PROTAC ternary complexes
A PROTAC's activity depends on a three-body equilibrium, not a simple one-to-one interaction.
Follow ternary complex formation, stability, and dissociation as a single continuous trace.
ternary kinetics
Measure PROTAC and molecular glue binding affinity and kinetics, label-free
Cooperativity, binding order, and complex stability decide whether a degrader works in cells. Conventional one-to-one binding assays were not built to show any of them. inQuiQ measures binary and ternary binding as it happens, label-free, on your own bench.
Label-free binding data across degrader chemistries
Every degrader program raises its own binding question. The inQuiQ answers them from one platform.
Molecular glues
A single endpoint reading can't separate glue candidates with similar apparent potency.
Rank candidates on complex stability and off-rate instead of one timepoint.
koff, half-life
E3 ligase engagement
Whether a recruiter binds VHL, CRBN, or another ligase is easy to assume and harder to confirm.
Quantify engagement to the ligase directly, as a real KD.
KD
Binary versus ternary affinity
Two arms of the same molecule, characterised separately, don't reveal cooperativity.
Measure both arms under the same conditions and derive cooperativity directly.
cooperativity (α)
Early degrader material
Early-stage compounds are often scarce and impure, which rules out a lot of conventional assays.
Screen crude, unpurified material before committing to degradation assays.
30 µL minimum
Don't see your degrader chemistry?
Discuss your assay with one of our application specialists.
Talk to a specialist
Benefits of the inQuiQ in molecular glue and PROTAC research
01 / 04
One injection reads sixteen sensors.
Target, E3 ligase, and multiple ternary complex conditions measured together, so a degrader series moves as a batch instead of a queue.
*spotter necessary for 16-sensor immobilisation
30 µL minimumrun in series
four channels, sixteen sensors
Same apparent affinity, different complex half-life.
The binary arm and the ternary complex are followed in the same run. Association and dissociation are resolved separately, so two degraders that plateau at the same response are still separated on off-rate and ternary complex half-life.
10 pM to 10 mMkon, koff, KD
slow off-rate
fast off-rate
same plateau, different off-rate
Measure in native, label-free conditions.
The degrader, the target, and the E3 ligase all meet unmodified, so nothing added to any of the three shifts the equilibrium being measured.
- No tag on the target, the degrader, or the ligase
- Ternary complex formation measured exactly as it happens in solution
tagged assay vs. label-free
See whether the third partner helps or hinders.
Inject the degrader alone, then pre-formed with its partner, and compare the response. A more stable ternary complex signals positive cooperativity; a weaker one signals negative cooperativity or steric clash, in the same real-time trace.
binary + ternary titrationcooperativity (α)
destabilized, or stabilized
How a targeted protein degradation run works
Every measurement follows the same steps, whether the analyte is a single arm or a fully formed complex. The target or the E3 ligase is immobilised on the sensor, the sample flows past, and the instrument records the response in real time. Two channels carry the same surface, so the binary arm and the pre-formed pair can be read side by side. An endpoint assay tells you a complex existed. The inQuiQ tells you how long it lasted.
Channel 1 degrader alone
Channel 2 pre-formed pair
Immobilisation
The target protein is attached to the sensor surface of both channels.
Amine coupling or capture through a tag holds the protein in place. Either partner can be immobilised: the target, to measure degrader engagement, or the E3 ligase, to measure recruiter engagement directly. Both channels carry the same surface, so anything that differs later is the sample and not the chemistry. Ligand density is set high enough that a weak binary arm still gives a readable response.
- amine coupling
- capture
- ligand density
Deactivation
Any activated site left unused is capped before the first compound arrives.
Without it the surface keeps reacting with whatever passes over, and non-specific binding shows up in the trace as signal that has nothing to do with the pair being measured. The response settles at a stable level, the immobilised amount.
- deactivation
- blocking
- non-specific binding
Channel 1: binary association
The degrader flows across the first channel on its own, and the response climbs as it engages the immobilised target.
The binary arm is injected alone to measure engagement with the immobilised partner. A reference channel subtracts what the surface contributes on its own. Flow between 1 and 100 µL/min sets contact time, up to 300 µL/min for low-viscosity samples. The rising phase gives an on-rate, kon.
- binary injection
- reference channel
- kon
Channel 2: ternary association
The pre-formed pair runs on the second channel over the same time window, and the response climbs much further.
The pre-formed pair is injected below saturation to avoid the hook effect. Because the recruited partner carries far more mass than the degrader alone, the ternary response sits well above the binary trace. Running both channels against the same surface at the same time makes the two traces directly comparable.
- ternary injection
- hook effect
- mass response
Dissociation
Buffer replaces the sample on both channels and the responses fall, but not at the same rate.
The falling phase gives the off-rate, koff, and 1/koff gives the ternary complex's dissociative half-life. Comparing the two channels gives cooperativity directly: α = KD,binary / KD,ternary. Fit a concentration series and you get kon, koff, and KD across 10 pM to 10 mM. Single-cycle kinetics runs the series uninterrupted when early material is scarce.
- koff
- half-life
- cooperativity (α)
- KD
- SCK
Regeneration
A regeneration buffer strips both channels and returns them to baseline, ready for the next injection.
The immobilised target stays in place, so every degrader in the series meets the same surface. Inject, read, regenerate, repeat, unattended. Candidates run one after another, and each injection is read by every sensor on the chip, so one sample can cover several targets, E3 ligases, or counter-screen controls at once.
- regeneration
- automated cycling
- saveable sequences
Response (RU)
Time
Channel 2
Channel 1
What the inQuiQ does for targeted protein degradation research
Six capabilities, one modular benchtop instrument, no labels anywhere in the workflow.
Many targets and ligases, one small sample
Four flexibly addressable channels for improved assay freedom, with 16 sensors to screen E3 ligases, targets, and controls efficiently.
16 sensors (spotter required)
30 µL
Resolve weak binary arms
Baseline noise stays low enough that a binary arm's small mass change is still readable.
0.1 RU RMS
Cover weak binary arms through to stable ternary complexes
One affinity range spans early degrader hits and optimised leads, with steady-state fitting where kinetics run out.
10 pM to 10 mM
Confirm cooperativity alongside affinity
Competitive assays show whether a ternary complex is more stable than its binary arms, and cooperativity is derived directly.
cooperativity (α)
KD
Add thermodynamic detail
The temperature-controlled flow cell runs a full temperature series on the same complex.
temp. control from 16 to 40 °C
Modular system for increased throughput
Add an autosampler and scale up your throughput for larger degrader or glue libraries.
2×96 wells
2×384 wells
Application notes, publications, and data
From small molecule kinetics to antibody affinity, explore real binding data generated on inQuiQ. Each application note pairs a sensorgram with the affinity and kinetic values behind it.
Small Molecule Kinetics on inQuiQ
This white paper showcases the high sensitivity of ring resonator technology for measuring low-molecular-weight interactions, using Carbonic Anhydrase II (CAII) and two small-molecule binders as a model system.
APPLICATION NOTE
Antibody interaction analysis
Kinetic characterisation of antibodoes and whatnot
APPLICATION NOTE
Small molecule interactions
Ka and Kd for very tiny small biomolecules.
APPLICATION NOTE
Small molecule interactions
Ka and Kd for very tiny small biomolecules.
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See the inQuiQ on your degrader chemistry
Send us your details and talk with an application scientist about your ternary complex assays.
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Download the inQuiQ brochure
Sensitivity, channel layout, footprint, and consumable formats in a couple of pages.
Delta Life Science
info@deltalifescience.nl
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info@deltalifescience.nl
Send us an email, and we will get back to you as soon as possible.
Questions researchers ask
Capture the E3 ligase or the target on the sensor, inject the PROTAC pre-incubated with its binding partner, then follow the dissociation phase. The off-rate (koff) gives the dissociative half-life of the ternary complex. The inQuiQ records this in real time, so stability is measured rather than inferred from an endpoint.
Cooperativity (α) compares binary and ternary affinity: α = KD,binary / KD,ternary. Above 1, the third partner stabilizes the complex and the degrader binds more tightly in the ternary state. Below 1, it interferes. The inQuiQ measures both arms under the same conditions, so α comes from one dataset.
At high degrader concentrations, binary complexes with the target and with the ligase outcompete the ternary complex, so signal falls as concentration rises. Avoid it by titrating the degrader across a wide range and keeping the ternary injection below saturation. A 10 pM to 10 mM range covers both sides of the curve.
Yes. Samples run directly after a 0.22 µm filter, with no buffer constraints across DMSO levels, additives, and lysate backgrounds. The antifouling hydrogel surface keeps non-specific binding low in complex material, which matters for early candidates that are not available as purified protein.
The minimum is 30 µL per sample, and up to 2 mL can be injected when a low-concentration analyte needs longer contact time. Early degrader campaigns usually have limited protein, so a small injection volume with a reusable chip keeps a full concentration series within reach.