Dynamic affinity capillary electrophoresis (ACE) was used for determining the binding constants between heparin-like glycosaminoglycans and the (96-110) heparin-binding domain of amyloid precursor protein (APP). The migration time shift of the (96-110) APP peptide was monitored as the concentration of heparin was increased in the background electrolyte. The compounds investigated included low-molecular-weight heparin, porcine mucosa heparin, and heparan sulfate. Change in mobility as a function of glycosaminoglycan concentration was plotted using both linear regression (Scatchard analysis) and nonlinear regression. Dissociation constants (K-d) were determined and compared for both sets of analyses with the low-molecular-weight heparin giving the most reproducible results and best fit with a K-d value of 3.9 mum.