Peptide arrays with designed secondary structures for protein characterization using fluorescent fingerprint patterns

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Abstract
To realize a practical high-throughput protein-detection system, novel peptide arrays have been constructed using designed peptide libraries with loop, α-helix, or β-strand structures. Here, we describe the overview of the reported deigned peptide arrays with loop and α-helix structures and the new results of those with β-strand structures. Initially, several model peptides known to interact with model structured proteins were selected to establish the present strategy for high-throughput detection of proteins. The fluorescent probes and suitable scaffolds of peptides were examined for the effective detection of proteins. The detection methods were established in solution and in an immobilized manner using the model systems. In the case of α-helix peptide, the response of a peptide with fluorescent resonance energy transfer between two probes at both termini was several times higher than that of a peptide with a single probe. In the cases of peptides with other structures, however, proteins were effectively detectable even by the fluorescent change of one probe. Furthermore, structurally focused libraries consisting of a total of ca. 250 different peptides based on the model peptides with secondary and/or tertiary structures were constructed with systematic replacement of residues. Using these libraries, various proteins were characterized effectively to give their own fluorescent “protein fingerprint” patterns. The resulting protein fingerprints correlated with the recognition properties of the proteins. These studies demonstrate that arrays with peptide libraries based on designed structures can be promising tools for detecting the target proteins. Designed synthetic peptides play roles as the capturing agents to be developed for practical protein chips. © 2004 Wiley Periodicals, Inc. Biopolymers (Pept Sci), 2004