Effect of divalent cations on the structure of the antibiotic daptomycin

Abstract

Daptomycin, a cyclic anionic lipopeptide antibiotic, whose three-dimensional structure was recently solved using solution state NMR (Ball et al. 2004; Jung et al. 2004; Rotondi and Gierasch 2005), requires calcium for function. To date, the exact nature of the interaction between divalent cations, such as Ca(2+) or Mg(2+), has not been fully characterized. It has, however, been suggested that addition of Ca(2+) to daptomycin in a 1:1 molar ratio induces aggregation. Moreover, it has been suggested that certain residues, e.g. Asp3 and Asp7, which are essential for activity (Grunewald et al. 2004; Kopp et al. 2006), may also be important for Ca(2+) binding (Jung et al. 2004). In this work, we have tried: (1) to further pinpoint how Ca(2+) affects daptomycin structure/oligomerization using analytical ultracentrifugation; and (2) to determine whether a specific calcium binding site exists, based on one-dimensional (13)C NMR spectra and molecular dynamics (MD) simulations. The centrifugation results indicated that daptomycin formed micelles of between 14 and 16 monomers in the presence of a 1:1 molar ratio of Ca(2+) and daptomycin. The (13)C NMR data indicated that addition of calcium had a significant effect on the Trp1 and Kyn13 residues, indicating that either calcium binds in this region or that these residues may be important for oligomerization. Finally, the molecular dynamics simulation results indicated that the conformational change of daptomycin upon calcium binding might not be as significant as originally proposed. Similar studies on the divalent cation Mg(2+) are also presented. The implication of these results for the biological function of daptomycin is discussed.

The action mechanism of daptomycin

“…They also determined the structure of daptomycin (2 mM) in the presence of 5 mM MgCl 2 . 37 No line broadening was observed, and the obtained structure closely resembled their previously reported apo-daptomycin structure. 42 Ball et al also reported the structure of Ca 2+ -bound daptomycin using an 0.8 mM solution of daptomycin at pH 5.3.…”

“…Realizing that daptomycin aggregation may have affected their results, Straus et al re-examined their Ca 2+ -bound daptomycin structure in detail. 37 Molecular dynamics (MD) simulations suggested that the conformational change in daptomycin upon binding Ca 2+ might not be as significant as originally proposed. It was concluded that none of the Ca 2+ -bound daptomycin models tested in the MD simulations were consistent with the NOE restraints reported earlier, and that the previously reported NOE restraints between residues Asp (3) and Ala (8) were intermolecular and should not been included during structure refinement.…”

Lipopeptides as anti-infectives: a practical perspective

“…in the presence of high concentrations of Ca 2+ [46][47][48]. With the Ca 2+ /daptomycin molar ratio at 1:1 under these conditions, oligomerization occurs, resulting in 14 to 16 monomers forming micelles [35,49,50]. The arrangement into micelles is not accompanied by a change in lipopeptide conformation, as originally proposed [36].…”

“…The anionic character of daptomycin is masked by its complexation with divalent cations such as Ca 2+ , enabling the lipopeptide to perturb bacterial membranes in a detergent-like manner, analogously to what has been suggested for cationic antimicrobial peptides [33][34][35].…”

Antimicrobial Properties of MX-2401, an Expanded-Spectrum Lipopeptide Active in the Presence of Lung Surfactant

“…The addition of one or more equivalents of Ca 2ϩ completely inverted the positive ellipticity at 230 nm in the absence of calcium. This effect has been interpreted as being due to a Ca 2ϩ -dependent change in structure (15,19) or daptomycin-mediated fusion of POPC-POPG liposomes in the presence of calcium (16) without a structural change (12).…”