Mapping the targeted membrane pore formation mechanism by solution NMR: the nisin Z and lipid II interaction in SDS micelles.
Nisin is an example of type-A lantibiotics that contain cyclic lanthionine rings and unusual dehydrated amino acids. Among the numerous pore-forming antimicrobial peptides, type-A lantibiotics form an unique family of post-translationally modified peptides. Via the recognition of cell wall precursor lipid II, nisin has the capacity to form pores against Gram-positive bacteria with an extremely high activity in the nanomolar (nM) range. Here we report a high-resolution NMR spectroscopy study of nisin/lipid II interactions in SDS micelles as a model membrane system in order to elucidate the mechanism of molecular recognition at residue level. The binding to lipid II was studied through (15)N-(1)H HSQC titration, backbone amide proton temperature coefficient analysis, and heteronuclear (15)N[(1)H]-NOE relaxation dynamics experiments. Upon the addition of lipid II, significant changes were monitored in the N-terminal part of nisin. An extremely low amide proton temperature coefficient (Delta delta/Delta T) was found for the amide proton of Ala3 (> -0.1 ppb/K) in the complex form. This suggests tight hydrogen bonding and/or isolation from the bulk solvent for this residue. Large chemical shift perturbations were also observed in the first two rings. In contrast, the C-terminal part of nisin was almost unaffected. This part of the molecule remains flexible and solvent-exposed. On the basis of our results, a multistep pore-forming mechanism is proposed. The N-terminal part of nisin first binds to lipid II, and a subsequent structural rearrangement takes place. The C-terminal part of nisin is possibly responsible for the activation of the pore formation. In light of the emerging antibiotic resistance problems, an understanding of the specific recognition mechanism of nisin with lipid II at the residue specific level may therefore aid in the development of novel antibiotics.
Hsu
Shang-Te
ST
Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Institute for Biomembranes, Utrecht University, 3584CH Utrecht, The Netherlands.
Breukink
Eefjan
E
de Kruijff
Ben
B
Kaptein
Robert
R
Bonvin
Alexandre M J J
AM
van Nuland
Nico A J
NA
D000577:Amides / Q000737:chemistry; D000595:Amino Acid Sequence; D000900:Anti-Bacterial Agents / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D002240:Carbohydrate Sequence; D007473:Ion Channels / Q000737:chemistry* / Q000378:metabolism; D008563:Membrane Lipids / Q000737:chemistry* / Q000378:metabolism; D008823:Micelles; D008969:Molecular Sequence Data; D009561:Nisin / Q000031:analogs & derivatives* / Q000737:chemistry* / Q000378:metabolism; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D010457:Peptidoglycan; D011104:Polyisoprenyl Phosphate Oligosaccharides / Q000737:chemistry* / Q000378:metabolism; D011487:Protein Conformation; D011522:Protons; D012967:Sodium Dodecyl Sulfate; D012996:Solutions; D012997:Solvents; D013696:Temperature; D013816:Thermodynamics; D017186:Titrimetry; D014538:Uridine Diphosphate N-Acetylmuramic Acid / Q000031:analogs & derivatives* / Q000737:chemistry* / Q000378:metabolism
D000577:Amides; D000900:Anti-Bacterial Agents; D007473:Ion Channels; D008563:Membrane Lipids; D008823:Micelles; D010457:Peptidoglycan; D011104:Polyisoprenyl Phosphate Oligosaccharides; D011522:Protons; D012996:Solutions; D012997:Solvents; D014538:Uridine Diphosphate N-Acetylmuramic Acid; C069249:muramyl-NAc-(pentapeptide)pyrophosphoryl-undecaprenol; D009561:Nisin; C062770:undecaprenyl diphosphate-(N-acetylglucosaminyl)(1-4)-N-acetylmuramoyl pentapeptide; D012967:Sodium Dodecyl Sulfate; C071364:nisin Z