Conventional end-point measurements can be misleading because the fluorescence intensity is influenced by both the peptide’s binding characteristics, as well as its synthesis yield.
As a result, peptides with different KD values can produce similar signals under saturated conditions, while peptides with similar affinities may yield different signals.
This makes it impossible to accurately rank or compare binding strengths without proper affinity measurements.
THE SOLUTION
Measure repeatedly, model correctly.
To overcome the limitations of end-point measurements, we perform a concentration series of the analyte and record binding signals across multiple concentrations.
By fitting the resulting curves to a 1:1 Langmuir binding model, we accurately extract dissociation constants KD for each peptide–protein interaction.
This allows for precise affinity ranking, even across peptides with varying synthesis yields or binding kinetics.