Solution Structure of Polymyxins B and E and Effect of Binding to Lipopolysaccharide: An NMR and Molecular Modeling Study

Abstract

The cyclic decapeptides polymyxin B (PmB) and E (PmE) (mo-K'TK'-cyclo-[K'K'XLK'K'T]; mo, methyl octanoate; K', diaminobutyric acid; X, D-Phe (PmB) or D-Leu (PmE)) display antimicrobial and lipopolysaccharide (LPS) antagonistic activities. We have investigated the conformational behavior of PmB and PmE in water solution, free and bound to LPS, by homonuclear NMR and molecular modeling methods. The free peptides exist in equilibria of fast exchanging conformations with local preferences for a distorted type II' beta-turn from residues 5-8, and/or a gamma-turn in residue 10. These two motifs are not present in the bound conformation of the peptides. The latter is amphiphilic separating the two hydrophobic residues in the cycle from the positively charged diaminobutyric acid side chains by an envelope-like fold of the cycle. The bound conformation is used for the derivation of a model of the PmB-lipid A complex based on electrostatic interactions and reduction of hydrophobic area. The proposed mode of binding breaks up the supramolecular structure of LPS connected with its toxicity. The model should contribute to the understanding of entropy-driven PmB-lipid A binding at the molecular level and assist the design of inhibitors of endotoxic activity.

Interaction of the HIV-1 gp120 Viral Protein V3 Loop with Bacterial Lipopolysaccharide

“…This pattern of interaction is similar to the one observed with antimicrobial peptides that interact with and neutralize LPS (39,53,54), where a strong induced fit has been observed in all cases, indicating that single point mutations within the V3 peptide are not likely to lead to a strong decrease of interaction, as observed already in LPS-antimicrobial peptide studies. Polymyxin B as a prototype of an endotoxin-neutralizing peptide also folds into a defined conformation in complex with LPS, segregating the cationic and lipophilic side chains (54). Similar results were obtained previously with LF11, a linear peptide based on human lactoferrin, where docking of LF11 to LPS demonstrates that cationic as well as hydrophobic residues interact with lipid A (39).…”

Isolation, Structural Characterization, and Properties of Mattacin (Polymyxin M), a Cyclic Peptide Antibiotic Produced byPaenibacillus kobensis M

“…The transferred NOE experiments performed with the mattacin/LPS mixture revealed a number of NOEs for the heptacyclic region of the peptide which were not visible before the addition of LPS. These NOEs (62 total) were used to produce a conformational model for comparison with that of polymyxin B (19). Matticin adopted a chair-like conformation with the side chains of A 2 bu-4 and -8 pointing downward from those of Thr-6 and Leu-7 (Fig.…”

“…Using transferred NOE two-dimensional NMR techniques, Pristovsek and Kidric (19) recently investigated the preferred conformation(s) induced in polymyxin B when in solution with LPS from E. coli. Their results indicate that although the peptide is highly flexible, the side chain of A 2 bu-8 and the ␥-amide NH of A 2 bu-4 as well as the amide NH of A 2 bu-8 with the side chain of A 2 bu-4 are in close proximity while bound to LPS.…”

“…Although polymyxins represent one of the earliest classes of commercially important antibiotics to be identified (17), and at least 15 unique polymyxins have been described (18), only polymyxin B is currently widely used and studied. In addition to efficient production and purification of mattacin, the present study describes its NMR solution structure and transfer NOE 1 determination of conformational changes that occur upon bind-ing to lipid A and compares these with previous results reported by others (19) with polymyxin B. Isothermal titration calorimetry was also employed to compare the binding of mattacin and polymyxin B to lipopolysaccharide (LPS), the major antigen of the outer membrane of Gram-negative bacteria. Finally, the biological potency of mattacin was assessed compared with that of polymyxin B, and the biosynthesis of mattacin was briefly examined.…”

Novel Des-Fatty Acyl-Polymyxin B Derivatives with Pseudomonas aeruginosa-Specific Antimicrobial Activity

“…24) Elimination of the positively charged Dab 1 residue, which interacts with the negatively charged phosphate group in the PMB-LPS complex, is not likely to significantly weaken the LPS-peptide interaction. This is because of the conformational change of the side chain at the Dab 3 residue, allowing for the efficient interaction of the Dab 3 residue with the negatively charged phosphate group.…”