Design and Production of Specifically and with High Affinity Reacting Peptides

TL;DR

This paper introduces a novel method for designing high-affinity peptides targeting specific proteins by leveraging the Proteomic Code and partial codon complementarity, enabling rapid and inexpensive affinity reagent production.

Contribution

It presents a new approach using partial codon complementarity and randomization to create specific affinity peptides for any protein target.

Findings

Achieved high-affinity peptides with Kd of 100 nM.

Demonstrated successful design for GAL4 protein.

Proposed a rapid, cost-effective alternative to antibodies.

Abstract

Background: A partially random target selection method was developed to design and produce affinity reagents (target) to any protein query. It is based on the recent concept of Proteomic Code (for review see Biro, 2007 [1]) which suggests that significant number of amino acids in specifically interacting proteins are coded by partially complementary codons. It means that the 1st and 3rd residues of codons coding many co-locating amino acids are complementary but the 2nd may but not necessarily complementary: like 5'-AXG-3'/3'-CXT-5' codon pair, where X is any nucleotide. Results: A mixture of 45 residue long, reverse, partially complementary oligonucleotide sequences (target pool) were synthesized to selected epitopes of query mRNA sequences. The 2nd codon residues were randomized. The target oligonucleotide pool was inserted into vectors, expressed and the protein products were screened for affinity to the query in Bacterial Two-Hybrid System. The best clones were used for larger-scale protein syntheses and characterization. It was possible to design and produce specific and with high affinity reacting (Kd:100 nM) oligopeptide reagents to GAL4 query oligopeptides. Conclusions: Second codon residue randomization is a promising method to design and produce affinity peptides to any protein sequences. The method has the potential to be a rapid, inexpensive, high throughput, non-immunoglobulin based alternative to recent in vivo antibody generating procedures.