Insights into Molecular Interactions between a GAPDH-Related Fish Antimicrobial Peptide, Analogs Thereof, and Bacterial Membranes

Abstract

Interactions between SJGAP (skipjack tuna GAPDH-related antimicrobial peptide) and four analogs thereof with model bacterial membranes were studied using Fourier-transform infrared spectroscopy (FTIR) and molecular dynamics (MD) simulations. MD trajectory analyses showed that the N-terminal segment of the peptide analogs has many contacts with the polar heads of membrane phospholipids, while the central α helix interacts strongly with the hydrophobic core of the membranes. The peptides also had a marked influence on the wave numbers associated with the phase transition of phospholipids organized as liposomes in both the interface and aliphatic chain regions of the infrared spectra, supporting the interactions observed in the MD trajectories. In addition, interesting links were found between peptide interactions with the aliphatic chains of membrane phospholipids, as determined by FTIR and from the MD trajectories, and the membrane permeabilization capacity of these peptide analogs, as previously demonstrated. To summarize, the combined experimental and computational efforts have provided insights into crucial aspects of the interactions between the investigated peptides and bacterial membranes. This work thus makes an original contribution to our understanding of the molecular interactions underlying the antimicrobial activity of these GAPDH-related antimicrobial peptides from Scombridae.

Figure 1

Lipid phase transition curves of DPPG, as shown by the [(υs)CH₂] wavenumbers as a function of temperature, in the presence or in the absence of the five studied peptide analogs.

Figure 2

Lipid phase transition curves of DPPE, as shown by the [(υs)CH₂] wavenumbers as a function of temperature, in the presence or in the absence of the five studied peptide analogs.

Figure 3

Relative contact times of peptide analogs’ residues with polar heads of phospholipids constituting the Gram-negative membrane model. Each value is the average of three independent trajectories.

Figure 4

Relative contact times of peptide analog residues with polar heads of phospholipids constituting the Gram-positive membrane model. Each value is the average of three independent trajectories.

Figure 5

Relative contact times between residue 26 of the peptide analogs and the phospholipid polar heads of the Gram-negative and Gram-positive membrane models. Each value is the average of three independent trajectories. The value obtained for analog 6 with the Gram-positive model is significantly higher than that of the other peptide analogs, according to a priori statistical comparison, as identified by the asterisk. Each value is the average of three independent trajectories, and error bars represent standard deviations.

Figure 6

Relative contact times of peptide analog residues with aliphatic chains of phospholipids constituting the Gram-negative membrane model. Each value is the average of three independent trajectories.

Figure 7

Relative contact times of peptide analog residues with aliphatic chains of phospholipids constituting the Gram-positive membrane model. Each value is the average of three independent trajectories.

Figure 8

Relative contact times between residue 19 of the peptide analogs and the phospholipid aliphatic chains of the Gram-negative and Gram-positive membrane models. Each value is the average of three independent trajectories. The values obtained for analog 7 with both membrane models are significantly higher than those of the other peptide analogs, according to a priori statistical comparisons, as identified by the asterisks. Each value is the average of three independent trajectories, and error bars represent standard deviations.

Figure 9

RMSF values of the residues constituting the five peptide analogs in the Gram-negative membrane model. Each value is the average of three independent trajectories.

Figure 10

RMSF values of the residues constituting the five peptide analogs in the Gram-positive membrane model. Each value is the average of three independent trajectories.

Figure 11

Cartoon representation of peptide analog 1 (SJGAP). Blue-colored residues and red-colored residues are at the N-terminal and C-terminal segments of the peptide chain, respectively.