Binding Kinetics Simulator

Binding Kinetics Simulator

Choose an example or build your own 1:1 kinetic binding experiment.

Examples

Sensorgram

Hover over the plot to read values

Results Summary

About this simulation

This tool simulates a surface-based kinetic binding experiment, such as Surface Plasmon Resonance or Biolayer Interferometry. Each analyte binds one independent, identical ligand site (1:1, Langmuir).

How it works

Curves are calculated exactly from the 1:1 rate equation for every concentration in the series, through baseline, association and dissociation. Each analyte has its own ka, kd and top concentration; all share the surface, timing, dilution factor and number of concentrations.

What it assumes

  • Identical, independent ligand sites.
  • Constant analyte concentration (pseudo-first-order).
  • No mass transport limitation.
  • Ideal injections and a flat, drift-free baseline.
  • Full regeneration between concentrations.

Key terms

  • ka (M⁻¹s⁻¹) — Association rate constant: how fast analyte binds free ligand at a given concentration.
  • kd (s⁻¹) — Dissociation rate constant: the fraction of complex that falls apart per second.
  • Association phase — Analyte is present at a constant concentration and complex builds up.
  • Dissociation phase — Analyte is replaced by buffer and bound complex decays.
  • Baseline — Buffer only, before analyte is added. Response stays at zero.
  • Analyte (A) — The binding partner in solution, flowed over the sensor (SPR) or into which the sensor is dipped (BLI).
  • Dilution series — The set of analyte concentrations, made by serial dilution of each analyte's top concentration by the shared fold factor.
  • Rmax (RU) — Response when every ligand site is occupied. Depends on how much ligand is immobilized.
  • KD (M) — Equilibrium dissociation constant, kd/ka. The analyte concentration that occupies half the sites at equilibrium. Lower means tighter binding.
  • teq (95%) — Time for association to reach 95% of Req: ln 20 / kobs ≈ 3/kobs. It is shortest at high concentration; the heading shows the value for the lowest concentration in the series, the slowest curve, and the table gives it for each concentration. As [A] → 0 it approaches ln 20 / kd.
  • Dissociation t½ — Time for half the complex to dissociate, ln 2 / kd.
  • Residence time — Average lifetime of a complex, 1/kd.
  • R (RU) — Response. Proportional to the mass of analyte bound: R = Rmax·f. SPR reports resonance units; BLI reports a wavelength shift in nm, which plays the same role.
  • kobs (s⁻¹) — Observed rate of the association curve, ka[A] + kd. It rises linearly with concentration.
  • feq — Req/Rmax: fraction bound at equilibrium. feq = [A] / ([A] + KD).
  • fend — Rend/Rmax: fraction bound at the end of the association phase. fend = feq·(1 − e−kobs·ta), where ta is the association time.
  • fend/feq (%) — How close each curve got to equilibrium. Values under 95%, shown in red, mean steady state was not reached.
  • Rt, ft, ft/feq — Shown when you hover over the plot: the response Rt and fraction bound ft = Rt/Rmax at time t, and ft/feq, how far each curve has progressed toward its equilibrium response at that moment.
  • Req — The response a curve would reach at equilibrium for a given concentration.
  • Steady state — The association phase has run long enough to reach equilibrium. Here, a curve counts as reached at 95% of Req.
  • Ligand (L) — The binding partner immobilized on the sensor surface.
  • f — Fraction of ligand sites occupied by analyte, from 0 to 1. f = [AL] / [L]T.
  • Pseudo-first-order — Analyte is in large excess, so binding does not deplete its concentration. The simulator assumes this.
  • Mass transport limitation — When analyte binds faster than diffusion can deliver it to the surface, slowing the apparent rates. Not modeled here.