Infrared spectroscopy of ‘forbidden’ peptide sequences

Abstract

Certain pentapeptide sequences are absent from all known universal protein primary structures, even though they are found in the non-coding regions of DNA. These ‘forbidden’ sequences may have been rejected by evolution because they disrupt the formation of functional secondary protein structures. The uncapped pentapeptides FFMCT and WCFNL, which model the two ‘most forbidden’ sequences, were studied in a cold molecular beam using IR/UV holeburning spectroscopy, and DFT calculations were carried out to help reveal their inherent conformational preferences. Computed IR spectra for different structures were compared to the experimental IR spectra in the Amide I/II and Amide A vibrational band regions. The conformational assignments based on this analysis provide preliminary clues for understanding how these peptides may form structures that hinder the desired protein folding process. For FFMCT the structural analysis indicates a strong preference for a β-turn conformation, where the C-terminal OH binds to the N-terminal F side chain. The WCFNL results show that the peptide adopts a 3₁₀-helical conformation with free N- and C-termini, and less backbone hydrogen bonding than in FFMCT. Both structural motifs could drastically disturb the overall folding process when being part of a peptide or protein.