Time-Resolved Atomistic Imaging and Statistical Analysis of Daptomycin Oligomers with and without Calcium Ions

Abstract

Daptomycin (DP) is effective against multiple drug-resistant Gram-positive pathogens because of its distinct mechanism of action. An accepted mechanism includes Ca2+-triggered aggregation of the DP molecule to form oligomers. DP and its oligomers have so far defied structural analysis at a molecular level. We studied the ability of DP molecule to aggregate by itself in water, the effects of Ca2+ ions to promote the aggregation, and the connectivity of the DP molecules in the oligomers by the combined use of dynamic light scattering in water and atomic-resolution cinematographic imaging of DP molecules captured on a carbon nanotube on which the DP molecule is installed as a fishhook. We found that the DP molecule aggregates weakly into dimers, trimers, and tetramers in water, and strongly in the presence of calcium ions, and that the tetramer is the largest oligomer in homogeneous aqueous solution. The dimer remains as the major species, and we propose a face-to-face stacked structure based on dynamic imaging using millisecond and angstrom resolution transmission electron microscopy. The tetramer in its cyclic form is the largest oligomer observed, while the trimer forms in its linear form. The study has shown that the DP molecule has an intrinsic property of forming tetramers in water, which is enhanced by the presence of calcium ions. Such experimental structural information will serve as a platform for future drug design. The data also illustrate the utility of cinematographic recording for the study of self-organization processes.

Cinematographic Recording of a Metastable Floating Island in Two- and Three-Dimensional Crystal Growth

“…Since 3-D crystal growth comprises a series of 2-D nucleation/growth events, the mechanism described here will be pertinent to a wide variety of 3-D crystal growth processes. The present work also provides a further demonstration of the value of the cinematographic study of stochastic chemical events to access hitherto unavailable information on the interactions of molecules and ion pairs , such as molecular shuttling, C–C bond-forming reactions, and 3-D crystal nucleation recorded with millisecond angstrom resolution …”

“…Since 3-D crystal growth comprises a series of 2-D nucleation/growth events, the mechanism described here will be pertinent to a wide variety of 3-D crystal growth processes. The present work also provides a further demonstration of the value of the cinematographic study of stochastic chemical events to access hitherto unavailable information on the interactions of molecules and ion pairs 21,22 We first discuss the uncatalyzed on-site epitaxy relevant to the scheme in Figure 1b. As previously reported, the NaCl@CNT specimen was prepared by first immersing water miscible aminated CNT 24 in aqueous NaCl followed by drying in a vacuum.…”

Electron beam-induced demetallation of Fe, Co, Ni, Cu, Zn, Pd, and Pt metalloporphyrins: insights in e-beam chemistry and metal cluster formations

“…We initiated our investigation with PtTPP , which features the Pt in the +II oxidation state. Upon examining the substrate for pristine graphene regions at high magnifications (×2 000 000) with a moderate electron flux of ∼10 −6 e − nm −2 s −1 for SMART-EM studies, 39–44 we discovered omnipresent single Pt atoms. As highlighted in the time-dependent image sequence of two Pt atoms in Fig.…”

Structural diversity, biosynthesis, and biological functions of lipopeptides fromStreptomyces

“…They discovered that the tetramer is the biggest oligomer in homogeneous aqueous solution, and the daptomycin molecule clusters was enhanced by the presence of Ca 2+ ions. 300 In 2016, the Schneider group investigated the biological model of daptomycin in B. subtilis, revealing that daptomycin decreased the membrane potential but no distinct membrane holes were detected during this process. They found that daptomycin affects cell wall formation whilst detecting no indication of altered membrane curvature.…”

“…They discovered that the tetramer is the biggest oligomer in homogeneous aqueous solution, and the daptomycin molecule clusters was enhanced by the presence of Ca 2+ ions. 300…”