Identification and sequence composition characterization of chondroitin sulfate-binding peptides through peptide array screening

Chondroitin sulfate (CS) is an important glycosaminoglycan that has been implicated in several disease processes, such as cancer and spinal cord injury. However, few studies have characterized CS-binding protein and peptide sequences for diagnostic and therapeutic use. In this study, peptide array screening, affinity capillary electrophoresis, and statistical analysis were used to both identify and characterize C6Sbinding peptides for sequence composition. The compositional characterization results showed that Phe, Arg, and Tyr all had a significantly high rate of occurrence in the "high binding " affinity peptides, while tryptophan and lysine were significantly underrepresented in this population. Peptides modified with alanine point mutations for Phe, Arg, and Tyr all had lower C6S-binding affinities than the original peptides, demonstrating that these amino acids are all important for C6S binding. Several peptides were designed that substituted Arg for Lys and Phe or Tyr for Trp to create peptides with higher binding affinity. The peptides with the Arg substitution all had improved binding affinities while the Phe/Tyr substitution decreased C6S-binding affinity. Further analysis showed that the increased occurrence of Phe and Tyr in the "high affinity " peptides was dependent upon their positions both within the peptide sequence and in relation to other critical amino acids. Finally, a motif (ABBAA) was suggested for C6S-binding peptides where A represents any aromatic amino acid and B any basic amino acid. The results demonstrate that the methodology developed in this study for sequence composition analysis is an effective technique for the characterization of the interaction between peptides and CS.