) | ||
|---|---|---|---|
| Ki | Inhibition constant Ki (mM) | the inhibitor concentration that halves the free enzyme; the lower it is, the stronger the inhibitor | |
| Km′, Vmax′ | apparent constants with the inhibitor | a competitive inhibitor can be outcompeted by more substrate, so Vmax is unchanged; a noncompetitive one cannot |
With the current values:
| 1 ÷ v | Lineweaver–Burk plot | a straight line: it crosses the y axis at 1 ÷ Vmax and the x axis at −1 ÷ Km, so inhibitors show as lines that pivot (competitive), shift up (noncompetitive) or move in parallel (uncompetitive) |
|---|
With the current values:
| fitted Km, Vmax | from the assay series | initial rates at eight substrate concentrations, each with a few percent of measuring noise, fitted by least squares |
|---|
With the current values:
How to use the enzyme kinetics simulator
- Set the substrate concentration, Km, kcat and the enzyme concentration. In the box, green substrate molecules are caught by the blue enzymes, held in the active site and released as yellow product; the readout and the charts show the rate falling as the substrate is used up.
- Press Run an assay series to measure the initial rate at eight substrate concentrations, with a little measuring noise, and fit the Michaelis–Menten curve to them. The fitted Km and Vmax appear under the picture; switch the chart to Lineweaver–Burk to see the same data as a straight line.
- Add an inhibitor and run the series again. A competitive inhibitor raises Km and leaves Vmax alone, a noncompetitive one lowers Vmax and leaves Km alone, and an uncompetitive one lowers both; the gray curve is the enzyme without the inhibitor. For the half-maximal inhibitor concentration from a dose-response series, use the IC50 Calculator.
Frequently asked questions
What do Km and Vmax mean?
Vmax is the fastest the enzyme can go, when every enzyme molecule is busy: Vmax = kcat × [E]. Km, the Michaelis constant, is the substrate concentration that gives half of Vmax. A low Km means the enzyme works well even when there is little substrate. Vmax depends on how much enzyme you add; Km does not.
Why does the rate level off?
At low substrate most enzymes are idle, so doubling the substrate nearly doubles the rate. At high substrate almost every enzyme is already holding a substrate molecule, so adding more cannot speed things up: the enzyme is saturated and the rate approaches Vmax.
How do the three kinds of inhibitor differ?
A competitive inhibitor sits in the active site, so it competes with the substrate: flood the enzyme with substrate and the inhibitor is pushed out, so Vmax is unchanged but more substrate is needed, a higher apparent Km. A noncompetitive inhibitor binds elsewhere and disables the enzyme whatever the substrate does, lowering Vmax. An uncompetitive inhibitor binds only the enzyme-substrate complex and lowers both.
Why fit the curve instead of using Lineweaver–Burk?
Taking 1/v magnifies the noise in the slowest measurements, which then dominate the straight-line fit. A direct least-squares fit of the Michaelis–Menten curve weighs all points fairly and gives better Km and Vmax. The double-reciprocal plot is still the clearest way to tell the inhibitor types apart by eye.
It says WebGL is turned off.
The 3D view needs WebGL, which every current browser has. It can be switched off by hardware acceleration being disabled in the browser settings, or by a very old graphics driver. Turn hardware acceleration on, or try another browser.
Is anything uploaded?
No. The simulation is drawn by your own browser with WebGL; nothing is sent anywhere, and it keeps working offline once the page has loaded.