Domain mapping for protein-protein interaction drug discovery
Compare truncations and mutants against the full-length protein, and localize where a protein-protein interaction inhibitor would have to bind.
competitive assays
Protein-protein interaction analysis: the kinetics your structure cannot show
A structure tells you what the complex looks like. It does not tell you how fast the partners find each other, how long they stay together, or whether your engineered variant still binds at all.
Where structural biologists use label-free binding data
Label-free interaction analysis measures binding between unmodified molecules in real time. For structural biology, it returns affinity, association and dissociation rates, and specificity in solution.
Predicted complexes
Test an AlphaFold or docking prediction at the bench.
Measure KD to test the predicted interface.
KD validation
Engineered variants
Confirm a construct still binds the way its parent does.
Compare stabilized, truncated, and mutated variants side by side.
variant ranking
Triage before structure determination
Check that the complex forms before structural work.
Confirm binding and complex stability before committing beam or microscope time.
complex stability
Thermodynamics
Measure the same interaction across temperatures.
Add a temperature series to the binding measurement.
16 to 40 °C
Don't see your system?
Protein-protein, protein-peptide, or a carbohydrate-protein interaction: discuss your assay with one of our application specialists.
Talk to a specialist
Benefits of the inQuiQ in structural biology
01 / 04
One injection, four channels, sixteen sensors
Four independently addressable flow channels, each carrying four sensors, with the sample flowing through the channels in series.
30 µL minimumsequential flow paths
Watch the complex form and come apart
A sensorgram gives the full kinetics data. Affinity runs from 10 pM to 10 mM, with steady-state fitting where dissociation is too fast for kinetics.
0.1 RU RMSka, kd, KD
association, then dissociation
Measure in label-free conditions
The analytes stay unmodified in solution, so it measures native interactions without label or tag artefacts.
- No tag on either partner to shift affinity or sit across an interface
- Solution-phase binding, measured in real time
the same binding event
See which domain carries the binding
Compare full-length protein with truncations and point mutants to identify the construct that retains affinity and localize the interaction.
competitive assaysblocking assays
full length, or domain removed
How a binding run works
Every measurement follows the same steps, whatever the complex, and the same run serves protein-ligand interaction analysis. One partner is immobilized on the sensor, the other flows past, and the instrument records the response in real time. An endpoint assay gives you one number. The inQuiQ gives you the full curve.
Immobilization
One binding partner is attached to the sensor surface first.
Amine coupling or tag capture immobilizes the protein. The more stable or readily produced partner is usually immobiliszd, while the other is injected. Ligand density is optimized to avoid mass-transport limitation.
- amine coupling
- capture
- ligand density
Deactivation
Any activated site left unused is deactivated before the first sample arrives.
Without it the surface keeps reacting with sample passing 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 immobilized amount.
- deactivation
- blocking
- non-specific binding
Association
The second partner flows across the surface and the response climbs.
During association, the injected analyte binds to the immobilized target, and the rising response reflects how quickly the complex forms. The association phase determines the on-rate, ka.
- solvent matching
- referencing
- ka
Dissociation
Buffer replaces the sample and the response falls as the complex comes apart.
The dissociation phase gives the off-rate, kd; 1/kd gives complex lifetime. A concentration series gives ka, kd, and KD across 10 pM to 10 mM. For fast dissociation, plateau responses give steady-state affinity. Single-cycle kinetics runs the series uninterrupted when protein is scarce.
- complex lifetime
- kd
- KD
- steady state
- SCK
Regeneration
A regeneration buffer strips the bound partner and returns the sensor to baseline, ready for the next injection.
The immobilized partner stays in place, so every variant meets the same surface. Inject, read, regenerate, repeat, unattended. Each injection is read by every sensor, so one sample can cover multiple constructs, mutants, or controls.
- regeneration
- automated cycling
- saveable sequences
Response (RU)
Time
What the inQuiQ does for structural biology
Six capabilities, one modular benchtop instrument, in a label-free workflow.
Many constructs, one small sample
4-plex with in-flow immobilization and 16-plex with a spotter lets you compare truncations, point mutants, and controls from one sample.
16 sensors (spotter required)
30 µL
Resolve weak and transient contacts
Baseline noise stays low enough that a small binding response is still readable.
0.1 RU RMS
From transient contacts to stable complexes
One affinity range covers weak contacts through tight complexes, with steady-state fitting when kinetics are too fast.
10 pM to 10 mM
Localise the interaction
Competitive and blocking assays identify the construct or domain carrying the binding.
competitive
blocking
Add thermodynamic detail
The temperature-controlled flow cell runs a full temperature series.
temp. control from 16 to 40 °C
Modular system for an increased throughput
Simply add an autosampler, and run a long variant or condition series unattended.
2×96 wells
2×384 wells
Explore the inQuiQ768
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.
Start A conversation
Talk to an application scientist
Bring your system. We will tell you honestly whether label-free is the right method for it, and how the assay would be built.
Ready to see the inQuiQ in action?
Talk to an application scientist
Thirty minutes to discuss your assay design, before anyone mentions an instrument.
Download the inQuiQ brochure
Sensitivity, channel layout, footprint, and consumable formats in a couple of pages.
Delta Life Science
request@deltalifescience.nl
Send us an email, and we will get back to you as soon as possible.
request@deltalifescience.nl
Send us an email, and we will get back to you as soon as possible.
Questions researchers ask
Cryo-EM, X-ray crystallography, and NMR give structure. Solution-phase protein interaction methods answer a different question: label-free interaction analysis, ITC, mass photometry, analytical ultracentrifugation, and SEC-MALS give function and behaviour in solution. Label-free analysis with the inQuiQ adds binding affinity (KD) and kinetics (kon, koff), so you can show that a modelled interface produces measurable, specific binding under native conditions.
Express the predicted partners, measure their binding in solution, and compare the result with the prediction. A measured KD and a clean sensorgram support the model. Competitive assays against truncations or point mutants then test whether the predicted interface is the one that actually drives binding.
The inQuiQ runs from 30 µL of sample. Sensors are regenerable, so the same chip carries a series of variants, mutants, and controls rather than one measurement per surface. That matters for structural constructs that are slow to express or purify.
Yes, indirectly and reliably. Run the full-length protein on the inQuiQ and its truncations or domain constructs as separate binding experiments, then use competitive and blocking assays to see which construct carries the affinity. The comparison localizes the interaction without needing a new structure for every variant.
Binding affinity (KD) says how tightly two molecules bind at equilibrium. Kinetics says how they get there: kon for how fast the complex forms, koff for how fast it falls apart. Two complexes can share a KD and behave differently, which is why structural work benefits from both.