RNA–peptide interactions are an important factor in the origin of the modern mechanism of translation and the genetic code. Despite great progress in the bioinformatics of RNA–peptide interactions due to the rapid growth in the number of known RNA–protein complexes, there is no comprehensive experimental method to take into account the influence of individual amino acids on non-covalent RNA–peptide bonds. First, we designed the combinatorial libraries of primordial peptides according to the combinatorial fusion rules based on Watson–Crick mutations. Next, we used high-density peptide arrays to investigate the interaction of primordial peptides with their cognate homo-oligonucleotides. We calculated the interaction scores of individual peptide fragments and evaluated the influence of the peptide length and its composition on the strength of RNA binding. The analysis shows that the amino acids phenylalanine, tyrosine, and proline contribute significantly to the strong binding between peptides and homo-oligonucleotides, while the sum charge of the peptide does not have a significant effect. We discuss the physicochemical implications of the combinatorial fusion cascade, a hypothesis that follows from the amino acid partition used in the work.
Fuel cells used for transport applications hold polymer membranes as a key element. Their efficiency can be significantly increased if structured ion channels are implemented at the molecular level into the proton‐conducting membrane. New functional molecules with selective affinity for ionomers are needed to obtain such a membrane design. This study presents a method to screen for selective peptide binders to perfluorinated sulfonic acid ionomers, e.g., Nafion using ultra‐high density peptide arrays with a spot size of up to 30 µm. First, the ionomer dispersion is incubated with the peptide chip containing 56014 randomly chosen 6‐mer peptides. Afterward, the peptide chip is washed. The peptide WIWHCW with the helix structure is identified as a selective binder to Nafion. The invariant amino acids responsible for binding are also determined using a peptide chip approach. The specific binding pocket of WIWHCW is formed by histidine and tryptophan. Its dissociation constant to the ionomer is measured at ≈140 µM.
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