Proline and alanine scanning analysis and structure-function relationships of the 11-residue lysine homopeptides

In a previous work we demonstrated that Lys homopeptides of odd number of residues were able to inhibit a wide range of both Gram (+and Gram-negative bacteria, especially with 11-residues, as opposite toLys homopeptides with an even number of residues [1].Here, we used alanine and proline scanning analogs to elucidate the contribution of the side chain of each e-aminogroup to the antibacterial and cytotoxic activity of the peptides. Hence, 11 peptides of scan Ala and the same number of scan Pro were synthesized by Fmoc solid-phase synthesis and subsequently tested for antibacterial activity against a wide range of bacteria. Lys residues at either the C-or N-terminal end of the peptide played a prominent role for bacterial inhibition compared to Lys residues located at the center of the chain, as demonstrated by Ala exchange. In general, substitution of Lys for Pro did not substantially change the bacterial inhibition pattern. Ala substitutions at any position of the homopeptide showed amore significant change of the polyproline II (PPII) structure compared to Pro substitutions. Indeed, Pro substitutions showed an increased propensity to form PPII structures. Besides providing insight into the biophysical attributes and the critical positions within the homopeptide sequence, which govern the antibacterial activity of cationic homopeptides, our studies assist in recognizing the key roles played by different amino acids in the antibacterial activity.