Role of clusters in nonclassical nucleation and growth of protein crystals

Initiation of hnRNPA1 Low-Complexity Domain Condensation Monitored by Dynamic Light Scattering

Biomolecular condensates (BMCs) exhibit physiological and pathological relevance in biological systems. Both liquid and solid condensates play significant roles in the spatiotemporal regulation and organization of macromolecules and their biological activities. Some pathological solid condensates, such as Lewy Bodies and other fibrillar aggregates, have been hypothesized to originate from liquid condensates. With the prevalence of BMCs having functional and dysfunctional roles, it is imperative to understand the mechanism of biomolecular condensate formation and initiation. Using the low-complexity domain (LCD) of heterogenous ribonuclear protein A1 (hnRNPA1) as our model, we monitored initial assembly events using dynamic light scattering (DLS) while modulating pH and salt conditions to perturb macromolecule and condensate properties. We observed the formation of nanometer-sized BMCs (nano-condensates) distinct from protein monomers and micron-sized condensates. We also observed that conditions that solubilize micron-sized protein condensates do not solubilize nano-condensates, indicating that the balance of forces that stabilize nano-condensates and micron-sized condensates are distinct. These findings provide insight into the forces that drive protein phase separation and potential nucleation structures of macromolecular condensation.

Local Structural Features Elucidate Crystallization of Complex Structures

Complex crystal structures are composed of multiple local environments, and how this type of order emerges spontaneously during crystal growth has yet to be fully understood. We study crystal growth across various structures and along different crystallization pathways, using self-assembly simulations of identical particles that interact via multiwell isotropic pair potentials. We apply an unsupervised machine learning method to features from bond-orientational order metrics to identify different local motifs present during a given structure's crystallization process. In this manner, we distinguish different crystallographic sites in highly complex structures. Tailoring this order parameter to structures of varying complexity and coordination number, we study the emergence of local order along a multistep crystal growth pathway─from a low-density fluid to a high-density, supercooled amorphous liquid droplet and to a bulk crystal. We find a consistent under-coordination of the liquid relative to the average coordination number in the bulk crystal. We use our order parameter to analyze the geometrically frustrated growth of a Frank-Kasper phase and discover how structural defects compete with the formation of crystallographic sites that are more high-coordinated than the liquid environments. The method presented here for classifying order on a particle-by-particle level has broad applicability to future studies of structural self-assembly and crystal growth, and they can aid in the design of building blocks and for targeting pathways of formation of soft-matter structures.

Classical and Nonclassical Nucleation Mechanisms of Insulin Crystals

Although the Classical Nucleation Theory (CNT) is the most consensual theory to explain protein nucleation mechanisms, experimental observations during the shear-induced assays suggest that the CNT does not always describe the insulin nucleation process. This is the case at intermediate precipitant (ZnCl2) solution concentrations (2.3 mM) and high-temperature values (20 and 40 °C) as well as at low precipitant solution concentrations (1.6 mM) and low-temperature values (5 °C). In this work, crystallization events following the CNT registered at high precipitant solution concentrations (3.1 and 4.7 mM) are typically described by a Newtonian response. On the other hand, crystallization events following a nonclassical nucleation pathway seem to involve the formation of a metastable intermediate state before crystal formation and are described by a transition from Newtonian to shear-thinning responses. A dominant shear-thinning behavior (shear viscosity values ranging more than 6 orders of magnitude) is found during aggregation/agglomeration events. The rheological analysis is complemented with different characterization techniques (Dynamic Light Scattering, Energy-Dispersive Spectroscopy, Circular Dichroism, and Differential Scanning Calorimetry) to understand the insulin behavior in solution, especially during the occurrence of aggregation/agglomeration events. To the best of our knowledge, the current work is the first study describing nonclassical nucleation mechanisms during shear-induced crystallization experiments, which reveals the potential of the interdisciplinary approach herein described and opens a window for a clear understanding of protein nucleation mechanisms.

Impact of molecular symmetry on crystallization pathways in highly supersaturated KH2PO4 solutions

Solute structure and its evolution in supersaturated aqueous solutions are key clues to understand Ostwald's step rule. Here, we measure the structural evolution of solute molecules in highly supersaturated solutions of KH2PO4 (KDP) and NH4H2PO4 (ADP) using a combination of electrostatic levitation and synchrotron X-ray scattering. The measurement reveals the existence of a solution-solution transition in KDP solution, caused by changing molecular symmetries and structural evolution of the solution with supersaturation. Moreover, we find that the molecular symmetry of H2PO4- impacts on phase selection. These findings manifest that molecular symmetry and its structural evolution can govern the crystallization pathways in aqueous solutions, explaining the microscopic origin of Ostwald's step rule.

Resolving Temperature-Dependent Hydrate Nucleation Pathway: The Role of "Transition Layer"

Understanding the nucleation of natural gas hydrate (NGH) at different conditions has important implications to NGH recovery and other industrial applications, such as gas storage and separation. Herein, vast numbers of hydrate nucleation events are traced via molecular dynamics (MD) simulations at different degrees of supercooling (or driving forces). Specifically, to precisely characterize a hydrate nucleus from an aqueous system during the MD simulation, we develop an evolutionary order parameter (OP) to recognize the nucleus size and shape. Subsequently, the free energy landscapes of hydrate during nucleation are explored by using the newly developed OP. The results suggest that at 270 K (or 0.92 Tm supercooling, where Tm is the melting point), the near-rounded nucleus prevails during the nucleation, as described from the classical nucleation theory. In contrast, at relatively strong driving forces of 0.85 and 0.88 Tm, nonclassical nucleation events arise. Specifically, the pathway toward an elongated nucleus becomes as important as the pathway toward a near-rounded nucleus. To explain the distinct nucleation phenomena at different supercoolings, a notion of a "transition layer" (or liquid-blob-like layer) is proposed. Here, the transition layer is to describe the interfacial region between the nucleus and aqueous solution, and this layer entails two functionalities: (1) it tends to retain CH4 depending on the degrees of supercooling and (2) it facilitates collision among CH4, which thus promote the incorporation of CH4 into nucleus. Our simulation indicates that compared to the near-rounded nucleus, the transition layer surrounding the elongated nucleus is more evident with the higher collision rate among CH4 molecules. As such, the transition layer tends to promote the elongated nucleus pathway, while offsetting the cost of larger surface free energy associated with the elongated nucleus. At 0.92 Tm, however, the transition layer gradually disappears, and classical nucleation events dominate. Overall, the notion of "transition layer" offers deeper insight into the NGH nucleation at different degrees of supercooling and could be extended to describe other types of hydrate nucleation.

Protein nanocondensates: the next frontier

Over the past decade, myriads of studies have highlighted the central role of protein condensation in subcellular compartmentalization and spatiotemporal organization of biological processes. Conceptually, protein condensation stands at the highest level in protein structure hierarchy, accounting for the assembly of bodies ranging from thousands to billions of molecules and for densities ranging from dense liquids to solid materials. In size, protein condensates range from nanocondensates of hundreds of nanometers (mesoscopic clusters) to phase-separated micron-sized condensates. In this review, we focus on protein nanocondensation, a process that can occur in subsaturated solutions and can nucleate dense liquid phases, crystals, amorphous aggregates, and fibers. We discuss the nanocondensation of proteins in the light of general physical principles and examine the biophysical properties of several outstanding examples of nanocondensation. We conclude that protein nanocondensation cannot be fully explained by the conceptual framework of micron-scale biomolecular condensation. The evolution of nanocondensates through changes in density and order is currently under intense investigation, and this should lead to the development of a general theoretical framework, capable of encompassing the full range of sizes and densities found in protein condensates.

Preparation and Characterization of Metal-Organic Framework Coatings for Improving Protein Crystallization Screening

Modifying crystallization plates can significantly impact the success rate and quality of protein crystal growth, making it a helpful strategy in protein crystallography. However, appropriate methods for preparing nano-sized particles with a high specific surface area and strategies for applying these nanoparticles to form suitable coatings on crystallization plate surfaces still need to be clarified. Here, we utilized both an ultrasonic crusher and a high-pressure homogenizer to create a nano metal-organic framework (MOF), specifically HKUST-1, and introduced a solvent evaporation method for producing MOF coatings on 96-well crystallization plates to induce protein crystal growth. The morphology of MOF coatings on the resin surface of the plate well was characterized using optical and scanning electron microscopy. Compared to the control group, crystallization screening experiments on nine proteins confirmed the effectiveness of plates with MOF coatings. Applying MOF coatings to crystallization plates is an easy-to-use, time-efficient, and potent tool for initiating crystallization experiments.

Strong, Chemically Stable, and Enzymatically On-Demand Detachable Hydrogel Adhesion Using Protein Crosslink

Achieving strong adhesion between hydrogels and diverse materials is greatly significant for emerging technologies yet remains challenging. Existing methods using non-covalent bonds have limited pH and ion stability, while those using covalent bonds typically lack on-demand detachment capability, limiting their applications. In this study, a general strategy of covalent bond-based and detachable adhesion by incorporating amine-rich proteins in various hydrogels and inducing the interfacial crosslinking of the hydrogels using a protein-crosslinking agent is demonstrated. The protein crosslink offers topological adhesion and can reach a strong adhesion energy of ≈750 J m^-2 . The chemistry of the adhesion is characterized and that the inclusion of proteins inside the hydrogels does not alter the hydrogels' properties is shown. The adhesion remains intact after treating the adhered hydrogels with various pH solutions and ions, even at an elevated temperature. The detachment is triggered by treating proteinase solution at the bonding front, causing the digestion of proteins, thus breaking up the interfacial crosslink network. In addition, that this approach can be used to adhere hydrogels to diverse dry surfaces, including glass, elastomers and plastics, is shown. The stable chemistry of protein crosslinks opens the door for various applications in a wide range of chemical environments.

Topological Considerations in Biomolecular Condensation

Biomolecular condensation and phase separation are increasingly understood to play crucial roles in cellular compartmentalization and spatiotemporal regulation of cell machinery implicated in function and pathology. A key aspect of current research is to gain insight into the underlying physical mechanisms of these processes. Accordingly, concepts of soft matter and polymer physics, the thermodynamics of mixing, and material science have been utilized for understanding condensation mechanisms of multivalent macromolecules resulting in viscoelastic mesoscopic supramolecular assemblies. Here, we focus on two topological concepts that have recently been providing key mechanistic understanding in the field. First, we will discuss how percolation provides a network-topology-related framework that offers an interesting paradigm to understand the complex networking of dense 'connected' condensate structures and, therefore, their phase behavior. Second, we will discuss the idea of entanglement as another topological concept that has deep roots in polymer physics and important implications for biomolecular condensates. We will first review some historical developments and fundamentals of these concepts, then we will discuss current advancements and recent examples. Our discussion ends with a few open questions and the challenges to address them, hinting at unveiling fresh possibilities for the modification of existing knowledge as well as the development of new concepts relevant to condensate science.

In Situ Kinetic Observations on Crystal Nucleation and Growth

Nucleation and growth are critical steps in crystallization, which plays an important role in determining crystal structure, size, morphology, and purity. Therefore, understanding the mechanisms of nucleation and growth is crucial to realize the controllable fabrication of crystalline products with desired and reproducible properties. Based on classical models, the initial crystal nucleus is formed by the spontaneous aggregation of ions, atoms, or molecules, and crystal growth is dependent on the monomer's diffusion and the surface reaction. Recently, numerous in situ investigations on crystallization dynamics have uncovered the existence of nonclassical mechanisms. This review provides a summary and highlights the in situ studies of crystal nucleation and growth, with a particular emphasis on the state-of-the-art research progress since the year 2016, and includes technological advances, atomic-scale observations, substrate- and temperature-dependent nucleation and growth, and the progress achieved in the various materials: metals, alloys, metallic compounds, colloids, and proteins. Finally, the forthcoming opportunities and challenges in this fascinating field are discussed.

Protein conformation and biomolecular condensates

Protein conformation and cell compartmentalization are fundamental concepts and subjects of vast scientific endeavors. In the last two decades, we have witnessed exciting advances that unveiled the conjunction of these concepts. An avalanche of studies highlighted the central role of biomolecular condensates in membraneless subcellular compartmentalization that permits the spatiotemporal organization and regulation of myriads of simultaneous biochemical reactions and macromolecular interactions. These studies have also shown that biomolecular condensation, driven by multivalent intermolecular interactions, is mediated by order-disorder transitions of protein conformation and by protein domain architecture. Conceptually, protein condensation is a distinct level in protein conformational landscape in which collective folding of large collections of molecules takes place. Biomolecular condensates arise by the physical process of phase separation and comprise a variety of bodies ranging from membraneless organelles to liquid condensates to solid-like conglomerates, spanning lengths from mesoscopic clusters (nanometers) to micrometer-sized objects. In this review, we summarize and discuss recent work on the assembly, composition, conformation, material properties, thermodynamics, regulation, and functions of these bodies. We also review the conceptual framework for future studies on the conformational dynamics of condensed proteins in the regulation of cellular processes.

Manipulating Reaction Intermediates to Aqueous-Phase ZnSe Magic-Size Clusters and Quantum Dots at Room Temperature

It is not resolved which model describes better the aqueous-phase nucleation and growth of semiconductor quantum dots (QDs), the classical one-step one or the nonclassical multi-step one. Here, we design a room-temperature reaction to trap reaction intermediates in the prenucleation stage of ZnSe QDs (as a model system). We show that the trapped intermediate can transform to magic-size clusters (MSCs) via intra-molecular reorganization and can fragment to enable the growth of QDs. The MSCs exhibit a sharp optical absorption peaking at 299 nm, labelled MSC-299. The intermediate, the precursor compound (PC-299) of MSC-299, is optically transparent at 299 nm and to longer wavelengths. This intermediate forms in various Zn and Se reaction systems. The present study provides unambiguous evidence that the nonclassical and classical pathways are both necessary to explain the nucleation and growth of aqueous-phase QDs, with the former pathway favored more by high reaction concentrations.

Atomic-Scale Tracking of Dynamic Nucleation and Growth of an Interfacial Lead Nanodroplet

Revealing the evolutional pathway of the nucleation and crystallization of nanostructures at the atomic scale is crucial for understanding the complex growth mechanisms at the early stage of new substances and spices. Real-time discrimination of the atomic mechanism of a nanodroplet transition is still a formidable challenge. Here, taking advantage of the high temporal and spatial resolution of transmission electron microscopy, the detailed growth pathway of Pb nanodroplets at the early stage of nucleation was directly observed by employing electron beams to induce the nucleation, growth, and fusion process of Pb nanodroplets based on PbTiO3 nanowires. Before the nucleation of Pb nanoparticles, the atoms began to precipitate when they were irradiated by electrons, forming a local crystal structure, and then rapidly and completely crystallized. Small nanodroplets maintain high activity and high density and gradually grow and merge into stable crystals. The whole process was recorded and imaged by HRTEM in real time. The growth of Pb nanodroplets advanced through the classical path and instantaneous droplet coalescence. These results provide an atomic-scale insight on the dynamic process of solid/solid interface, which has implications in thin-film growth and advanced nanomanufacturing.

Exploring Nucleation Pathways in Distinct Physicochemical Environments Unveiling Novel Options to Modulate and Optimize Protein Crystallization

The scientific discussion about classical and nonclassical nucleation theories has lasted for two decades so far. Recently, multiple nucleation pathways and the occurrence and role of metastable intermediates in crystallization processes have attracted increasing attention, following the discovery of functional phase separation, which is now under investigation in different fields of cellular life sciences, providing interesting and novel aspects for conventional crystallization experiments. In this context, more systematic investigations need to be carried out to extend the current knowledge about nucleation processes. In terms of the data we present, a well-studied model protein, glucose isomerase (GI), was employed first to investigate systematically the early stages of the crystallization process, covering condensing and prenucleation ordering of protein molecules in diverse scenarios, including varying ionic and crowding agent conditions, as well as the application of a pulsed electric field (pEF). The main method used to characterize the early events of nucleation was synchronized polarized and depolarized dynamic light scattering (DLS/DDLS), which is capable of collecting the polarized and depolarized component of scattered light from a sample suspension in parallel, thus monitoring the time-resolved evolution of the condensation and geometrical ordering of proteins at the early stages of nucleation. A diffusion interaction parameter, KD, of GI under varying salt conditions was evaluated to discuss how the proportion of specific and non-specific protein–protein interactions affects the nucleation process. The effect of mesoscopic ordered clusters (MOCs) on protein crystallization was explored further by adding different ratios of MOCs induced by a pEF to fresh GI droplets in solution with different PEG concentrations. To emphasize and complement the data and results obtained with GI, a recombinant pyridoxal 5-phosphate (vitamin B6) synthase (Pdx) complex of Staphylococcus aureus assembled from twelve monomers of Pdx1 and twelve monomers of Pdx2 was employed to validate the ability of the pEF influencing the nucleation of complex macromolecules and the effect of MOCs on adjusting the crystallization pathway. In summary, our data revealed multiple nucleation pathways by tuning the proportion of specific and non-specific protein interactions, or by utilizing a pEF which turned out to be efficient to accelerate the nucleation process. Finally, a novel and reproducible experimental strategy, which can adjust and facilitate a crystallization process by pEF-induced MOCs, was summarized and reported for the first time.

Formation and stabilization mechanism of mesoscale clusters in solution

To understand the existence of complex meso-sized solute-rich clusters, which challenge the understanding of phases and phase equilibria, the formation and stabilization mechanisms of clusters in solution during nucleation of crystals and the associated physico-chemical rules are studied in detail. An essential part of the mechanism is the formation of long-lived oligomers between solute molecules. By means of density functional theory simulation and nuclear magnetic resonance experiments, this work showed that the oligomers in solution tend to be π-π stacking dimers. Clusters are formed under the combined effect of diffusion and monomer-dimer reaction. The physically meaningful quantities such as the monomer-dimer reaction rate constants and the diffusion coefficients of both species were obtained by reaction-diffusion kinetics and diffusion-ordered spectroscopy results. The evolution of cluster radius as a function of time, and the qualitative spatial distributions of monomer and dimer densities under steady-state were plotted to better understand the formation process and the nature of the clusters.

A Two-Pathway Model for the Evolution of Colloidal Compound Semiconductor Quantum Dots and Magic-Size Clusters

A fundamental understanding of formation pathways is critical to the controlled synthesis of colloidal semiconductor nanocrystals. As ultrasmall-size quantum dots (QDs) sometimes emerge in reactions along with magic-size clusters (MSCs), distinguishing their individual pathway of evolution is important, but has proven difficult. To decouple the evolution of QDs and MSCs, an unconventional, selective approach has been developed, along with a two-pathway model that provides a fundamental understanding of production selectivity. For on-demand production of either ultrasmall QDs or MSCs, the key enabler is in how to allow a reaction to proceed in the time prior to nucleation and growth of QDs. In this prenucleation stage, an intermediate compound forms, which is the precursor compound (PC) to the MSC. Here, the two-pathway model and the manipulation of such PCs to synthesize either ultrasmall QDs or binary and ternary MSCs are highlighted. The two-pathway model will assist the development of nucleation theory as well as provide a basis for a mechanism-enabled design and predictive synthesis of functional nanomaterials.

Nucleation of glucose isomerase protein crystals in a nonclassical disguise: The role of crystalline precursors

The ability of proteins to self-assemble into complex, hierarchical structures has been the inspiration for the bottom-up design of a class of biomaterials with proteins as their building blocks. The earliest stages of formation often involve the passing of an activation barrier under the form of nucleus formation, a quaternary protein complex that templates incoming molecules to proper registry. For protein crystallization, the consensus has emerged that the fastest route toward a nucleus follows a winding path: first, densification, followed by symmetry formation. In this contribution, we show that this need not be the case for the protein glucose isomerase, which seems to follow the simplest path to a nucleus, making crystalline clusters from the earliest detectable beginnings.

Protein crystallization is an astounding feat of nature. Even though proteins are large, anisotropic molecules with complex, heterogeneous surfaces, they can spontaneously group into two- and three-dimensional arrays with high precision. And yet, the biggest hurdle in this assembly process, the formation of a nucleus, is still poorly understood. In recent years, the two-step nucleation model has emerged as the consensus on the subject, but it still awaits extensive experimental verification. Here, we set out to reconstruct the nucleation pathway of the candidate protein glucose isomerase (GI), for which there have been indications that it may follow a two-step nucleation pathway under certain conditions. We find that the precursor phase present during the early stages of the reaction process is nanoscopic crystallites that have lattice symmetry equivalent to the mature crystals found at the end of a crystallization experiment. Our observations underscore the need for experimental data at a lattice-resolving resolution on other proteins so that a general picture of protein crystal nucleation can be formed.

Transformation Pathways in Colloidal CdTeSe Magic-Size Clusters

A rarely studied transformation in colloidal ternary magic-size clusters (MSCs) is addressed. We report the first observation of the transformation from ternary CdTeSe MSC-399 to MSC-422, which occurs at room temperature. These two MSC types display sharp optical absorption resonances at 399 and 422 nm, respectively, and are related in that they are quasi isomers, together with their counterpart precursor compounds (PCs). Binary CdTe and CdSe samples were prepared in the prenucleation stage also called the induction period (IP). After they were mixed and placed in a mixture of toluene and octylamine, the transformation was found to take place and to be assisted by the addition of the CdSe IP sample. A binary IP sample contains corresponding binary PCs and monomers (Mo) and fragments (Fr). We argue that the transformation pathway is enabled by the corresponding ternary PCs, involving the substitution reaction, namely CdTeSe PC-399 + CdSe (Mo/Fr)-1 ⇒ CdTeSe PC-422 + CdSe (Mo/Fr)-2. The present study provides an in-depth understanding of the formation characteristics of the MSCs.

Direct observation of the moment of nucleation from a solution by TEM

Recent discoveries of various nucleation processes make understanding the initial processes of crystallization, where atoms and molecules come together to form a crystal nucleus, difficult. Herein, transmission electron microscopy is used to directly visualize the moment of nucleation from a solution and to show that the singular phenomena of nanoparticles are critical to understanding nucleation. Our work revealed that nanoparticles undergo precipitation and dissolution even in undersaturated and equilibrium conditions, that crystal polymorphs formed at different frequencies compete, that molecules follow various nucleation pathways in the same solution, and that the hydration layer plays a critical role in crystallization. The observations visually support the common belief that dehydration is the greatest barrier to crystallization in an aqueous solution. These results are expected to contribute to the development of a unified nucleation model.

Temperature-dependent kinetic pathways of heterogeneous ice nucleation competing between classical and non-classical nucleation

Ice nucleation on the surface plays a vital role in diverse areas, ranging from physics and cryobiology to atmospheric science. Compared to ice nucleation in the bulk, the water-surface interactions present in heterogeneous ice nucleation complicate the nucleation process, making heterogeneous ice nucleation less comprehended, especially the relationship between the kinetics and the structures of the critical ice nucleus. Here we combine Markov State Models and transition path theory to elucidate the ensemble pathways of heterogeneous ice nucleation. Our Markov State Models reveal that the classical one-step and non-classical two-step nucleation pathways can surprisingly co-exist with comparable fluxes at T = 230 K. Interestingly, we find that the disordered mixing of rhombic and hexagonal ice leads to a favorable configurational entropy that stabilizes the critical nucleus, facilitating the non-classical pathway. In contrast, the favorable energetics promotes the formation of hexagonal ice, resulting in the classical pathway. Furthermore, we discover that, at elevated temperatures, the nucleation process prefers to proceed via the classical pathway, as opposed to the non-classical pathway, since the potential energy contributions override the configurational entropy compensation. This study provides insights into the mechanisms of heterogeneous ice nucleation and sheds light on the rational designs to control crystallization processes.

Patterns in Nature—S-Layer Lattices of Bacterial and Archaeal Cells

Bacterial surface layers (S-layers) have been observed as the outermost cell envelope component in a wide range of bacteria and most archaea. S-layers are monomolecular lattices composed of a single protein or glycoprotein species and have either oblique, square or hexagonal lattice symmetry with unit cell dimensions ranging from 3 to 30 nm. They are generally 5 to 10 nm thick (up to 70 nm in archaea) and represent highly porous protein lattices (30–70% porosity) with pores of uniform size and morphology in the range of 2 to 8 nm. Since S-layers can be considered as one of the simplest protein lattices found in nature and the constituent units are probably the most abundantly expressed proteins on earth, it seems justified to briefly review the different S-layer lattice types, the need for lattice imperfections and the discussion of S-layers from the perspective of an isoporous protein network in the ultrafiltration region. Finally, basic research on S-layers laid the foundation for applications in biotechnology, synthetic biology, and biomimetics.

The Ambiguous Functions of the Precursors That Enable Nonclassical Modes of Olanzapine Nucleation and Growth

One of the most consequential assumptions of the classical theories of crystal nucleation and growth is the Szilard postulate, which states that molecules from a supersaturated phase join a nucleus or a growing crystal individually. In the last 20 years, observations in complex biological, geological, and engineered environments have brought to light violations of the Szilard rule, whereby molecules assemble into ordered or disordered precursors that then host and promote nucleation or contribute to fast crystal growth. Nonclassical crystallization has risen to a default mode presumed to operate in the majority of the inspected crystallizing systems. In some cases, the existence of precursors in the growth media is admitted as proof for their role in nucleation and growth. With the example of olanzapine, a marketed drug for schizophrenia and bipolar disorder, we demonstrate that molecular assemblies in the solution selectively participate in crystal nucleation and growth. In aqueous and organic solutions, olanzapine assembles into both mesoscopic solute-rich clusters and dimers. The clusters facilitate nucleation of crystals and crystal form transformations. During growth, however, the clusters land on the crystal surface and transform into defects, but do not support step growth. The dimers are present at low concentrations in the supersaturated solution, yet the crystals grow by the association of dimers, and not of the majority monomers. The observations with olanzapine emphasize that detailed studies of the crystal and solution structures and the dynamics of molecular association may empower classical and nonclassical models that advance the understanding of natural crystallization, and support the design and manufacture of promising functional materials.

Nucleation of protein mesocrystals via oriented attachment

Self-assembly of proteins holds great promise for the bottom-up design and production of synthetic biomaterials. In conventional approaches, designer proteins are pre-programmed with specific recognition sites that drive the association process towards a desired organized state. Although proven effective, this approach poses restrictions on the complexity and material properties of the end-state. An alternative, hierarchical approach that has found wide adoption for inorganic systems, relies on the production of crystalline nanoparticles that become the building blocks of a next-level assembly process driven by oriented attachment (OA). As it stands, OA has not yet been observed for protein systems. Here we employ cryo-transmission electron microscopy (cryoEM) in the high nucleation rate limit of protein crystals and map the self-assembly route at molecular resolution. We observe the initial formation of facetted nanocrystals that merge lattices by means of OA alignment well before contact is made, satisfying non-trivial symmetry rules in the process. As these nanocrystalline assemblies grow larger we witness imperfect docking events leading to oriented aggregation into mesocrystalline assemblies. These observations highlight the underappreciated role of the interaction between crystalline nuclei, and the impact of OA on the crystallization process of proteins.

A New Method for Dispersing Pristine Carbon Nanotubes Using Regularly Arranged S-Layer Proteins

Homogeneous and stable dispersions of functionalized carbon nanotubes (CNTs) in aqueous solutions are imperative for a wide range of applications, especially in life and medical sciences. Various covalent and non-covalent approaches were published to separate the bundles into individual tubes. In this context, this work demonstrates the non-covalent modification and dispersion of pristine multi-walled carbon nanotubes (MWNTs) using two S-layer proteins, namely, SbpA from Lysinibacillus sphaericus CCM2177 and SbsB from Geobacillus stearothermophilus PV72/p2. Both the S-layer proteins coated the MWNTs completely. Furthermore, it was shown that SbpA can form caps at the ends of MWNTs. Reassembly experiments involving a mixture of both S-layer proteins in the same solution showed that the MWNTs were primarily coated with SbsB, whereas SbpA formed self-assembled layers. The dispersibility of the pristine nanotubes coated with SbpA was determined by zeta potential measurements (−24.4 +/− 0.6 mV, pH = 7). Finally, the SbpA-coated MWNTs were silicified with tetramethoxysilane (TMOS) using a mild biogenic approach. As expected, the thickness of the silica layer could be controlled by the reaction time and was 6.3 +/− 1.25 nm after 5 min and 25.0 +/− 5.9 nm after 15 min. Since S-layer proteins have already demonstrated their capability to bind (bio)molecules in dense packing or to act as catalytic sites in biomineralization processes, the successful coating of pristine MWNTs has great potential in the development of new materials, such as biosensor architectures.

Mesoscopic protein-rich clusters host the nucleation of mutant p53 amyloid fibrils

The protein p53 is a crucial tumor suppressor, often called "the guardian of the genome"; however, mutations transform p53 into a powerful cancer promoter. The oncogenic capacity of mutant p53 has been ascribed to enhanced propensity to fibrillize and recruit other cancer fighting proteins in the fibrils, yet the pathways of fibril nucleation and growth remain obscure. Here, we combine immunofluorescence three-dimensional confocal microscopy of human breast cancer cells with light scattering and transmission electron microscopy of solutions of the purified protein and molecular simulations to illuminate the mechanisms of phase transformations across multiple length scales, from cellular to molecular. We report that the p53 mutant R248Q (R, arginine; Q, glutamine) forms, both in cancer cells and in solutions, a condensate with unique properties, mesoscopic protein-rich clusters. The clusters dramatically diverge from other protein condensates. The cluster sizes are decoupled from the total cluster population volume and independent of the p53 concentration and the solution concentration at equilibrium with the clusters varies. We demonstrate that the clusters carry out a crucial biological function: they host and facilitate the nucleation of amyloid fibrils. We demonstrate that the p53 clusters are driven by structural destabilization of the core domain and not by interactions of its extensive unstructured region, in contradistinction to the dense liquids typical of disordered and partially disordered proteins. Two-step nucleation of mutant p53 amyloids suggests means to control fibrillization and the associated pathologies through modifying the cluster characteristics. Our findings exemplify interactions between distinct protein phases that activate complex physicochemical mechanisms operating in biological systems.

Nonclassical Nucleation—Role of Metastable Intermediate Phase in Crystal Nucleation: An Editorial Prefix

Classical nucleation theory (CNT), which was established about 90 years ago, represents the most commonly used theory in describing nucleation processes. For a fluid-to-solid phase transition, CNT states that the solutes in a supersaturated solution reversibly form small clusters. Once a cluster reaches its critical size, it becomes thermodynamically stable and is favored for further growth. One of the most important assumptions of CNT is that the nucleation process is described by one reaction coordinate and all order parameters proceed simultaneously. Recent studies in experiments, computer simulations, and theory have revealed nonclassical features in the early stage of nucleation. In particular, the decoupling of order parameters involved during a fluid-to-solid transition leads to the so-called two-step nucleation mechanism, in which a metastable intermediate phase (MIP) exists in parallel to the initial supersaturated solution and the final crystals. These MIPs can be high-density liquid phases, mesoscopic clusters, or preordered states. In this Special Issue, we focus on the role of the various MIPs in the early stage of crystal nucleation of organic materials, metals and alloys, aqueous solutions, minerals, colloids, and proteins, and thus on various scenarios of nonclassical pathways of crystallization.

The crystallization enthalpy and entropy of protein solutions: microcalorimetry, van't Hoff determination and linearized Poisson–Boltzmann model of tetragonal lysozyme crystals

Microcalorimetric and van't Hoff determinations as well as a theoretical description provide a consistent picture of the crystallization enthalpy and entropy of protein solutions and their dependence on physicochemical solution parameters.

Room-temperature formation of CdS magic-size clusters in aqueous solutions assisted by primary amines

Aqueous-phase approaches to semiconductor CdS magic-size clusters (MSCs) and the formation pathway have remained relatively unexplored. Here, we report the demonstration of an aqueous-phase, room-temperature approach to CdS MSCs, together with an exploration of their evolution pathway. The resulting CdS MSCs display a sharp optical absorption peak at about 360 nm and are labeled MSC-360. With CdCl₂ and thiourea as the respective Cd and S sources, and 3-mercarpotopropionic acid as the ligand, CdS MSC-360 develops in a mixture of a primary amine and water. We argue that the primary amine facilitates room-temperature decomposition of thiourea when CdCl₂ is present, and the formation pathway of MSCs is similar to that in organic-phase approaches. Our findings show there is a viable avenue to room-temperature aqueous-phase formation of CdS MSCs. Providing explanations of the procedure developed including the formation of large aggregates, the present study represents an important advance towards a mechanistic understanding of nanocrystal synthesis.

CdS magic-size clusters have, so far, been prepared only in organic solvents. Here, the authors report an aqueous-phase synthesis for CdS magic-size clusters at room temperature and reveal insights into the formation mechanism, including the key role of primary amines.

Evolution of CdTe Magic-Size Clusters with Single Absorption Doublet Assisted by Adding Small Molecules during Prenucleation

An approach is reported for the exclusive production of CdTe magic-size clusters (MSCs) that exhibit an optical absorption doublet peaking at 385/427 nm, with an explanation of the synthesis procedure. The MSCs, defined as dMSC-427, were produced from the reaction of cadmium oleate (Cd(OA)₂) and tri-n-octylphosphine telluride in octadecene at 100 °C, with the addition of acetic acid (HOAc) or acetate (M(OAc)₂) during the prenucleation stage (40 °C). Without such an addition or when it was performed in the postnucleation stage (100 °C), quantum dots (QDs) developed. The production of dMSC-427 or QDs is hypothesized to be related to the solubility of the Cd precursor, such as Cd(OA)₁(OAc)₁ or Cd(OA)₂, respectively. Also, the reactions that lead to Cd(OA)₁(OAc)₁ are proposed. The present study provides an in-depth understanding of the two-pathway model proposed for the prenucleation stage of binary colloidal QDs, as well as of the formation of MSCs and/or QDs.

Thermal Effects on the Crystallization Kinetics, and Interfacial Adhesion of Single-Crystal Phase-Change Gallium

Although substrates play an important role upon crystallization of supercooled liquids, the influences of surface temperature and thermal property have remained elusive. Here, the crystallization of supercooled phase-change gallium (Ga) on substrates with different thermal conductivity is studied. The effect of interfacial temperature on the crystallization kinetics, which dictates thermo-mechanical stresses between the substrate and the crystallized Ga, is investigated. At an elevated surface temperature, close to the melting point of Ga, an extended single-crystal growth of Ga on dielectric substrates due to layering effect and annealing is realized without the application of external fields. Adhesive strength at the interfaces depends on the thermal conductivity and initial surface temperature of the substrates. This insight can be applicable to other liquid metals for industrial applications, and sheds more light on phase-change memory crystallization.

Delayed nucleation in lipid particles

Metastable states in first-order phase-transitions have been traditionally described by classical nucleation theory (CNT). However, recently an increasing number of systems displaying such a transition have not been successfully modelled by CNT. The delayed crystallization of phospholipids upon super-cooling is an interesting case, since the extended timescales allow access into the dynamics. Herein, we demonstrate the controllable behavior of the long-lived metastable liquid-crystalline phase of dilauroyl-phosphatidylethanolamine (DLPE), arranged in multi-lamellar vesicles, and the ensuing cooperative transition to the crystalline state. Experimentally, we find that the delay in crystallization is a bulk phenomenon, which is tunable and can be manipulated to span two orders of magnitude in time by changing the quenching temperature, solution salinity, or adding a secondary phospholipid. Our results reveal the robust persistence of the metastability, and showcase the apparent deviation from CNT. This distinctive suppression of the transition may be explained by the resistance of the multi-lamellar vesicle to deformations caused by nucleated crystalline domains. Since phospholipids are used as a platform for drug-delivery, a programmable design of cargo hold and release can be of great benefit.

Recent experimental explorations of non-classical nucleation

This work provides a clearer picture for non-classical nucleation by revealing the presence of various intermediates using advanced characterization techniques.

New insights into the spatial confinement mechanism of nucleation of biogenic aragonite crystals from bivalve nacre

Nacreous aragonite crystals nucleate on the margin of the underlying tablets: a spatial confinement mechanism.

A mechanism for reversible mesoscopic aggregation in liquid solutions

Solutions of proteins and other molecules exhibit puzzling, mesoscopically sized inclusions of a solute-rich liquid, well outside the region of stability of the solute-rich phase. This mesoscopic size is in conflict with existing views on heterophase fluctuations. Here we systematically work out a microscopic mechanism by which a metastable solute-rich phase can readily nucleate in a liquid solution. A requisite component of the mechanism is that the solute form long-lived complexes with itself or other molecules. After nucleated in this non-classical fashion, individual droplets grow until becoming mechanically unstable because of a concomitant drop in the internal pressure, the drop caused by the metastability of the solute-rich phase. The ensemble of the droplets is steady-state. In a freshly prepared solution, the ensemble is predicted to evolve in a way similar to the conventional Ostwald ripening, during which larger droplets grow at the expense of smaller droplets.

How crystals form: A theory of nucleation pathways

Recent advances in classical density functional theory are combined with stochastic process theory and rare event techniques to formulate a theoretical description of nucleation, including crystallization, that can predict nonclassical nucleation pathways based on no input other than the interaction potential of the particles making up the system. The theory is formulated directly in terms of the density field, thus forgoing the need to define collective variables. It is illustrated by application to diffusion-limited nucleation of macromolecules in solution for both liquid-liquid separation and crystallization. Both involve nonclassical pathways with crystallization, in particular, proceeding by a two-step mechanism consisting of the formation of a dense-solution droplet followed by ordering originating at the core of the droplet. Furthermore, during the ordering, the free-energy surface shows shallow minima associated with the freezing of liquid into solid shells, which may shed light on the widely observed metastability of nanoscale clusters.

Supercluster-coupled crystal growth in metallic glass forming liquids

While common growth models assume a structure-less liquid composed of atomic flow units, structural ordering has been shown in liquid metals. Here, we conduct in situ transmission electron microscopy crystallization experiments on metallic glass nanorods, and show that structural ordering strongly affects crystal growth and is controlled by nanorod thermal history. Direct visualization reveals structural ordering as densely populated small clusters in a nanorod heated from the glass state, and similar behavior is found in molecular dynamics simulations of model metallic glasses. At the same growth temperature, the asymmetry in growth rate for rods that are heated versus cooled decreases with nanorod diameter and vanishes for very small rods. We hypothesize that structural ordering enhances crystal growth, in contrast to assumptions from common growth models. The asymmetric growth rate is attributed to the difference in the degree of the structural ordering, which is pronounced in the heated glass but sparse in the cooled liquid.

Conventional crystal growth models assume crystals grow into a structure-less liquid, even though liquid metals have shown evidence of structural ordering. Here, the authors show crystal growth can be influenced by the presence of thermodynamically unstable local structural order in the liquid.

Anomalous Dense Liquid Condensates Host the Nucleation of Tumor Suppressor p53 Fibrils

About half of human cancers are associated with mutations of the tumor suppressor p53. Gained oncogenic functions of the mutants have been related to aggregation behaviors of wild-type and mutant p53. The thermodynamic and kinetic mechanisms of p53 aggregation are poorly understood. Here we find that wild-type p53 forms an anomalous liquid phase. The liquid condensates exhibit several behaviors beyond the scope of classical phase transition theories: their size, ca. 100 nm, is independent of the p53 concentration and decoupled from the protein mass held in the liquid phase. Furthermore, the liquid phase lacks constant solubility. The nucleation of p53 fibrils deviates from the accepted mechanism of sequential association of single solute molecules. We find that the liquid condensates serve as pre-assembled precursors of high p53 concentration that facilitate fibril assembly. Fibril nucleation hosted by precursors represents a novel biological pathway, which opens avenues to suppress protein fibrillation in aggregation diseases.

Precursor Self-Assembly Identified as a General Pathway for Colloidal Semiconductor Magic-Size Clusters

Little is known about the formation pathway of colloidal semiconductor magic-size clusters (MSCs). Here, the synthesis of the first single-ensemble ZnSe MSCs, which exhibit a sharp optical absorption singlet peaking at 299 nm, is reported; their formation is independent of Zn and Se precursors used. It is proposed that the formation of MSCs starts with precursor self-assembly followed by Zn and Se covalent bond formation to result in immediate precursors (IPs) which can transform into the MSCs. It is demonstrated that the IPs in cyclohexane appear transparent in optical absorption, and become visible as MSCs exhibiting one sharp optical absorption peak when a primary amine is added at room temperature. It is shown that when the preparation of the IP is controlled to be within the induction period, which occurs prior to nucleation and growth of conventional quantum dots (QDs), the resulting MSCs can be produced without the complication of the simultaneous coproduction of conventional QDs. The present study reveals the existence of precursor self-assembly which leads to the formation of colloidal semiconductor MSCs and provides insights into a multistep nucleation process in cluster science.

Crystallization of Organic Molecules: Nonclassical Mechanism Revealed by Direct Imaging

Organic crystals are of primary importance in pharmaceuticals, functional materials, and biological systems; however, organic crystallization mechanisms are not well-understood. It has been recognized that "nonclassical" organic crystallization from solution involving transient amorphous precursors is ubiquitous. Understanding how these precursors evolve into crystals is a key challenge. Here, we uncover the crystallization mechanisms of two simple aromatic compounds (perylene diimides), employing direct structural imaging by cryogenic electron microscopy. We reveal the continuous evolution of density, morphology, and order during the crystallization of very different amorphous precursors (well-defined aggregates and diffuse dense liquid phase). Crystallization starts from initial densification of the precursors. Subsequent evolution of crystalline order is gradual, involving further densification concurrent with optimization of molecular ordering and morphology. These findings may have implications for the rational design of organic crystals.

Growing Protein Crystals with Distinct Dimensions Using Automated Crystallization Coupled with In Situ Dynamic Light Scattering

The automated crystallization device is a patented technique1 especially developed for monitoring protein crystallization experiments with the aim to precisely maneuver the nucleation and crystal growth towards desired sizes of protein crystals. The controlled crystallization is based on sample investigation with in situ Dynamic Light Scattering (DLS) while all visual changes in the droplet are monitored online with the help of a microscope coupled to a CCD camera, thus enabling a full investigation of the protein droplet during all stages of crystallization. The use of in situ DLS measurements throughout the entire experiment allows a precise identification of the highly supersaturated protein solution transitioning to a new phase – the formation of crystal nuclei. By identifying the protein nucleation stage, the crystallization can be optimized from large protein crystals to the production of protein microcrystals. The experimental protocol shows an interactive crystallization approach based on precise automated steps such as precipitant addition, water evaporation for inducing high supersaturation, and sample dilution for slowing induced homogeneous nucleation or reversing phase transitions.

Experimental measurement of the diamond nucleation landscape reveals classical and nonclassical features

Nucleation is a core scientific concept that describes the formation of new phases and materials. While classical nucleation theory is applied across wide-ranging fields, nucleation energy landscapes have never been directly measured at the atomic level, and experiments suggest that nucleation rates often greatly exceed the predictions of classical nucleation theory. Multistep nucleation via metastable states could explain unexpectedly rapid nucleation in many contexts, yet experimental energy landscapes supporting such mechanisms are scarce, particularly at nanoscale dimensions. In this work, we measured the nucleation energy landscape of diamond during chemical vapor deposition, using a series of diamondoid molecules as atomically defined protonuclei. We find that 26-carbon atom clusters, which do not contain a single bulk atom, are postcritical nuclei and measure the nucleation barrier to be more than four orders of magnitude smaller than prior bulk estimations. These data support both classical and nonclassical concepts for multistep nucleation and growth during the gas-phase synthesis of diamond and other semiconductors. More broadly, these measurements provide experimental evidence that agrees with recent conceptual proposals of multistep nucleation pathways with metastable molecular precursors in diverse processes, ranging from cloud formation to protein crystallization, and nanoparticle synthesis.