Peptides antimicrobial activities are correlated to their spatial location in the first two principal components derived from DSC data.

<p>Antimicrobial activity is represented as the anti-log of the minimum inhibitory concentration (MIC) in micromoles 1/log(MIC(µM)). Peptides MICs can be verified in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0045848#pone-0045848-t002" target="_blank">Table 2</a>. Tested microorganisms were (a) <i>Escherichia coli</i>, (b) <i>Staphylococcus aureus</i>, (c) <i>Pseudomonas aeruginosa</i> and the phytopathogenic bacterium (d) <i>Xanthomonas axonopodis</i> pv. <i>glycines</i>.</p

IAPs-induced inhibition of fixation of <i>Pahakopsora pachyrhizi</i> spores on soy bean leaves and tolerance of <i>G. max</i> transformed with gb|ABM17058.1|(213–231) to the Asian rust in the greenhouse.

<p>(a) AMPs and IAPs at 8 to 128 µg/mL were co-incubated with 3.5×10⁵/ml <i>P. pachyrhizi</i> spores for seven days on the surface of <i>G. max</i> leaves, followed by the estimation of the infected area (represented as a histogram graph). Bars correspond to the sample standard deviation (<i>n</i> = 3). All peptides at all tested concentrations resulted in significantly different pustule areas at a 95% confidence interval except for those marked with an asterisk (*). Wild type and <i>G. max</i> plants transformed with a vector containing gb|ABM17058.1|(213–231) were grown to the V3 stage and sprayed with a suspension of <i>P. pachyrhizi</i> spores (10⁶ spores/mL). (b) Transformed plants (72.14.5 and 72.14.9) were co-cultivated with control plants (wt/+) for 15 days. (c) Control lineages, designated as wt/− and wt/+, correspond to wild-type plants subjected to spraying with water alone or the Asian rust spore suspension, respectively. Intragenic lineages 72.14.5 and 72.14.9 presented a significant reduction in the number of uredia per foliar area (see text).</p

Peptides filtered by Kamal are physicochemically more similar to a sample of antimicrobial peptides than randomly chosen molecules from the same EST database.

<p>A principal component analysis was applied to calculated physicochemical properties (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0045848#pone.0045848.s005" target="_blank">Table S1</a>) of five hundred randomly chosen protein fragments and five hundred putative IAPs filtered from an EST database of <i>G. max</i> proteins <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0045848#pone.0045848-Schmutz1" target="_blank">[14]</a>, represented as green and grey spheres respectively, as well as naturally occurring antimicrobial molecules from the Antimicrobial Peptide Database <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0045848#pone.0045848-Wang1" target="_blank">[15]</a>, in black. Component loadings are available in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0045848#pone-0045848-t001" target="_blank">Table 1</a>.</p

The helicity of peptides in buffer and at 1 mol% DMPC or 2∶1 DMPC:DMPG LUVs are correlated to peptides spatial location in the first two principal components derived from DSC data.

<p>Far-UV CD spectra of selected cases for each of the three peptide clusters are shown. Insets (a), (c) and (e) depict the far-UV CD spectra for HSP-4, penetratin and the IAP Q8RW88(70–95), respectively, in buffer (hollow spheres) and titrated with DMPC LUVs (filled spheres). Insets (b), (d) and (f) demonstrate the CD spectra of the same peptides in buffer and added with 2∶1 DMPC:DMPG LUVs. MREs were similar for 0.01 and 0.005 peptide/phospholipids molar ratios, indicating that secondary structure changes reached a plateau under these conditions.</p

Peptide search criteria and illustrative data for the filtering of putative IAPs from the soybean (<i>Glycine max</i>) genome project [14].

<p>-Parameter not used.</p>*<p>no Cys or Pro.</p

Peptides primary structures, source proteins, organisms and minimum inhibitory activity (MIC) against pathogenic bacteria.

<p>NDA  =  Non-detectable activity.</p>*<p>publication names, UniprotKB or genebank entries followed by the first and last residues in brackets.</p>**<p>free carboxy-terminus peptide.</p

Principal component analysis of the model fitted main phase transitions of LUVs added with peptides at 4 mol% highlight similarities on membranes thermal behaviors.

<p>A matrix describing the effect of peptides on the transition temperature (Tm), enthalpy (ΔH) and cooperativity (ΔH_VH) of the broad and sharp components of DMPC and 2∶1 DMPC:DMPG LUV thermal transitions was assembled and standardized (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0045848#pone.0045848.s006" target="_blank">Table S2</a>) and a PCA was applied to the resulting data. Additionally, the coordinates of peptides in the first three principal components were submitted to a mixture modeling clustering algorithm, resulting in an optimal of three peptide clusters, shown here in different colors (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0045848#pone.0045848.s003" target="_blank">Fig. S3</a>). Thermograms demonstrating the effect of selected peptides on the main phase transition of membranes are shown as representative examples: HSP-4 on (a) 2∶1 DMPC:DMPG and (b) DMPC LUVs represents cluster 3, in black, the IAP Q8RW88(70–95) on (c) 2∶1 DMPC:DMPG and (d) DMPC LUVs represents cluster 1, in green, and penetratin added to (e) DMPC and (f) 2∶1 DMPC:DMPG LUVs represents cluster 2, in grey. Group borders are illustrational.</p

Thermal scans of 2∶1 DMPC:DMPG LUVs enriched with increasing concentrations of DS 01 show the effect of frog skin antimicrobial peptides on the main phase transition of phospholipids.

<p>Non two-state model fitting of the P’_β→Lα phase transition of a solution of 0.5 mM 2∶1 DMPC:DMPG LUVs enriched with a) pure phospholipids, b) 1 mol% DS 01, c) 2 mol% DS 01 and d) 4 mol% DS 01.</p

Modulation of cytokine IL-8 production by LAB isolates.

<p>A: modulation of IL-8 production by the PS cell line in the presence of LAB isolates (MOI 100:1). Bars represent the mean IL-8 production ± standard deviation for four assays (two biological and two technical replicates), normalized with regard to IL-8 production by unstimulated PS cells (76 +/-16 pg/mL as a mean); B: modulation of IL-8 production by the <i>E</i>. <i>coli</i>-stimulated PS cell line in the presence of LAB isolates. <i>E</i>. <i>coli</i> was used at MOI 1:1 and LAB at MOI 100:1. Bars represent the mean IL-8 production ± standard deviation for four assays, normalized with regard to IL-8 production by <i>E</i>. <i>coli</i>-stimulated PS cells (368 ± 88 pg/mL as a mean). Differences in IL-8 production with regard to the reference condition were assessed using the Mann-Whitney test (* p < 0.05).</p

Internalization of lactic acid bacteria into bovine mammary epithelial cells.

<p>Lactic acid bacteria populations internalized into bMEC were determined after 2 h of interaction at a MOI of 400:1 (A) and 2000:1 (B), respectively. Data are presented as mean population per well (i.e., corresponding to 2.5x10⁵ bMEC) ± standard deviation. Each experiment was done in triplicate and differences between strains were assessed using one-way analysis of variance, followed by Tukey’s range test. Letters a, b, c and d indicate homogeneous statistical processing groups that were significantly different according to Tukey’s range test.</p