Nanoscale assembly in biological systems: from neuronal cytoskeletal proteins to curvature stabilizing lipids

Hierarchical assembly and modeling of DNA nanotube networks using Y-shaped DNA origami seeds

DNA nanotechnology offers many means to synthesize custom nanostructured materials from the ground up in a hierarchical fashion. While the assembly of DNA nanostructures from small (nanometer-scale) monomeric components has been studied extensively, how the hierarchical assembly of rigid or semi-flexible units produces multi-micron scale structures is less understood. Here we demonstrate a mechanism for assembling micron-scale semi-flexible DNA nanotubes into extended structures. These nanotubes assemble from nanometer-scale tile monomers into materials via heterogeneous nucleation from rigid, Y-shaped DNA origami seeds to form Y-seeded nanotube architectures. These structures then assemble into networks via nanotube end-to-end joining. We measure the kinetics of network growth and find that the assembly of networks can be approximated by a model of hierarchical assembly that assumes a single joining rate between DNA nanotube ends. Because the number of nucleation sites on Y-seeds and their spatial arrangement can be systematically varied by design, this hierarchical assembly process could be used to form a wide variety of networks and to understand the assembly mechanisms that lead to different types of material architectures at length scales of tens to hundreds of microns.

Ca2+ and Ag+ orient low-molecular weight amphiphile self-assembly into "nano-fishnet" fibrillar hydrogels with unusual β-sheet-like raft domains

Low-molecular weight gelators (LMWGs) are small molecules (M_w < ∼1 kDa), which form self-assembled fibrillar network (SAFiN) hydrogels in water when triggered by an external stimulus. A great majority of SAFiN gels involve an entangled network of self-assembled fibers, in analogy to a polymer in a good solvent. In some rare cases, a combination of attractive van der Waals and repulsive electrostatic forces drives the formation of bundles with a suprafibrillar hexagonal order. In this work, an unexpected micelle-to-fiber transition is triggered by Ca²⁺ or Ag⁺ ions added to a micellar solution of a novel glycolipid surfactant, whereas salt-induced fibrillation is not common for surfactants. The resulting SAFiN, which forms a hydrogel above 0.5 wt%, has a "nano-fishnet" structure, characterized by a fibrous network of both entangled fibers and β-sheet-like rafts, generally observed for silk fibroin, actin hydrogels or mineral imogolite nanotubes, but not known for SAFiNs. The β-sheet-like raft domains are characterized by a combination of cryo-TEM and SAXS and seem to contribute to the stability of glycolipid gels. Furthermore, glycolipid is obtained by fermentation from natural resources (glucose, rapeseed oil), thus showing that naturally engineered compounds can have unprecedented properties, when compared to the wide range of chemically derived amphiphiles.

Topological Connection between Vesicles and Nanotubes in Single-Molecule Lipid Membranes Driven by Head-Tail Interactions

Lipid nanotube-vesicle networks are important channels for intercellular communication and transport of matter. Experimentally observed in neighboring mammalian cells but also reproduced in model membrane systems, a broad consensus exists on their formation and stability. Lipid membranes must be composed of at least two molecular components, each stabilizing low (generally a phospholipid) and high curvatures. Strong anisotropy or enhanced conical shape of the second amphiphile is crucial for the formation of nanotunnels. Anisotropic driving forces generally favor nanotube protrusions from vesicles. In this work, we report the unique case of topologically connected nanotubes-vesicles obtained in the absence of directional forces, in single-molecule membranes, composed of an anisotropic bolaform glucolipid, above its melting temperature, T_m. Cryo-TEM and fluorescence confocal microscopy show the interconnection between vesicles and nanotubes in a single-phase region, between 60 and 90 °C under diluted conditions. Solid-state NMR demonstrates that the glucolipid can assume two distinct configurations, head-head and head-tail. These arrangements, seemingly of comparable energy above the T_m, could explain the existence and stability of the topologically connected vesicles and nanotubes, which are generally not observed for classical single-molecule phospholipid-based membranes above their T_m.

Identification of Lipid Heterogeneity and Diversity in the Developing Human Brain

The lipidome is currently understudied but fundamental to life. Within the brain, little is known about cell-type lipid heterogeneity, and even less is known about cell-to-cell lipid diversity because it is difficult to study the lipids within individual cells. Here, we used single-cell mass spectrometry-based protocols to profile the lipidomes of 154 910 single cells across ten individuals consisting of five developmental ages and five brain regions, resulting in a unique lipid atlas available via a web browser of the developing human brain. From these data, we identify differentially expressed lipids across brain structures, cortical areas, and developmental ages. We inferred lipid profiles of several major cell types from this data set and additionally detected putative cell-type specific lipids. This data set will enable further interrogation of the developing human brain lipidome.

Physical and chemical properties of carbon nanotubes in view of mechanistic neuroscience investigations. Some outlook from condensed matter, materials science and physical chemistry

The open border between non-living and living matter, suggested by increasingly emerging fields of nanoscience interfaced to biological systems, requires a detailed knowledge of nanomaterials properties. An account of the wide spectrum of phenomena, belonging to physical chemistry of interfaces, materials science, solid state physics at the nanoscale and bioelectrochemistry, thus is acquainted for a comprehensive application of carbon nanotubes interphased with neuron cells. This review points out a number of conceptual tools to further address the ongoing advances in coupling neuronal networks with (carbon) nanotube meshworks, and to deepen the basic issues that govern a biological cell or tissue interacting with a nanomaterial. Emphasis is given here to the properties and roles of carbon nanotube systems at relevant spatiotemporal scales of individual molecules, junctions and molecular layers, as well as to the point of view of a condensed matter or materials scientist. Carbon nanotube interactions with blood-brain barrier, drug delivery, biocompatibility and functionalization issues are also regarded.

Synchrotron small-angle X-ray scattering and electron microscopy characterization of structures and forces in microtubule/Tau mixtures

Tau, a neuronal protein known to bind to microtubules and thereby regulate microtubule dynamic instability, has been shown recently to not only undergo conformational transitions on the microtubule surface as a function of increasing microtubule coverage density (i.e., with increasing molar ratio of Tau to tubulin dimers) but also to mediate higher-order microtubule architectures, mimicking fascicles of microtubules found in the axon initial segment. These discoveries would not have been possible without fine structure characterization of microtubules, with and without applied osmotic pressure through the use of depletants. Herein, we discuss the two primary techniques used to elucidate the structure, phase behavior, and interactions in microtubule/Tau mixtures: transmission electron microscopy and synchrotron small-angle X-ray scattering. While the former is able to provide striking qualitative images of bundle morphologies and vacancies, the latter provides angstrom-level resolution of bundle structures and allows measurements in the presence of in situ probes, such as osmotic depletants. The presented structural characterization methods have been applied both to equilibrium mixtures, where paclitaxel is used to stabilize microtubules, and also to dissipative nonequilibrium mixtures at 37°C in the presence of GTP and lacking paclitaxel.

Polyelectrolyte properties of filamentous biopolymers and their consequences in biological fluids

Anionic polyelectrolyte filaments are common in biological cells. DNA, RNA, the cytoskeletal filaments F-actin, microtubules, and intermediate filaments, and polysaccharides such as hyaluronan that form the pericellular matrix all have large net negative charge densities distributed over their surfaces. Several filamentous viruses with diameters and stiffnesses similar to those of cytoskeletal polymers also have similar negative charge densities. Extracellular protein filaments such collagen, fibrin and elastin, in contrast, have notably smaller charge densities and do not behave as highly charged polyelectrolytes in solution. This review summarizes data that demonstrate generic counterion-mediated effects on four structurally unrelated biopolymers of similar charge density: F-actin, vimentin, Pf1 virus, and DNA, and explores the possible biological and pathophysiological consequences of the polyelectrolyte properties of biological filaments.

Tuning nanostructure dimensions with supramolecular twisting

Peptide amphiphiles are molecules containing a peptide segment covalently bonded to a hydrophobic tail and are known to self-assemble in water into supramolecular nanostructures with shape diversity ranging from spheres to cylinders, twisted ribbons, belts, and tubes. Understanding the self-assembly mechanisms to control dimensions and shapes of the nanostructures remains a grand challenge. We report here on a systematic study of peptide amphiphiles containing valine-glutamic acid dimeric repeats known to promote self-assembly into belt-like flat assemblies. We find that the lateral growth of the assemblies can be controlled in the range of 100 nm down to 10 nm as the number of dimeric repeats is increased from two to six. Using circular dichroism, the degree of β-sheet twisting within the supramolecular assemblies was found to be directly proportional to the number of dimeric repeats in the PA molecule. Interestingly, as twisting increased, a threshold is reached where cylinders rather than flat assemblies become the dominant morphology. We also show that in the belt regime, the width of the nanostructures can be decreased by raising the pH to increase charge density and therefore electrostatic repulsion among glutamic acid residues. The control of size and shape of these nanostructures should affect their functions in biological signaling and drug delivery.

Liquid crystal assemblies in biologically inspired systems

In this paper, which is part of a collection in honor of Noel Clark's remarkable career on liquid crystal and soft matter research, we present examples of biologically inspired systems, which form liquid crystal (LC) phases with their LC nature impacting biological function in cells or being important in biomedical applications. One area focuses on understanding network and bundle formation of cytoskeletal polyampholytes (filamentous-actin, microtubules, and neurofilaments). Here, we describe studies on neurofilaments (NFs), the intermediate filaments of neurons, which form open network nematic liquid crystal hydrogels in axons. Synchrotron small-angle-x-ray scattering studies of NF-protein dilution experiments and NF hydrogels subjected to osmotic stress show that neurofilament networks are stabilized by competing long-range repulsion and attractions mediated by the neurofilament's polyampholytic sidearms. The attractions are present both at very large interfilament spacings, in the weak sidearm-interpenetrating regime, and at smaller interfilament spacings, in the strong sidearm-interpenetrating regime. A second series of experiments will describe the structure and properties of cationic liposomes (CLs) complexed with nucleic acids (NAs). CL-NA complexes form liquid crystalline phases, which interact in a structure-dependent manner with cellular membranes enabling the design of complexes for efficient delivery of nucleic acid (DNA, RNA) in therapeutic applications.