The role of d - allo -isoleucine in the deposition of the anti- Leishmania peptide bombinin H4 as revealed by 31 P solid-state NMR, VCD spectroscopy, and MD simulation

Abstract

Bombinin H4 is an antimicrobial peptide that was isolated from the toad Bombina variegata. Bombinin H family peptides are active against gram-positive, gram-negative bacteria, and fungi as well as the parasite Leishmania. Among them, bombinin H4 (H4), which contains d-allo-isoleucine (d-allo-Ile) as the second residue in its sequence, is the most active, and its l-isomer is bombinin H2 (H2). H4 has a significantly lower LC50 than H2 against Leishmania. However, the atomic-level mechanism of the membrane interaction and higher activity of H4 has not been clarified. In this work, we investigated the behavior of the conformations and interactions of H2 and H4 with the Leishmania membrane using P solid-state nuclear magnetic resonance (NMR), vibrational circular dichroism (VCD) spectroscopy, and molecular dynamics (MD) simulations. The generation of isotropicP NMR signals depending on the peptide concentration indicated the abilities of H2 and H4 to exert antimicrobial activity via membrane disruption. The VCD experiment and density functional theory calculation confirmed the different stability and conformations of the N-termini of H2 and H4. MD simulations revealed that the N-terminus of H4 is more stable than that of H2 in the membrane, in line with the VCD experiment data. VCD and MD analyses demonstrated that the first l-Ile and second d-allo-Ile of H4 tend to take a cis conformation. These residues function as an anchor and facilitate the easy winding of the helical conformation of H4 in the membrane. It may assist to quickly reach to the threshold concentration of H4 on the Leishmania membrane. This article is part of a Special Issue entitled: d-Amino acids: biology in the mirror, edited by Dr. Loredano Pollegioni, Dr. Jean-Pierre Mothet and Dr. Molla Gianluca.

A Comparative Study on Interactions of Antimicrobial Peptides L- and D-phenylseptin with 1,2-dimyristoyl-sn-glycero-3-phosphocholine

“…However, the intensity of the amide I couplet and amide II of D-Phes was significantly decreased, indicating that the conformation of N-terminal part is different between the two peptides; while the N-terminus of L-Phes adopts a helical conformation, the same region in D-Phes is disordered. Previously, we have reported the differences in the VCD spectra of bombinin H4, containing D-allo-isoleucine at the second residue, and its diastereomer H2, and showed differences in the structure of the N-terminal region [21]. Thus, our CD and VCD experiments of the phenylseptin showed that both peptides form similar α-helical structures, however in the N-terminal region, the conformation is quite different for the two peptides.…”

“…reported the differences in the VCD spectra of bombinin H4, containing D-allo-isoleucine at the second residue, and its diastereomer H2, and showed differences in the structure of the N-terminal region [21]. Thus, our CD and VCD experiments of the phenylseptin showed that both peptides form similar α-helical structures, however in the N-terminal region, the conformation is quite different for the two peptides.…”

“…In this work, we performed a comparative analysis of the membrane interactions of the L-Phes and D-Phes peptides with the 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) membrane using quartz crystal microbalance (QCM), circular dichroism (CD), vibrational circular dichroism (VCD), solid-state nuclear magnetic resonance (NMR), and molecular dynamics (MD) simulations. The combination of these techniques are widely applied to monitor and study the membrane interactions, secondary structures, and the structural dynamics of the antimicrobial peptides [21,23,24].…”

Structural Characterization of a Cyclodextrin/l-menthol Inclusion Complex in the Solid-state by Solid-state NMR and Vibrational Circular Dichroism

“…[34][35][36] VCD can observe characteristic intense signals and positive/negative signs depending on the crystal packing of amino acids, secondary structure of proteins, and the supramolecular chirality. [37][38][39][40][41] Solid-state NMR allows one to determine the structure of target molecule in the solid-state at atomic resolution. 42 VCD allows one to determine the absolute configuration of enantiomers and vibrational mode on the basis of intermolecular interactions.…”

Molecular dynamic simulations, GIAO‐NMR and TD‐DFT spectroscopy analyze for zwitterionic isoleucine (ILE)N, 1 ≤ N ≤ 6, in water solution

“…In recent years, there has been an increase in interest for biological molecules especially amino acids, which has had great appeal for the manufacture of new nanomaterials and applications. In this regard, the determination of spectroscopic properties and the possible dependence of these properties on amino acid chain growth becomes an important point for applications of these new nanomaterials whether in the membranes research [1][2][3][4] or self-assemble properties [5][6][7][8] , energy storage 9 or even pharmaceutical applications [10][11][12] . In this article, we focus on the amino acid Isoleucine (ILE) which has a characteristic hydrophobic structure and has a high β-sheet formation potential compared to the other amino acids.…”