Taylor Dispersion-Induced Phase Separation for the Efficient Characterisation of Protein Condensate Formation.

Biomolecular condensates have emerged as important structures in cellular function and disease, and are thought to form through liquid-liquid phase separation (LLPS). Thorough and efficient in vitro experiments are therefore needed to elucidate the driving forces of protein LLPS and the possibility to modulate it with drugs. Here we present Taylor dispersion-induced phase separation (TDIPS), a method to robustly measure condensation phenomena using a commercially available microfluidic platform. It uses only nanoliters of sample, does not require extrinsic fluorescent labels, and is straightforward to implement. We demonstrate TDIPS by screening the phase behaviour of two proteins that form biomolecular condensates in vivo, PGL-3 and Ddx4. Uniquely accessible to this method, we find an unexpected re-entrant behaviour at very low ionic strength, where LLPS is inhibited for both proteins. TDIPS can also probe the reversibility of assemblies, which was shown for both α-synuclein and for lysozyme, relevant for health and biotechnology, respectively. Finally, we highlight how effective inhibition concentrations and partitioning of LLPS-modifying compounds can be screened highly efficiently.

Mass photometric detection and quantification of nanoscale α-synuclein phase separation.

Protein liquid-liquid phase separation can lead to disease-related amyloid fibril formation. The mechanisms of conversion of monomeric protein into condensate droplets and of the latter into fibrils remain elusive. Here, using mass photometry, we demonstrate that the Parkinson's disease-related protein, α-synuclein, can form dynamic nanoscale clusters at physiologically relevant, sub-saturated concentrations. Nanoclusters nucleate in bulk solution and promote amyloid fibril formation of the dilute-phase monomers upon ageing. Their formation is instantaneous, even under conditions where macroscopic assemblies appear only after several days. The slow growth of the nanoclusters can be attributed to a kinetic barrier, probably due to an interfacial penalty from the charged C terminus of α-synuclein. Our findings reveal that α-synuclein phase separation occurs at much wider ranges of solution conditions than reported so far. Importantly, we establish mass photometry as a promising methodology to detect and quantify nanoscale precursors of phase separation. We also demonstrate its general applicability by probing the existence of nanoclusters of a non-amyloidogenic protein, Ddx4n1.

Protein nanofibril design via manipulation of hydrogen bonds.

The process of amyloid nanofibril formation has broad implications including the generation of the strongest natural materials, namely silk fibers, and their major contribution to the progression of many degenerative diseases. The key question that remains unanswered is whether the amyloidogenic nature, which includes the characteristic H-bonded ß-sheet structure and physical characteristics of protein assemblies, can be modified via controlled intervention of the molecular interactions. Here we show that tailored changes in molecular interactions, specifically in the H-bonded network, do not affect the nature of amyloidogenic fibrillation, and even have minimal effect on the initial nucleation events of self-assembly. However, they do trigger changes in networks at a higher hierarchical level, namely enhanced 2D packaging which is rationalized by the 3D hierarchy of ß-sheet assembly, leading to variations in fibril morphology, structural composition and, remarkably, nanomechanical properties. These results pave the way to a better understanding of the role of molecular interactions in sculpting the structural and physical properties of protein supramolecular constructs.

The Kinetics, Thermodynamics and Mechanisms of Short Aromatic Peptide Self-Assembly.

The self-assembly of short aromatic peptides and peptide derivatives into a variety of different nano- and microstructures (fibrillar gels, crystals, spheres, plates) is a promising route toward the creation of bio-compatible materials with often unexpected and useful properties. Furthermore, such simple self-assembling systems have been proposed as model systems for the self-assembly of longer peptides, a process that can be linked to biological function and malfunction. Much effort has been made in the last 15 years to explore the space of peptide sequences, chemical modifications and solvent conditions in order to maximise the diversity of assembly morphologies and properties. However, quantitative studies of the corresponding mechanisms of, and driving forces for, peptide self-assembly have remained relatively scarce until recently. In this chapter we review the current state of understanding of the thermodynamic driving forces and self-assembly mechanisms of short aromatic peptides into supramolecular structures. We will focus on experimental studies of the assembly process and our perspective will be centered around diphenylalanine (FF), a key motif of the amyloid ß sequence and a paradigmatic self-assembly building block. Our main focus is the basic physical chemistry and key structural aspects of such systems, and we will also compare the mechanism of dipeptide aggregation with that of longer peptide sequences into amyloid fibrils, with discussion on how these mechanisms may be revealed through detailed analysis of growth kinetics, thermodynamics and other fundamental properties of the aggregation process.

Self-Assembly-Mediated Release of Peptide Nanoparticles through Jets Across Microdroplet Interfaces.

The release of nanoscale structures from microcapsules, triggered by changes in the capsule in response to external stimuli, has significant potential for active component delivery. Here, we describe an orthogonal strategy for controlling molecular species' release across oil/water interfaces by modulating their intrinsic self-assembly state. We show that although the soluble peptide Boc-FF can be stably encapsulated for days, its self-assembly into nanostructures triggers jet-like release within seconds. Moreover, we exploit this self-assembly-mediated release to deliver other molecular species that are transported as cargo. These results demonstrate the role of self-assembly in modulating the transport of peptides across interfaces.

Fibrous Protein Self-Assembly in Biomimetic Materials.

Protein self-assembly processes, by which polypeptides interact and independently form multimeric structures, lead to a wide array of different endpoints. Structures formed range from highly ordered molecular crystals to amorphous aggregates. Order arises in the system from a balance between many low-energy processes occurring due to a set of interactions between residues in a chain, between residues in different chains, and between solute and solvent. In Nature, self-assembling protein systems have evolved over millions of years to organize into supramolecular structures, optimized for specific functions, with this propensity determined by the sequence of their constituent amino acids, of which only 20 are encoded in DNA. The structural materials that arise from biological self-assembly can display remarkable mechanical properties, often as a result of hierarchical structure on the nano- and microscales, and much research has been devoted to mimicking and exploiting these properties for a variety of end uses. This work presents a review of a range of studies in which biological functions are effectively reproduced through the design of self-assembling fibrous protein systems.

Thermodynamics of Polypeptide Supramolecular Assembly in the Short-Chain Limit.

The self-assembly of peptides into ordered supramolecular structures, such as fibrils and crystals, is of relevance in such diverse areas as molecular medicine and materials science. However, little information is available about the fundamental thermodynamic driving forces of these types of self-assembly processes. Here, we investigate in detail the thermodynamics of assembly of diphenylalanine (FF). This dipeptide forms the central motif of the Aß peptides, which are associated with Alzheimer's disease through their presence in amyloid plaques in the nervous systems of affected individuals. We identify the molecular origins of the self-assembly of FF in aqueous solution, and we evaluate these findings in the context of the aggregation free energies of longer peptides that are able to form amyloid fibrils. We find that the thermodynamics of FF assembly displays the typical characteristics of hydrophobic desolvation processes, and detailed analysis of the temperature dependence of the kinetics of assembly within the framework of crystallization theories reveals that the transition state from solution to crystalline aggregates is enthalpically unfavorable and entropically favorable, qualitatively similar to what has been found for longer sequences. This quantitative comparison of aggregating peptides of very different lengths is the basis of an in-depth understanding of the relationship between sequence and assembly behavior.

Synthesis of Nonequilibrium Supramolecular Peptide Polymers on a Microfluidic Platform.

The self-assembly of peptides and peptide mimetics into supramolecular polymers has been established in recent years as a route to biocompatible nanomaterials with novel mechanical, optical, and electronic properties. The morphologies of the resulting polymers are usually dictated by the strengths as well as lifetimes of the noncovalent bonds that lead to the formation of the structures. Together with an often incomplete understanding of the assembly mechanisms, these factors limit the control over the formation of polymers with tailored structures. Here, we have developed a microfluidic flow reactor to measure growth rates directly and accurately on the axial and radial faces of crystalline peptide supramolecular polymers. We show that the structures grow through two-dimensional nucleation mechanisms, with rates that depend exponentially on the concentration of soluble peptide. Using these mechanistic insights into the growth behavior of the axial and radial faces, we have been able to tune the aspect ratio of populations of dipeptide assemblies. These results demonstrate a general strategy to control kinetically self-assembly beyond thermodynamic products governed by the intrinsic properties of the building blocks in order to attain the required morphology and function.

Discovery of a ternary pseudobrookite phase in the earth-abundant Ti-Zn-O system.

We combine theory with experiment in searching for "missing", stable materials within the Zn-Ti-O chemical system, leading to the discovery of a new pseudobrookite phase, ZnxTi3-xO5-δ. This ternary system was chosen for (1) technological relevance, (2) earth abundance, and (3) the fact that many compounds in this system are predicted from enthalpies of formation to be borderline stable, suggesting an important role of entropic contributions in their stabilization and making this chemical system a perfect test bed for exploring the limits of theoretical predictions. The initial set of exploratory experimental syntheses, via sintering in evacuated ampoules and quenching, resulted in a single phase ZnxTi3-xO5-δ composition with x ≈ 0.6 and an almost stoichiometric oxygen content, as evaluated by X-ray fluorescence, energy dispersive spectroscopy, thermogravimetric analysis, and X-ray photoelectron spectroscopy. The theoretically calculated lowest energy crystal structure for the closest stoichiometric ZnTi5O10 composition matched that measured experimentally by synchrotron X-ray diffraction (allowing for differences attributable to cation disorder). The measured broad optical absorption, n-type electrical conductivity, and stability in acidic media are comparable to those of other ternary pseudobrookites and Ti-O Magnéli phases, suggesting comparable applicability as a robust electrode or catalyst support in electrochemical devices or water remediation. However, the new phase decomposes upon heating in air as it oxidizes. The success of the present approach to identify a "missing material" in an earth-abundant and applications-rich system suggests that future efforts to experimentally realize and theoretically confirm missing materials in this and similar systems are warranted, both scientifically and technologically.

Micro- and nanoscale hierarchical structure of core-shell protein microgels.

Protein nanofibrils were first discovered in the context of misfolding and neurodegenerative diseases but have recently been found in naturally occurring functional materials including algal adhesives, bacterial coatings, and even mammalian melanosomes. These physiologically beneficial roles have led to the exploration of their use as the basis for artificial protein-based functional materials for a range of applications as bioscaffolds and carrier agents. In this work, we fabricate core-shell protein microgels stabilized by protein fibrillation with hierarchical structuring on scales ranging from a few nanometers to tens of microns. With the aid of droplet microfluidics, we exploit fibrillar protein self-assembly together with the aqueous phase separation of a polysaccharide and polyethylene glycol to control the internal structure of the microgels on the micro- and nanoscales. We further elucidate the local composition, morphology, and structural characteristics of the microgels and demonstrate a potential application of core-shell protein microgels for controlling the storage and sequential release of small drug-like molecules. The controlled self-assembly of protein nanofibrils into hierarchical structures can be used in this manner to generate a class of nanomaterials with a range of potential functions and applications.

Design and discovery of a novel half-Heusler transparent hole conductor made of all-metallic heavy elements.

Transparent conductors combine two generally contradictory physical properties, but there are numerous applications where both functionalities are crucial. Previous searches focused on doping wide-gap metal oxides. Focusing instead on the family of 18 valence electron ternary ABX compounds that consist of elements A, B and X in 1:1:1 stoichiometry, we search theoretically for electronic structures that simultaneously lead to optical transparency while accommodating intrinsic defect structures that produce uncompensated free holes. This leads to the prediction of a stable, never before synthesized TaIrGe compound made of all-metal heavy atom compound. Laboratory synthesis then found it to be stable in the predicted crystal structure and p-type transparent conductor with a strong optical absorption peak at 3.36 eV and remarkably high hole mobility of 2,730 cm(2) V(-1) s(-1) at room temperature. This methodology opens the way to future searches of transparent conductors in unexpected chemical groups.

Protein microgels from amyloid fibril networks.

Nanofibrillar forms of proteins were initially recognized in the context of pathology, but more recently have been discovered in a range of functional roles in nature, including as active catalytic scaffolds and bacterial coatings. Here we show that protein nanofibrils can be used to form the basis of monodisperse microgels and gel shells composed of naturally occurring proteins. We explore the potential of these protein microgels to act as drug carrier agents, and demonstrate the controlled release of four different encapsulated drug-like small molecules, as well as the component proteins themselves. Furthermore, we show that protein nanofibril self-assembly can continue after the initial formation of the microgel particles, and that this process results in active materials with network densities that can be modulated in situ. We demonstrate that these materials are nontoxic to human cells and that they can be used to enhance the efficacy of antibiotics relative to delivery in homogeneous solution. Because of the biocompatibility and biodegradability of natural proteins used in the fabrication of the microgels, as well as their ability to control the release of small molecules and biopolymers, protein nanofibril microgels represent a promising class of functional artificial multiscale materials generated from natural building blocks.

Ostwald's rule of stages governs structural transitions and morphology of dipeptide supramolecular polymers.

The self-assembly of molecular building blocks into nano- and micro-scale supramolecular architectures has opened up new frontiers in polymer science. Such supramolecular species not only possess a rich set of dynamic features as a consequence of the non-covalent nature of their core interactions, but also afford unique structural characteristics. Although much is now known about the manner in which such structures adopt their morphologies and size distributions in response to external stimuli, the kinetic and thermodynamic driving forces that lead to their transformation from soluble monomeric species into ordered supramolecular entities have remained elusive. Here we focus on Boc-diphenylalanine, an archetypical example of a peptide with a high propensity towards supramolecular self-organization, and describe the pathway through which it forms a range of nano-assemblies with different structural characteristics. Our results reveal that the nucleation process is multi-step in nature and proceeds by Ostwald's step rule through which coalescence of soluble monomers leads to the formation of nanospheres, which then undergo ripening and structural conversions to form the final supramolecular assemblies. We characterize the structures and thermodynamics of the different phases involved in this process and reveal the intricate nature of the transitions that can occur between discrete structural states of this class of supramolecular polymers.

Nanoscale spatially resolved infrared spectra from single microdroplets.

Droplet microfluidics has emerged as a powerful platform allowing a large number of individual reactions to be carried out in spatially distinct microcompartments. Due to their small size, however, the spectroscopic characterisation of species encapsulated in such systems remains challenging. In this paper, we demonstrate the acquisition of infrared spectra from single microdroplets containing aggregation-prone proteins. To this effect, droplets are generated in a microfluidic flow-focussing device and subsequently deposited in a square array onto a ZnSe prism using a micro stamp. After drying, the solutes present in the droplets are illuminated locally by an infrared laser through the prism, and their thermal expansion upon absorption of infrared radiation is measured with an atomic force microscopy tip, granting nanoscale resolution. Using this approach, we resolve structural differences in the amide bands of the spectra of monomeric and aggregated lysozyme from single microdroplets with picolitre volume.

Expanding the solvent chemical space for self-assembly of dipeptide nanostructures.

Nanostructures composed of short, noncyclic peptides represent a growing field of research in nanotechnology due to their ease of production, often remarkable material properties, and biocompatibility. Such structures have so far been almost exclusively obtained through self-assembly from aqueous solution, and their morphologies are determined by the interactions between building blocks as well as interactions between building blocks and water. Using the diphenylalanine system, we demonstrate here that, in order to achieve structural and morphological control, a change in the solvent environment represents a simple and convenient alternative strategy to the chemical modification of the building blocks. Diphenylalanine (FF) is a dipeptide capable of self-assembly in aqueous solution into needle-like hollow micro- and nanocrystals with continuous nanoscale channels that possess advantageous properties such as high stiffness and piezoelectricity and have so emerged as attractive candidates for functional nanomaterials. We investigate systematically the solubility of diphenylalanine in a range of organic solvents and probe the role of the solvent in the kinetics of self-assembly and the structures of the final materials. Finally, we report the crystal structure of the FF peptide in microcrystalline form grown from MeOH solution at 1 Å resolution and discuss the structural changes relative to the conventional materials self-assembled in aqueous solution. These findings provide a significant expansion of the structures and morphologies that are accessible through FF self-assembly for existing and future nanotechnological applications of this peptide. Solvent mediation of molecular recognition and self-association processes represents an important route to the design of new supramolecular architectures deriving their functionality from the nanoscale ordering of their components.

Self-Assembly of Amyloid Fibrils That Display Active Enzymes.

Enzyme immobilization is an important strategy to enhance the stability and recoverability of enzymes and to facilitate the separation of enzymes from reaction products. However, enzyme purification followed by separate chemical steps to allow immobilization on a solid support reduces the efficiency and yield of the active enzyme. Here we describe polypeptide constructs that self-assemble spontaneously into nanofibrils with fused active enzyme subunits displayed on the amyloid fibril surface. We measured the steady-state kinetic parameters for the appended enzymes in situ within fibrils and compare these with the identical protein constructs in solution. Finally, we demonstrated that the fibrils can be recycled and reused in functional assays both in conventional batch processes and in a continuous-flow microreactor.

Theoretical prediction and experimental realization of new stable inorganic materials using the inverse design approach.

Discovery of new materials is important for all fields of chemistry. Yet, existing compilations of all known ternary inorganic solids still miss many possible combinations. Here, we present an example of accelerated discovery of the missing materials using the inverse design approach, which couples predictive first-principles theoretical calculations with combinatorial and traditional experimental synthesis and characterization. The compounds in focus belong to the equiatomic (1:1:1) ABX family of ternary materials with 18 valence electrons per formula unit. Of the 45 possible V-IX-IV compounds, 29 are missing. Theoretical screening of their thermodynamic stability revealed eight new stable 1:1:1 compounds, including TaCoSn. Experimental synthesis of TaCoSn, the first ternary in the Ta-Co-Sn system, confirmed its predicted zincblende-derived crystal structure. These results demonstrate how discovery of new materials can be accelerated by the combination of high-throughput theoretical and experimental methods. Despite being made of three metallic elements, TaCoSn is predicted and explained to be a semiconductor. The band gap of this material is difficult to measure experimentally, probably due to a high concentration of interstitial cobalt defects.

Carrier generation in multicomponent wide-bandgap oxides: InGaZnO4.

To exploit the full potential of multicomponent wide-bandgap oxides, an in-depth understanding of the complex defect chemistry and of the role played by the constituent oxides is required. In this work, thorough theoretical and experimental investigations are combined in order to explain the carrier generation and transport in crystalline InGaZnO4. Using first-principles density functional approach, we calculate the formation energies and transition levels of possible acceptor and donor point defects as well as the implied defect complexes in InGaZnO4 and determine the equilibrium defect and electron densities as a function of growth temperature and oxygen partial pressure. An excellent agreement of the theoretical results with our Brouwer analysis of the bulk electrical measurements for InGaZnO4 establishes the Ga antisite defect, GaZn, as the major electron donor in InGaZnO4. Moreover, we show that the oxygen vacancies, long believed to be the carrier source in this oxide, are scarce. The proposed carrier generation mechanism also explains the observed intriguing behavior of the conductivity in In-rich vs Ga-rich InGaZnO4.

Transparent Conducting Oxides for Photovoltaics: Manipulation of Fermi Level, Work Function and Energy Band Alignment.

Doping limits, band gaps, work functions and energy band alignments of undoped and donor-doped transparent conducting oxides Zn0, In2O3, and SnO2 as accessed by X-ray and ultraviolet photoelectron spectroscopy (XPS/UPS) are summarized and compared. The presented collection provides an extensive data set of technologically relevant electronic properties of photovoltaic transparent electrode materials and illustrates how these relate to the underlying defect chemistry, the dependence of surface dipoles on crystallographic orientation and/or surface termination, and Fermi level pinning.

Bulk defect chemistry and surface electronic behavior of Zn,Sn codoped In(2)O(3) transparent conducting oxides.

The electrical properties of the zinc and tin codoped indium oxide, In((2-2x))Sn(x)Zn(x)O(3) or ZITO, were investigated via high temperature electrical measurements over a range of pO(2). Results indicate the presence of the (2Sn(In) O(i)'')(x) neutral defect cluster, which is also prevalent in indium-tin-oxide. Thin films of ZITO were deposited, annealed, and analyzed via photoelectron spectroscopy. Changes in the Fermi level position and core level binding energies were attributed to the neutral defect cluster affecting the free carrier content. An important correlation has been observed for the bixbyite structure transparent conducting oxides relating the crystal structure, the bulk defect chemistry, and the surface electronic properties.