Helical preferences of alanine,glycine, and aminoisobutyric homopeptides

The stability between helical conformations of homopeptides of alanine, glycine, and aminoisobutyric acid has been studied by means of quantum-mechanical methods. The influence of peptide length on the relative stability between helical conformations has also been analyzed by means of systematic studies for peptides of size up to 11 residues. Finally, the influence of the solvent has been examined by using self-consistent reaction field methods. The results provide a detailed picture of the modulation exerted by these factors on the helical preferences of these peptides. © 1997 Wiley-Liss Inc.     

Inhibitory effect of short cationic homopeptides against Gram‐positive bacteria

In the selection or design of antimicrobial peptides, the key role played by cationic amino acids and chain length on the inhibitory potency and specificity is not clear. A fundamental study was conducted using chemically synthesized homopeptides of l ‐Lys and l ‐Arg ranging from 7 to 14 residues. Their effect on growth inhibition was evaluated over a wide range of Gram‐positive bacteria at different levels of concentration. Interestingly, at lower concentrations (10 μM), Lys homopeptides with odd number of residues, especially with 11 residues, showed a broader inhibitory activity than those with even number of residues. At higher peptide concentrations (>20 μM), the inhibitory activity of Lys homopeptides was directly related to the number of residues in the chain. In contrast, Arg homopeptides, at lower concentrations, did not exhibit a defined pattern of bacterial inhibition related to the number of residues; however, at higher concentrations (>20 μM), the inhibitory effects were more pronounced. Lys homopeptides at concentrations up to 300 μM showed a remarkably lower toxicity against CHSE‐214 cells. Arg homopeptides exhibited negligible cytotoxicity up to chain length of 11 residues at concentrations lower than 100 μM, but an abrupt increase in toxicity resulted when the peptide chain length reached 12 amino acid residues and higher concentrations. All synthesized homopeptides displayed characteristic polyproline II helix conformation in both buffer and liposomes, as shown by CD spectroscopy. This result suggests that short Lys homopeptides with an odd number of residues (9 and 11) have a broad spectrum of activity against Gram‐positive bacterial cells compared with Arg homopeptides, which in turn showed a considerably higher selectivity toward those cells. By investigating the differences between Lys and Arg homopeptides, this study contributes to the understanding of their mechanism of growth inhibition and selectivity. Thus, it provides further guidelines for a rational design of short antimicrobial peptides. Copyright © 2013 European Peptide Society and John Wiley & Sons, Ltd.     

Structural versatility of peptides containing C-dialkylated glycines: conformational energy computations, i.r. absorption and H n.m.r. analysis of 1-aminocyclopropane-1-carboxylic acid homopeptides

Conformational energy computations on the 1-aminocyclopropane-1-carboxylic acid mono-, di-, and tripeptide amides, (Ac-(Ac₃c)_n---NHMe (n=1−3), indicate that this C^,-dialkylated, cyclic -amino acid residue is conformally restricted and that type-I(I′) β-bends and distorted 3₁₀-helices are particularly stable conformations for the di- and tripeptide amides, respectively. The results of the theoretical analysis are in agreement with those obtained in an i.r. absorption and ¹H n.m.r. investigation in chloroform solution of A.c.₃c-rich tri- and tetrapeptide esters. A comparisons is also made with the conclusions extracted from our previous work on peptides rich in Aib (-aminoisobutyric acid), Ac₅c(1-aminocyclopentane-1-carboxylic acid), and Ac₆c (1-aminocyclohexane-1-carboxylic acid).     

Evolutionary analysis of amino acid repeats across the genomes of 12 Drosophila species

Repeated motifs of amino acids within proteins are an abundant feature of eukaryotic sequences and may catalyze the rapid production of genetic and even phenotypic variation among organisms. The completion of the genome sequencing projects of 12 distinct Drosophila species provides a unique dataset to study these intriguing sequence features on a phylogeny with a variety of timescales. We show that there is a higher percentage of proteins containing repeats within the Drosophila genus than most other eukaryotes, including non-Drosphila insects, which makes this collection of species particularly useful for the study of protein repeats. We also find that proteins containing repeats are overrepresented in functional categories involving developmental processes, signaling, and gene regulation. Using the set of 1-to-1 ortholog alignments for the 12 Drosophila species, we test the ability of repeats to act as reliable phylogenetic signals and find that they resolve the generally accepted phylogeny despite the noise caused by their accelerated rate of evolution. We also determine that in general the position of repeats within a protein sequence is non-random, with repeats more often being absent from the middle regions of sequences. Finally we find evidence to suggest that the presence of repeats is associated with an increase in evolutionary rate upon the entire sequence in which they are embedded. With additional evidence to suggest a corresponding elevation in positive selection we propose that some repeats may be inducing compensatory substitutions in their surrounding sequence.