Automated analysis of transmission electron micrographs of metallic nanoparticles by machine learning

Metallic nanoparticles were analysed with respect to size and shape by a machine learning approach. This involved a separation of particles from the background (segmentation), a separation of overlapping particles, and the identification of individual particles. An algorithm to separate overlapping particles, based on ultimate erosion of convex shapes (UECS), was implemented. Finally, particle properties like size, circularity, equivalent diameter, and Feret diameter were computed for each particle of the whole particle population. Thus, particle size distributions can be easily created based on the various parameters. However, strongly overlapping particles are difficult and sometimes impossible to separate because of an a priori unknown shape of a particle that is partially lying in the shadow of another particle. The program is able to extract information from a sequence of images of the same sample, thereby increasing the number of analysed nanoparticles to several thousands. The machine learning approach is well-suited to identify particles at only limited particle-to-background contrast as is demonstrated for ultrasmall gold nanoparticles (2 nm)

Viscoelastic dynamics of actin filaments coupled to rotary F-ATPase: angular torque profile of the enzyme.

ATP synthase (F(O)F(1)) operates as two rotary motor/generators coupled by a common shaft. Both portions, F(1) and F(O), are rotary steppers. Their symmetries are mismatched (C(3) versus C(10-14)). We used the curvature of fluorescent actin filaments, attached to the rotating c-ring, as a spring balance (flexural rigidity of 8. 10(-26) Nm(2)) to gauge the angular profile of the output torque at F(O) during ATP hydrolysis by F(1) (see theoretical companion article (. Biophys. J. 81:1234-1244.)). The large average output torque (50 +/- 6 pN. nm) proved the absence of any slip. Variations of the torque were small, and the output free energy of the loaded enzyme decayed almost linearly over the angular reaction coordinate. Considering the threefold stepping and high activation barrier of the driving motor proper, the rather constant output torque implied a soft elastic power transmission between F(1) and F(O). It is considered as essential, not only for the robust operation of this ubiquitous enzyme under symmetry mismatch, but also for a high turnover rate of the two counteracting and stepping motor/generators

Water-Based Synthesis of Ultrasmall Nanoparticles of Platinum Group Metal Oxides (1.8 nm)

Ultrasmall nanoparticles of platinum group metal oxides (core diameter of about 1.8 nm) were prepared by alkaline hydrolysis of metal precursors in the presence of NaBH4 and by colloidal stabilization with tripeptide glutathione. We obtained water-dispersed nanoparticles of Rh2O3, PdO, RuO2, IrO2, Os/OsO2, and Pt/PtO. Their size was probed using high-resolution transmission electron microscopy, differential centrifugal sedimentation, small-angle X-ray scattering, and diffusion-ordered 1H NMR spectroscopy (1H DOSY). Their oxidation state was clearly determined using X-ray photoelectron spectroscopy, X-ray powder diffraction, and electron diffraction. The chemical composition of the nanoparticles, that is, the ratio of the metal oxide core and glutathione capping agent, was quantitatively determined by a combination of these methods

Subunit Movements in Single Membrane-bound H+-ATP Synthases from Chloroplasts during ATP Synthesis

Subunit movements within the H+-ATP synthase from chloroplasts (CF0F1) are investigated during ATP synthesis. The γ-subunit (γCys-322) is covalently labeled with a fluorescence donor (ATTO532). A fluorescence acceptor (adenosine 5′-(β,γ-imino)triphosphate (AMPPNP)-ATTO665) is noncovalently bound to a noncatalytic site at one α-subunit. The labeled CF0F1 is integrated into liposomes, and a transmembrane pH difference is generated by an acid base transition. Single-pair fluorescence resonance energy transfer is measured in freely diffusing proteoliposomes with a confocal two-channel microscope. The fluorescence time traces reveal a repetitive three-step rotation of the γ-subunit relative to the α-subunit during ATP synthesis. Some traces show splitting into sublevels with fluctuations between the sublevels. During catalysis the central stalk interacts, with equal probability, with each αβ-pair. Without catalysis the central stalk interacts with only one specific αβ-pair, and no stepping between FRET levels is observed. Two inactive states of the enzyme are identified: one in the presence of AMPPNP and one in the presence of ADP

Torque Generation in F1-ATPase Devoid of the Entire Amino-Terminal Helix of the Rotor That Fills Half of the Stator Orifice

F1-ATPase is an ATP-driven rotary molecular motor in which the central γ-subunit rotates inside a cylinder made of α3β3 subunits. The amino and carboxyl termini of the γ rotor form a coiled coil of α-helices that penetrates the stator cylinder to serve as an axle. Crystal structures indicate that the axle is supported by the stator at two positions, at the orifice and by the hydrophobic sleeve surrounding the axle tip. The sleeve contacts are almost exclusively to the longer carboxyl-terminal helix, whereas nearly half the orifice contacts are to the amino-terminal helix. Here, we truncated the amino-terminal helix stepwise up to 50 residues, removing one half of the axle all the way up and far beyond the orifice. The half-sliced axle still rotated with an unloaded speed a quarter of the wild-type speed, with torque nearly half the wild-type torque. The truncations were made in a construct where the rotor tip was connected to a β-subunit via a short peptide linker. Linking alone did not change the rotational characteristics significantly. These and previous results show that nearly half the normal torque is generated if rotor-stator interactions either at the orifice or at the sleeve are preserved, suggesting that the make of the motor is quite robust