Time-resolved Atomistic Imaging and Statistical Analysis of Daptomycin Oligomers with and without Calcium Ion

13 April 2022, Version 2
This content is a preprint and has not undergone peer review at the time of posting.


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, and we studied the process 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 a homogeneous aqueous solution. The dimer remains as the major species under a variety of conditions, and we propose a face-to-face stacked structure based on dynamic imaging using millisecond and angstrom resolution transmission electron microscopy. The tetramer is the largest oligomer observed both in the absence and in the presence of a large excess of calcium ions. Taken together with statistical data, the microscopic structural information obtained at a single-molecule level favors a cyclic form of the dimer and the tetramer over a linear or stacked form. Such experimental structural information is new and will serve as a platform for future drug design. The data also illustrate the utility of cinematographic recording of dynamic motions of molecules for the study of self-organization processes.


transmission electron microscopy
single molecule


Comments are not moderated before they are posted, but they can be removed by the site moderators if they are found to be in contravention of our Commenting Policy [opens in a new tab] - please read this policy before you post. Comments should be used for scholarly discussion of the content in question. You can find more information about how to use the commenting feature here [opens in a new tab] .
This site is protected by reCAPTCHA and the Google Privacy Policy [opens in a new tab] and Terms of Service [opens in a new tab] apply.