ISDA

Entry Detail

PDB ID:

5NF0

Keywords:

Title:

Discovery, crystal structures and atomic force microscopy study of thioether ligated D,L-cyclic antimicrobial peptides against multidrug resistant Pseudomonas aeruginosa

Biological Source:

Source Organism:

Pseudomonas aeruginosa, synthetic construct

Host Organism:

Escherichia coli

PDB Version:

Deposition Date:

2017-03-13

Release Date:

2017-09-13

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.27 Å

R-Value Free:

0.18

R-Value Work:

0.16

R-Value Observed:

0.16

Space Group:

P 21 21 21

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:Fucose-binding lectin II (PA-IIL)
Chain IDs:A, B, C, D
Chain Length:114
Number of Molecules:4
Biological Source:Pseudomonas aeruginosa

UniProt ID:Q9HYN5 Pfam ID:PF07472

Polymer Type:polypeptide(L)
Description:CYD-TRP-TRD-LYS-LYD-LYS-LYD-LYS-TRD-TRP-CYD-GLY
Chain IDs:E, G, H
Chain Length:12
Number of Molecules:3
Biological Source:synthetic construct

Polymer Type:polypeptide(L)
Description:Fragment of ligand
Chain IDs:F
Chain Length:5
Number of Molecules:1
Biological Source:synthetic construct

Ligand Molecules

OXE

ZDC

Primary Citation

Design, crystal structure and atomic force microscopy study of thioether ligated d,l-cyclic antimicrobial peptides against multidrug resistant Pseudomonas aeruginosa.

He, R, Di Bonaventura, I, Visini, R, Gan, B.H, Fu, Y, Probst, D, Luscher, A, Kohler, T, van Delden, C, Stocker, A, Hong, W, Darbre, T, Reymond, J.L.Show

Chem Sci 8 7464 7475 (2017)

PMID: 29163899 DOI: 10.1039/c7sc01599b

Abstact

Here we report a new family of cyclic antimicrobial peptides (CAMPs) targeting MDR strains of Pseudomonas aeruginosa. These CAMPs are cyclized via a xylene double thioether bridge connecting two cysteines placed at the ends of a linear amphiphilic alternating d,l-sequence composed of lysines and tryptophans. Investigations by transmission electron microscopy (TEM), dynamic light scattering and atomic force microscopy (AFM) suggest that these peptide macrocycles interact with the membrane to form lipid-peptide aggregates. Amphiphilic conformations compatible with membrane disruption are observed in high resolution X-ray crystal structures of fucosylated derivatives in complex with lectin LecB. The potential for optimization is highlighted by N-methylation of backbone amides leading to derivatives with similar antimicrobial activity but lower hemolysis.

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Primary Citation of related structures