A well-defined amphipathic conformation for the calcium-free cyclic lipopeptide antibiotic, daptomycin, in aqueous solution.

Daptomycin is a 13-residue cyclic lipopeptide with Ca2+-dependent bactericidal activity against a variety of high-risk pathogens. Ring closure in daptomycin is via an ester linkage between the side chain of Thr4 and the C-terminal carboxyl of the main chain; the N-terminal residue is capped by a decanoyl aliphatic chain. Extensive NMR data obtained under solution conditions that minimize aggregation have provided constraints for a detailed conformational analysis of daptomycin in aqueous solution, which should facilitate the rational design of improved analogs and enhance understanding of its mode of action. Transannular and shorter-range nuclear Overhauser effects (NOEs) as well as amide temperature shifts and 3J(NH alpha) coupling constants indicate that daptomycin adopts a well-defined conformation containing a distorted hairpin formed by Gly5-D-Ala6 type II' beta-turn. A number of hydrophobic moieties (the lipid N-cap and the Trp1 and Kyn13 side chains) are clustered at one end of the hairpin, while neutral polar and anionic residues are localized on the other end, leading to amphipathicity in the molecule. These features suggest a mode of action in which the large hydrophobic cluster of the peptide interacts with the acyl chain region of a membrane. This interaction may be facilitated by Ca2+ ions, both by neutralizing the anionic charges and by favoring association with the membrane head groups. Interestingly, our findings differ from two recent articles in which the aqueous conformation of Ca2+-free daptomycin is reported to lack a well-defined conformation (D. Jung, A. Rozek, M. Okron, and R. E. W. Hancock, Chemistry & Biology, 2004, Vol. 11, pp. 949-957) or is suggested to populate an alternate conformation (L.-J. Ball, C. M. Goult, J. A. Donarski, J. Micklefield, and V. Ramesh, Organic & Biomolecular Chemistry, 2004, Vol. 2, pp. 1872-1878).