6Q6W

Structure of Fucosylated D-antimicrobial peptide SB5 in complex with the Fucose-binding lectin PA-IIL at 1.438 Angstrom resolution

Summary for 6Q6W

• Entry DOI: 10.2210/pdb6q6w/pdb
• Descriptor: Fucose-binding lectin, SB5, CALCIUM ION, ... (6 entities in total)
• Functional Keywords: antimicrobial, lectin, complex, antibiotic
• Biological source: Pseudomonas aeruginosa; More
• Total number of polymer chains: 2
• Total formula weight: 13453.92

Authors

Baeriswyl, S.,Stocker, A.,Reymond, J.L. (deposition date: 2018-12-12, release date: 2019-03-20, Last modification date: 2024-01-24)

Primary citation

Baeriswyl, S.,Gan, B.H.,Siriwardena, T.N.,Visini, R.,Robadey, M.,Javor, S.,Stocker, A.,Darbre, T.,Reymond, J.L.
X-ray Crystal Structures of Short Antimicrobial Peptides as Pseudomonas aeruginosa Lectin B Complexes.
Acs Chem.Biol., 14:758-766, 2019

PubMed Abstract: Herein, we report X-ray crystal structures of 11-13 residue antimicrobial peptides (AMPs) active against Pseudomonas aeruginosa as complexes of fucosylated d-enantiomeric sequences with the P. aeruginosa lectin LecB. These represent the first crystal structures of short AMPs. In 24 individual structures of eight different peptides, we found mostly α-helices assembled as two-helix or four-helix bundles with a hydrophobic core and cationic residues pointing outside. Two of the analogs formed an extended structure engaging in multiple contacts with the lectin. Molecular dynamics (MD) simulations showed that α-helices are stabilized by bundle formation and suggested that the N-terminal acyl group present in the linker to the fucosyl group can extend the helix by one additional H-bond and increase α-helix amphiphilicity. Investigating N-terminal acylation led to AMPs with equivalent and partly stronger antibacterial effects compared to the free peptide.

PubMed: 30830745
DOI: 10.1021/acschembio.9b00047

Experimental method

X-RAY DIFFRACTION (1.438 Å)