Rational and Combinatorial Design of Peptide Affinity Ligands for Troponin I

Peptides are promising affinity ligands for detection of proteins in biological samples. We describe a synergistic approach to peptide ligand design based on rational and combinatorial peptide design strategies. Troponin I, a biologically relevant marker of cardiac injury was used as a model protein analyte in this system. Under physiological conditions, endogenous Troponin C and Troponin T bind to Troponin I with very high affinities. Based on the previously published crystal structure of the complexes of Troponin I, T and C, we designed candidate libraries of short linear peptides (15 amino acids in length) for screening against Troponin I. Peptide libraries were synthesized using a high throughput peptide synthesizer, and screened for binding to Troponin I using high density peptide microarrays. We have discovered a wide range of peptides derived from Troponin C and T that bind to Troponin I with varying binding affinities (1 nM – 1 uM). These peptides are excellent candidates for use in biological assays for the quantitative determination of Troponin I from human serum samples. This study elucidates a systematic approach for the design and discovery of peptide affinity ligands for the detection of protein biomarkers of interest.