The enzyme is drawn as two residue lobes with a cleft (the active site) between them. Free substrate spheres (green) diffuse by Brownian motion; when one wanders into the capture radius of the open site, it can bind to form the ES complex. Binding triggers induced fit: the lobes flex inward around the substrate, which is the mechanism this sim visualizes (as opposed to the older, rigid "lock-and-key" idea — set flexibility to 0% to see the rigid-pocket limit instead).
E + S ⇌(k1,k-1) ES --kcat--> E + P
v = kcat·[E]T·[S] / (Km + [S]) Km = (k-1 + kcat) / k1
- [S] slider — sets how many substrate spheres are active in the diffusion box, i.e. substrate concentration.
- Flexibility slider — a more flexible (higher induced-fit) active site widens the capture radius and closes deeper around the substrate, raising the effective k1 and kcat: tighter transition-state stabilization means faster, more efficient catalysis (lower apparent Km, higher kcat/Km).
- Temperature slider — raises molecular motion and the catalytic rate up to the enzyme's optimum (~37 °C here), then the rate collapses as the protein denatures — shown live as the rate factor f(T) and as the lobes losing their ability to close above ~55 °C.
- Inhibitor slider — spawns red inhibitor spheres that compete for the same active site without being converted to product (competitive inhibition): v = Vmax[S] / (Km(1+[I]/Ki) + [S]).
Each catalytic cycle is drawn out in full — binding, lobe closure, a catalysis delay, product release (purple) and lobe reopening — then the released particle re-enters the free-substrate pool so [S] stays constant, the standard simplification used to hold substrate concentration fixed in a Michaelis-Menten demonstration.