Magnetosomes are lipid-bound organelles that direct the biomineralization of magnetic nanoparticles in magnetotactic bacteria. Magnetosome membranes are not uniform in size and can grow in a biomineralization-dependent manner. However, the underlying mechanisms of magnetosome membrane growth regulation remain unclear. Using cryoelectron tomography, we systematically examined mutants with defects at various stages of magnetosome formation to identify factors involved in controlling membrane growth. We found that a conserved serine protease, MamE, plays a key role in magnetosome membrane growth regulation. When the protease activity of MamE is disrupted, magnetosome membrane growth is restricted, which, in turn, limits the size of the magnetite particles. Consistent with this finding, the upstream regulators of MamE protease activity, MamO and MamM, are also required for magnetosome membrane growth. We then used a combination of candidate and comparative proteomics approaches to identify Mms6 and MamD as two MamE substrates. Mms6 does not appear to participate in magnetosome membrane growth. However, in the absence of MamD, magnetosome membranes grow to a larger size than the wild type. Furthermore, when the cleavage of MamD by MamE protease is blocked, magnetosome membrane growth and biomineralization are severely inhibited, phenocopying the MamE protease-inactive mutant. We therefore propose that the growth of magnetosome membranes is controlled by a protease-mediated switch through processing of MamD. Overall, our work shows that, like many eukaryotic systems, bacteria control the growth and size of biominerals by manipulating the physical properties of intracellular organelles.

We apply electron microscopy to evaluate the structure of spherulites in films of linear low density polyethylene (LLDPE). Improvements in this imaging technique allow us to show that the spherulites consist of two crossing patterns of lamellar stacks; one type of stack is composed of the usual radial lamellae while the second type of lamellae stacks is tangential. Radial lamellae are thicker and have a helical twist while tangential lamellae do not twist but rather create parallel stacks. The observed structure is akin to the structure frequently encountered in spherulites of polypropylene and shows the same dependence on crystallization temperature. At the same time the formation mechanism must be different from widely discussed epitaxial overgrowth in polypropylene because the polyethylene orthorhombic crystal lattice does not provide the same matching of lattice parameters as alpha phase of polypropylene.

We introduce a novel composite holey gold support that prevents cryo-crinkling and reduces beam-induced motion of soft specimens, building on the previously introduced all-gold support. The composite holey gold support for high-resolution cryogenic electron microscopy of soft crystalline membranes was fabricated in two steps. In the first step, a holey gold film was transferred on top of a molybdenum grid. In the second step, a continuous thin carbon film was transferred onto the holey gold film. This support (Au/Mo grid) was used to image crystalline synthetic polymer membranes. The low thermal expansion of Mo is not only expected to avoid cryo-crinkling of the membrane when the grids are cooled to cryogenic temperatures, but it may also act to reduce whatever crinkling existed even before cooling. The Au/Mo grid exhibits excellent performance with specimens tilted to 45°. This is demonstrated by quantifying beam-induced motion and differences in local defocus values. In addition, images of specimens on the Au/Mo grids that are tilted at 45° show high-resolution information of the crystalline membranes that, after lattice-unbending, extends beyond 1.5 Å in the direction perpendicular to the tilt axis.

The essential 2D crystalline nanostructure comprising synthetic polymers is single crystal that was observed in solution and in melt. The structure of polyethylene (PE) single crystal lamellae grown from solution was studied by using electron diffraction in landmark studies dating back to 1938[1]. Protein-based 2D crystalline membranes, such like purple membrane, were intensively investigated as early as 1975 by Handerson and Unwin[2]. It was later resolved at 3.5 Å resolution in Henderson, Baldwin, Downing, Lepault and Zemlin’s co-authored work by applying crystal unbending protocols to the low-dose electron micrographs[3]. The resolution of structures resolved from radiation sensitive soft materials, in particular biomaterials, has been significantly improved years to the introduction of direct electron detectors and the development of novel image processing algorithms for cryo-EM imaging. Imaging synthetic soft materials with atomic resolution using electron microscopy is still challenging because synthetic soft materials are heterogeneous as compared to natural biomaterials. We designed a series of hydrophilic poly(N-2-(2-(2-methoxyethoxy)ethoxy)ethylglycine) Our experiments conducted on the crystalline nanosheets formed by self-assembly of these

Vesicle formation in a series of amphiphilic sequence-defined polypeptoid block co-polymers comprising a phosphonated hydrophilic block and an amorphous hydrophobic block, poly- N-(2-ethyl)hexylglycine- block-poly- N-phosphonomethylglycine (pNeh- b-pNpm), is studied. The hydrophobic/hydrophilic block ratio was varied keeping the total chain length of the co-polymers constant. A new approach for characterizing the vesicle membrane morphology based on low-dose cryogenic electron microscopy (cryo-EM) is described. The individual low-dose micrographs cannot be interpreted directly due to low signal-to-noise ratio. Sorting and averaging techniques, developed in the context of protein structure determination, were thus applied to vesicle micrographs. Molecular dynamic simulations of the vesicles were used to establish the relationship between membrane morphology and averaged cryo-EM images. This approach enables resolution of the local thickness of the hydrophobic membrane core at the 1 nm length scale. The thickness of the hydrophobic core of the pNeh- b-pNpm membranes increases linearly with the length of the hydrophobic block.

The self-assembly of micellar structures from diblock polymers that contain hydrophilic and hydrophobic domains has been of great interest for the encapsulation of drugs and other hydrophobic molecules. While most commercially used surfactants are derived from hydrocarbon sources, there have been recent efforts to replace these with biodegradable, nontoxic, biologically synthesized alternatives. Previous examples have primarily examined naturally occurring self-assembling proteins, such as silk and elastin-like sequences. Herein, we describe a new series of fusion proteins that have been developed to self-assemble spontaneously into stable micelles that are 27 nm in diameter after enzymatic cleavage of a solubilizing protein tag. The sequences of the proteins are based on a human intrinsically disordered protein, which has been appended with a hydrophobic segment. The micelles were found to form across a broad range of pH, ionic strength, and temperature conditions, with critical micelle concentration (CMC) values in the low micromolar range, 3 orders of magnitude lower than the CMC of commonly used surfactant sodium dodecyl sulfate (SDS). The reported micelles were found to solubilize hydrophobic metal complexes and organic molecules, suggesting their potential suitability for catalysis and drug delivery applications. Furthermore, the inherent flexibility in the design of these protein sequences enables the encoding of additional functionalities for many future applications. Overall, this work represents a new biomolecular alternative to traditional surfactants that are based on nonrenewable and poorly biodegradable hydrocarbon sources.

When polymer melt is subjected to stress, molecular chains become aligned along the elongation direction. However, when polyethylene film crystallizes under stress, molecular chains frequently align perpendicular to the elongation direction. In this paper we investigate why this happens. Evaluating metallocene LLDPE film we show that under the stress lamellae rotate to accommodate geometrical changes. Quantitative analysis of SAXS data explains the mechanism of this rotation. The lamellae rotation presents an opportunity to reexamine the strain-induced structure and crystallization mechanism. For the first time we apply 3D visualization to shishkebab like structure in bulk samples and support visualization with Fourier analysis to relate the microscopy data to large body of evidence reported earlier by SAXS. Obtained evidence reveals that our samples do not contain extended chain precursors. Reevaluation of the equatorial streak, frequently interpreted as evidence of extended chain precursors or voids, suggests that in our sample the streak originates from rotated lamellae. Our findings indicate that strain-induced crystallization does not have to rely on the existence of extended chains precursors, as is widely assumed. While the major findings from this work are derived from microscopy investigations we supplement these with limited amount of SAXS and WAXS experiments to help elucidate the rotation mechanism and crystalline orientation. The insight dervied from this study reconciles seemingly contradictory SAXS, WAXS, TEM and optical microscopy data collected from polyethylene film.

Calcium calmodulin dependent kinase (CaMKII) has an important role in dendritic spine remodelling upon synaptic stimulation. Using fluorescence video microscopy and image analysis, we investigated the architectural dynamics of rhodamine-phalloidin stabilized F-actin networks cross-linked by CaMKII. We used automated image analysis to identify F-actin bundles and cross-over junctions and developed a dimensionless metric to characterize network architecture. Similar networks were formed by three different CaMKII species with ten-fold length difference in the linker region between the kinase domain and holoenzyme hub; implying linker length is not a primary determinant of F-actin binding. Electron micrographs showed that, at physiological molar ratios, single CaMKII holoenzymes cross-linked multiple F-actin filaments in random networks, whereas at higher CaMKII / F-actin ratios filaments bundled. Light microscopy established that random networks resisted macromolecular crowding, with polyethylene glycol mimicking cytoplasmic osmolarity, and blocked ATP-powered compaction by myosin-2 mini-filaments. Importantly, the networks disassembled following addition of calcium calmodulin and were then rapidly spaced into compacted foci by myosin motors or, more slowly, aggregated by crowding. Single molecule TIRF microscopy showed CaMKII dissociation from surface-immobilized G-actin exhibited a mono-exponential dwell-time distribution, whereas CaMKII bound to F-actin networks had a long-lived fraction, trapped at cross-over junctions. Release of CaMKII from F-actin, triggered by calcium calmodulin did not require ATP (hence phosphorylation) and was too rapid to measure with video-rate imaging. The residual bound-fraction was reduced substantially upon addition of an NMDA receptor peptide analogue. These results provide mechanistic insights to CaMKII-actin interactions at the collective network and single molecule level. Our findings argue that CaMKII-actin networks in dendritic spines are stable enough to protect the basal network architecture against physical stress but once CaMKII is disengaged by calcium calmodulin and sequestered by receptors at the synapse; F-actin compaction by myosin motors stabilizes the expanded spine compatible with the recorded times.

The extent to which the resolution varies within a three-dimensional (3-D) reconstruction, when the diameter of an object is large, is investigated computationally. Numerical simulation is used to model ideal three-dimensional point-spread functions at different radial positions within an object. It is shown that reconstructed density maps are affected less than might have been expected when particles are larger than the depth of field. This favorable outcome is attributed mainly to the fact that a point which lies outside the depth of field relative to the center, for some orientations of the object, will also lie within the depth of field for other orientations. We find, as a result, that the diameter of a particle can be as much as four times the depth of field (as defined by a 90° phase-error criterion) before curvature of the Ewald sphere becomes a limiting factor in determining the resolution that can be achieved.

Properties of soft crystalline materials such as synthetic polymers are governed by locations of constituent atoms. Determining atomic-scale structures in these materials is difficult because they degrade rapidly when studied by electron microscopy, and techniques such as X-ray scattering average over volumes much larger than coherent blocks of the unit cells. We obtained cryo-electron microscopy images of self-assembled nanosheets of a peptoid polymer, made by solid-phase synthesis, in which we see a variety of crystalline motifs. A combination of crystallographic and single-particle methods, developed for cryo-electron microscopy of biological macromolecules, was used to obtain high-resolution images of the crystals. Individual crystals contain grains that are mirror images of each other with concomitant grain boundaries. We have used molecular dynamic simulations to build an atomic model of the crystal structure to facilitate the interpretation of electron micrographs. Direct visualization of crystalline grains and grain boundaries on atomic length scales represents a new level of information for the polymer field.

It is known that the addition of salts to symmetric block copolymers leads to stabilization of ordered phases and an increase in domain spacing; both trends are consistent with an increase in the effective Flory-Huggins interaction parameter between the blocks, χ. In this work, we show that the addition of salt to a disordered asymmetric block copolymer first leads to the formation of coexisting ordered phases which give way to a reentrant disordered phase at a higher salt concentration. The coexisting phases are both body centered cubic (BCC) with different domain spacings, stabilized by partitioning of the salt. Further increase in salt concentration results in yet another disorder-to-order transition; hexagonally packed cylinders are obtained in the high salt concentration limit. The coexisting phases formed at intermediate salt concentration, elucidated by electron tomography, showed the absence of macroscopic regions with distinct BCC lattices. A different asymmetric block copolymer with composition in the vicinity of the sample described above only showed only a single disorder-to-order transition. However, the dependence of domain spacing on salt concentration was distinctly non-monotonic, and similar to that of the sample with the reentrant phase behavior. This dependence appears to be an announcement of reentrant phase transitions in asymmetric block copolymer electrolytes. These results cannot be mapped on to the traditional theory of block copolymer electrolyte self-assembly based on an effective χ.

Calcium-calmodulin-dependent kinase II (CaMKII) has an important role in dendritic spine remodeling upon synaptic stimulation. Using fluorescence video microscopy and image analysis, we investigated the architectural dynamics of rhodamine-phalloidin stabilized filamentous actin (F-actin) networks cross-linked by CaMKII. We used automated image analysis to identify F-actin bundles and crossover junctions and developed a dimensionless metric to characterize network architecture. Similar networks were formed by three different CaMKII species with a 10-fold length difference in the linker region between the kinase domain and holoenzyme hub, implying linker length is not a primary determinant of F-actin cross-linking. Electron micrographs showed that at physiological molar ratios, single CaMKII holoenzymes cross-linked multiple F-actin filaments at random, whereas at higher CaMKII/F-actin ratios, filaments bundled. Light microscopy established that the random network architecture resisted macromolecular crowding with polyethylene glycol and blocked ATP-powered compaction by myosin-II miniature filaments. Importantly, the networks disassembled after the addition of calcium-calmodulin and were then spaced within 3 min into compacted foci by myosin motors or more slowly (30 min) aggregated by crowding. Single-molecule total internal reflection fluorescence microscopy showed CaMKII dissociation from surface-immobilized globular actin exhibited a monoexponential dwell-time distribution, whereas CaMKII bound to F-actin networks had a long-lived fraction, trapped at crossover junctions. Release of CaMKII from F-actin, triggered by calcium-calmodulin, was too rapid to measure with flow-cell exchange (<20 s). The residual bound fraction was reduced substantially upon addition of an N-methyl-D-aspartate receptor peptide analog but not ATP. These results provide mechanistic insights to CaMKII-actin interactions at the collective network and single-molecule level. Our findings argue that CaMKII-actin networks in dendritic spines maintain spine size against physical stress. Upon synaptic stimulation, CaMKII is disengaged by calcium-calmodulin, triggering network disassembly, expansion, and subsequent compaction by myosin motors with kinetics compatible with the times recorded for the poststimulus changes in spine volume.

Tau is a developmentally regulated protein found in axons, whose physiological role is to stabilize and bundle microtubules (MTs). Hyper-phosphorylation of tau is thought to cause its detachment from MTs and subsequent aggregation into pathological fibrils that have been implicated in Alzheimer’s disease pathogenesis. Despite its known MT binding role, there is no consensus regarding which tau residues are crucial for tau-MT interactions, where on the MT tau binds, and how binding results in MT stabilization. We have used cryo-EM to visualize the interaction of different tau constructs with MTs at high resolution (3.2-4.8 Å) and used computational approaches to generate atomic models of tau-tubulin interactions. Our work shows that the highly conserved tubulin-binding repeats within tau adopt very similar structures in their interactions with the MT. Each tau repeat binds the MT exterior and adopts an extended structure along the crest of the protofilament (PF), interacting with both α- and β-tubulin, thus stabilizing the interface between tubulin dimers. Our structures agree with and explain previous biochemical data concerning the effect of phosphorylation on MT affinity and lead to a model in which tau repeats bind in tandem along a PF, tethering together tubulin dimers and stabilizing longitudinal polymerization interfaces. These structural findings could establish a basis of future treatments aiming at the selective stabilization of tau-MT interactions.

Tau is a developmentally regulated axonal protein that stabilizes and bundles microtubules (MTs). Its hyperphosphorylation is thought to cause detachment from MTs and subsequent aggregation into fibrils implicated in Alzheimer's disease. It is unclear which tau residues are crucial for tau-MT interactions, where tau binds on MTs, and how it stabilizes them. We used cryo-electron microscopy to visualize different tau constructs on MTs and computational approaches to generate atomic models of tau-tubulin interactions. The conserved tubulin-binding repeats within tau adopt similar extended structures along the crest of the protofilament, stabilizing the interface between tubulin dimers. Our structures explain the effect of phosphorylation on MT affinity and lead to a model of tau repeats binding in tandem along protofilaments, tethering together tubulin dimers and stabilizing polymerization interfaces.

Herein, we describe a new series of fusion proteins that have been developed to self-assemble spontaneously into stable micelles that are 27 nm in diameter after enzymatic cleavage of a solubilizing protein tag. The sequences of the proteins are based on a human intrinsically disordered protein, which has been appended with a hydrophobic segment. The micelles were found to form across a broad range of pH, ionic strength, and temperature conditions, with critical micelle concentration (CMC) values below 1 µM being observed in some cases. The reported micelles were found to solubilize hydrophobic metal complexes and organic molecules, suggesting their potential suitability for catalysis and drug delivery applications.

Mammalian diacylglycerol kinases (DGKs) are a group of enzymes that catalyze the ATP-dependent phosphorylation of diacylglycerol (DAG) to produce phosphatidic acid (PtdOH). In doing so, they modulate the levels of these two important signaling lipids. Currently, ten mammalian DGKs are organized into five classes that vary with respect to domain organization, regulation, and cellular/subcellular distribution.As lipids play critical roles in cells, it is not surprising that there is increasing interest in understanding the mechanism underlying the catalysis and regulation of lipid modulating enzymes such as DGKs. However, there are no solved 3D structures for any of the eukaryotic DGKs. In this review, we summarize what is known and the current challenges in determining the structures of these important enzymes. In addition to gain critical insights into their mechanisms of catalysis and regulation, DGK structures will provide a platform for the design of isoform specific inhibitors.

Journal Article Accurate Cryo-EM Characterizations of Polypeptoid Vesicles Get access Xi Jiang, Xi Jiang Materials Science Division Search for other works by this author on: Oxford Academic Google Scholar Jing Sun, Jing Sun Molecular FoundryQingdao University of Science and Technology, Qingdao, China 266042 Search for other works by this author on: Oxford Academic Google Scholar Ronald N Zuckermann, Ronald N Zuckermann Molecular Foundry Search for other works by this author on: Oxford Academic Google Scholar Nitash P Balsara, Nitash P Balsara Materials Science DivisionDepartment of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720 Search for other works by this author on: Oxford Academic Google Scholar Kenneth H Downing Kenneth H Downing Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Lab, Berkeley CA, 94720 Search for other works by this author on: Oxford Academic Google Scholar Microscopy and Microanalysis, Volume 23, Issue S1, 1 July 2017, Pages 836–837, https://doi.org/10.1017/S1431927617004846 Published: 04 August 2017