Fig. 3: Sub-MIC Dap on POPG at 37 °C. First minutes. Initial stages.
From: High-speed atomic force microscopy highlights new molecular mechanism of daptomycin action
a Oligomers of Dap in diffusion on a membrane (slashed circles). The upper left image shows the membrane and the underlying mica substrate (colour scale: 4 nm). The rest of the images are close-ups on top of the membrane (colour scale: 2 nm): The oligomers formed temporary ensembles (slashed ellipses), but they did not form permanent clusters. Movie details: frame rate 74 ms; full image size 180 nm × 60 nm; full-frame size 256 × 80 pixels. a, right, The particle analysis (right bottom, one of the frames analysed; right top, histogram) shows a spread in the area of the oligomers from 2 to 10 nm2, a peak value of 4.3 nm2, and a mean and standard deviation of 5.4 ± 3.2 nm2; which corresponds to a stoichiometric variability maximal of 1 to 6 monomers, and mean and standard deviation of 3.6 ± 2.1 monomers. The oligomers experience mutual attraction at short distances. b, left, Oligomer-oligomer energy profile obtained from the spatial distribution of oligomer-oligomer distances. The area fraction of the oligomers on the membrane is of ~0.04. b, centre, Minima are found at distances between oligomers of ~7 and ~16 nm. The count at far distance (count ∞) can be calculated to be ~1.12 (area fraction occupied by the oligomers (0.04; ~4% of the total membrane area) multiplied by the number of frames counted (n = 28), horizontal white line at d > 30 nm) in agreement with the count at d > 30 nm. b, right, Equilibrium Boltzmann distribution energy profile derived from U(d) = −kbTln[count (d)/count ∞]; the depthless of the energy wells is estimated to be of −3.4 kBT at d = 7 nm and −2.8 kBT at d = 16 nm. c These 32 frames (2.821 s) show a pair of oligomers in interaction. c, right, From the count of d, the energy profile features one global (d = 7 nm) and one local (d = 16 nm) minima. Because the oligomer-oligomer interaction is ergodic and, as expected, the interaction profile in space is similar to interaction profile in time. This allows to derive the energy values of the interaction profile in time from the in space results.
