Effects of sequence context on the binding of tryptophan- containing peptides by the cucurbit[8] uril- methyl viologen complex

This paper describes a novel assay for measuring the relative extent of peptide binding in a large parallel format and the use of this assay to explore the effects of sequence context on the binding of tryptophan (Trp)-containing peptides by the synthetic receptor comprising the noncovalent complex between cucurbit[8]uril and methyl viologen (i.e. Q8MV). The extent of quenching of Trp fluorescence upon binding to Q8MV was used to measure the relative extent of binding and thus the relative affinities of 104 Trp-containing peptides, in parallel, using a fluorescence plate reader. This study resulted in the remarkable observation that the identity of the amino acid residues at positions adjacent to the Trp-binding site has little if any influence on the binding affinity. This finding suggests that Q8MV should be effective for the recognition of Trp residues within a broad range of peptide sequences.