Solid-liquid phase boundaries of lens protein solutions

Effects of tamarind seed polysaccharides on physicochemical characteristics of frozen dough: structure-function relationship

BACKGROUND

Recently, frozen dough has become more popular because of its ability to be quickly transformed into freshly baked foods. During the storage and transport process, frozen dough can suffer some degree of damage caused by ice crystallization and recrystallization. Adding polysaccharides to frozen dough is a good way to solve this problem. Tamarind seed polysaccharide (TSP) has excellent ice crystal steady ability and has also been widely used in frozen foods. However, there is no study on the use of TSP in frozen dough.

RESULTS

TSP can stabilize the bound water content, inhibit the freezable water content, and increase elasticity. However, the dough with different structures of TSP added was less firm after 30 days of freezing compared to the dough without TSP, and the porosity and stomatal density of the prepared steamed bread gradually decreased. The addition of TSP reduced gluten deterioration during the freezing process, thus decreasing the collapse and uneven porosity of the steamed bread.

CONCLUSIONS

The results could provide new insights into the structure of TSP and its effect on the quality characteristics of frozen dough. © 2023 Society of Chemical Industry.

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.

Biomolecular phase separation in stress granule assembly and virus infection

Liquid-liquid phase separation (LLPS) has emerged as a crucial mechanism for cellular compartmentalization. One prominent example of this is the stress granule. Found in various types of cells, stress granule is a biomolecular condensate formed through phase separation. It comprises numerous RNA and RNA-binding proteins. Over the past decades, substantial knowledge has been gained about the composition and dynamics of stress granules. SGs can regulate various signaling pathways and have been associated with numerous human diseases, such as neurodegenerative diseases, cancer, and infectious diseases. The threat of viral infections continues to loom over society. Both DNA and RNA viruses depend on host cells for replication. Intriguingly, many stages of the viral life cycle are closely tied to RNA metabolism in human cells. The field of biomolecular condensates has rapidly advanced in recent times. In this context, we aim to summarize research on stress granules and their link to viral infections. Notably, stress granules triggered by viral infections behave differently from the canonical stress granules triggered by sodium arsenite (SA) and heat shock. Studying stress granules in the context of viral infections could offer a valuable platform to link viral replication processes and host anti-viral responses. A deeper understanding of these biological processes could pave the way for innovative interventions and treatments for viral infectious diseases. They could potentially bridge the gap between basic biological processes and interactions between viruses and their hosts.

Insights into the solubility of γ $$ \gamma $$ D-crystallin from multiscale atomistic simulations

The molecular basis underlying the rich phase behavior of globular proteins remains poorly understood. We use atomistic multiscale molecular simulations to model the solution-state conformational dynamics and interprotein interactions of γ $$ \gamma $$ D-crystallin and its P23T-R36S mutant, which drastically limits the protein solubility, at both infinite dilution and at a concentration where the mutant fluid phase and crystalline phase coexist. We find that while the mutant conserves the protein fold, changes to the surface exposure of residues in the neighborhood of residue-36 enhance protein-protein interactions and develop specific protein-protein contacts found in the protein crystal lattice.

Coexistence of Transient Liquid Droplets and Amorphous Solid Particles in Nonclassical Crystallization of Cerium Oxalate

Crystallization from solution often occurs via "nonclassical" routes; that is, it involves transient, non-crystalline states like reactant-rich liquid droplets and amorphous particles. However, in mineral crystals, the well-defined thermodynamic character of liquid droplets and whether they convert─or not─into amorphous phases have remained unassessed. Here, by combining cryo-transmission electron microscopy and X-ray scattering down to a 250 ms reaction time, we unveil that crystallization of cerium oxalate involves a metastable chemical equilibrium between transient liquid droplets and solid amorphous particles: contrary to the usual expectation, reactant-rich droplets do not evolve into amorphous solids. Instead, at concentrations above 2.5 to 10 mmol L^-1, both amorphous and reactant-rich liquid phases coexist for several tens of seconds and their molar fractions remain constant and follow the lever rule in a multicomponent phase diagram. Such a metastable chemical equilibrium between solid and liquid precursors has been so far overlooked in multistep nucleation theories and highlights the interest of rationalizing phase transformations using multicomponent phase diagrams not only when designing and recycling rare earths materials but also more generally when describing nonclassical crystallization.

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.

Automated matching of two-time X-ray photon correlation maps from phase-separating proteins with Cahn-Hilliard-type simulations using auto-encoder networks

Machine learning methods are used for an automated classification of experimental two-time X-ray photon correlation maps from an arrested liquid-liquid phase separation of a protein solution. The correlation maps are matched with correlation maps generated with Cahn-Hilliard-type simulations of liquid-liquid phase separations according to two simulation parameters and in the last step interpreted in the framework of the simulation. The matching routine employs an auto-encoder network and a differential evolution based algorithm. The method presented here is a first step towards handling large amounts of dynamic data measured at high-brilliance synchrotron and X-ray free-electron laser sources, facilitating fast comparison with phase field models of phase separation.

Spontaneous formation of barium sulfate crystals at liquid–liquid interfaces

Interfacial ion transfer from organic phase to aqueous phase is employed as the basis for formation of barium sulfate crystals close to the interface.

Homogeneous nucleation of sheared liquids: advances and insights from simulations and theory

One of the most ubiquitous and technologically important phenomena in nature is the nucleation of homogeneous flowing systems. The microscopic effects of shear on a nucleating system are still imperfectly understood, although in recent years a consistent picture has emerged. The opposing effects of shear can be split into two major contributions for simple atomic and molecular liquids: increase of the energetic cost of nucleation, and enhancement of the kinetics. In this perspective, we describe the latest computational and theoretical techniques which have been developed over the past two decades. We collate and unify the overarching influences of shear, temperature, and supersaturation on the process of homogeneous nucleation. Experimental techniques and capabilities are discussed, against the backdrop of results from simulations and theory. Although we primarily focus on simple systems, we also touch upon the sheared nucleation of more complex systems, including glasses and polymer melts. We speculate on the promising directions and possible advances that could come to fruition in the future.

Multivalent ions and biomolecules: Attempting a comprehensive perspective

Ions are ubiquitous in nature. They play a key role for many biological processes on the molecular scale, from molecular interactions, to mechanical properties, to folding, to self-organisation and assembly, to reaction equilibria, to signalling, to energy and material transport, to recognition etc. Going beyond monovalent ions to multivalent ions, the effects of the ions are frequently not only stronger (due to the obviously higher charge), but qualitatively different. A typical example is the process of binding of multivalent ions, such as Ca2+ , to a macromolecule and the consequences of this ion binding such as compaction, collapse, potential charge inversion and precipitation of the macromolecule. Here we review these effects and phenomena induced by multivalent ions for biological (macro)molecules, from the "atomistic/molecular" local picture of (potentially specific) interactions to the more global picture of phase behaviour including, e. g., crystallisation, phase separation, oligomerisation etc. Rather than attempting an encyclopedic list of systems, we rather aim for an embracing discussion using typical case studies. We try to cover predominantly three main classes: proteins, nucleic acids, and amphiphilic molecules including interface effects. We do not cover in detail, but make some comparisons to, ion channels, colloidal systems, and synthetic polymers. While there are obvious differences in the behaviour of, and the relevance of multivalent ions for, the three main classes of systems, we also point out analogies. Our attempt of a comprehensive discussion is guided by the idea that there are not only important differences and specific phenomena with regard to the effects of multivalent ions on the main systems, but also important similarities. We hope to bridge physico-chemical mechanisms, concepts of soft matter, and biological observations and connect the different communities further.

Measuring Protein Solubility

Protein solubility determines the conditions under which the protein will remain in solution. As a result, it is an important quantity in applications that involve concentrated protein solutions. Here I describe the solubility measurement of the protein thaumatin in the presence of tartrate ions as a function of temperature. This method can be used to measure the solubility of other proteins.

Fractal self-assembly and aggregation of human amylin

Human amylin is an intrinsically disordered protein believed to have a central role in Type-II diabetes mellitus (T2DM). The formation of intermediate oligomers is a seminal event in the eventual self-assembled fibril structures of amylin. However, the recent experimental investigations have shown the presence of different self-assembled (oligomers, protofilaments, and fibrils) and aggregated structures (amorphous aggregates) of amylin formed during its aggregation. Here, we show that amylin under diffusion-limited conditions leads to fractal self-assembly. The pH and solvent sensitive fractal self-assemblies of amylin were observed using an optical microscope. Confocal microscopy and scanning electron microscopy (SEM) with energy dispersion X-ray analysis (EDAX) were used to confirm the fractal self-assembly of amylin in water and PBS buffer, respectively. The fractal characteristics of the self-assemblies and the aggregates formed during the aggregation of amylin under different pH conditions were investigated using laser light scattering. The hydropathy and the docking study indicated the interactions between the anisotropically distributed hydrophobic residues and polar/ionic residues on the solvent-accessible surface of the protein as the crucial interaction hot-spots for driving the self-assembly and aggregation of human amylin. The simultaneous presence of various self-assemblies of human amylin was observed through different microscopy techniques. The present study may help in designing different fractal-like nanomaterials with potential applications in drug delivery, sensing, and tissue engineering.

Potential and limits of a colloid approach to protein solutions

Looking at globular proteins with the eyes of a colloid scientist has a long tradition, in fact a significant part of the early colloid literature was focused on protein solutions. However, it has also been recognized that proteins are much more complex than the typical hard sphere-like synthetic model colloids. Proteins are not perfect spheres, their interaction potentials are in general not isotropic, and using theories developed for such particles are thus clearly inadequate in many cases. In this perspective article, we now take a closer look at the field. In particular, we reflect on the fact that modern colloid science has been undergoing a tremendous development, where a multitude of novel systems have been developed in the lab and in silico. During the last decade we have seen a rapidly increasing number of reports on the synthesis of anisotropic, patchy and/or responsive synthetic colloids, that start to resemble their complex biological counterparts. This experimental development is also reflected in a corresponding theoretical and simulation effort. The experimental and theoretical toolbox of colloid science has thus rapidly expanded, and there is obviously an enormous potential for an application of these new concepts to protein solutions, which has already been realized and harvested in recent years. In this perspective article we make an attempt to critically discuss the exploitation of colloid science concepts to better understand protein solutions. We not only consider classical applications such as the attempt to understand and predict solution stability and phase behaviour, but also discuss new challenges related to the dynamics, flow behaviour and liquid-solid transitions found in concentrated or crowded protein solutions. It not only aims to provide an overview on the progress in experimental and theoretical (bio)colloid science, but also discusses current shortcomings in our ability to correctly reproduce and predict the structural and dynamic properties of protein solutions based on such a colloid approach.

On the theory of crystal growth in metastable systems with biomedical applications: protein and insulin crystallization

A generalized theory of nucleation and growth of crystals in a metastable (supercooled or supersaturated) liquid is developed taking into account two principal effects: the diffusion mechanism of the particle-size distribution function in the space of particle radii and the unsteady-state growth rates of individual crystals induced by fluctuations in external temperature or concentration field. A system of the Fokker-Planck and balance integro-differential equations is formulated and analytically solved in a parametric form for arbitrary nucleation kinetics and arbitrary growth rates of individual crystals. The particle-size distribution function and system metastability are found in an explicit form. The Weber-Volmer-Frenkel-Zel'dovich and Meirs kinetic mechanisms, as well as the unsteady-state growth rates of nuclei (Alexandrov & Alexandrova 2019 Phil. Trans. R. Soc. A 377, 20180209 ( doi:10.1098/rsta.2018.0209 )), are considered as special cases. Some potential biomedical applications of the present theory for crystal growth from supersaturated solutions are discussed. The theory is compared with experimental data on protein and insulin crystallization (growth dynamics of the proteins lysozyme and canavalin as well as of bovine and porcine insulin is considered). The hat-shaped particle-size distribution functions for lysozyme and canavalin crystals as well as for bovine and porcine insulin are found. This article is part of the theme issue 'Heterogeneous materials: metastable and non-ergodic internal structures'.

Controlling Phase Separation of Lysozyme with Polyvalent Anions

The ability of polyvalent anions to influence protein-protein interactions and protein net charge was investigated through solubility and turbidity experiments, determination of osmotic second virial coefficients ( B₂₂), and ζ-potential values for lysozyme solutions.  B₂₂ values showed that all anions reduce protein-protein repulsion between positively charged lysozyme molecules, and those anions with higher net valencies are more effective. The polyvalent anions pyrophosphate and tripolyphosphate were observed to induce protein reentrant condensation, which has been previously observed with negatively charged proteins in the presence of trivalent cations. Reentrant condensation is a phenomenon in which low concentrations of polyvalent ions induce protein precipitation, but further increasing polyvalent ion concentration causes the protein precipitate to resolubilize. Interestingly, citrate does not induce lysozyme reentrant condensation despite having a similar charge, size, and shape to pyrophosphate. We observe qualitative differences in protein behavior when compared against negatively charged proteins in solutions of trivalent cations. The polyphosphate ions induce a much stronger protein-protein attraction, which correlates with the occurrence of a liquid-gel transition that replaces the liquid-liquid transition observed with trivalent cations. The results indicate that solutions of polyphosphate ions provide a model system for exploring the link between the protein-phase diagram and model interaction potentials and also highlight the importance that ion-specific effects can have on protein solubility.

Tuning phase transitions of aqueous protein solutions by multivalent cations

In the presence of trivalent cations, negatively charged globular proteins show a rich phase behaviour including reentrant condensation, crystallisation, clustering and lower critical solution temperature metastable liquid-liquid phase separation (LCST-LLPS). Here, we present a systematic study on how different multivalent cations can be employed to tune the interactions and the associated phase behaviour of proteins. We focus our investigations on the protein bovine serum albumin (BSA) in the presence of HoCl3, LaCl3 and YCl3. Using UV-Vis spectroscopy and small-angle X-ray scattering (SAXS), we find that the interprotein attraction induced by Ho3+ is very strong, while the one induced by La3+ is comparatively weak when comparing the data to BSA-Y3+ systems based on our previous work. Using zeta potential and isothermal titration calorimetry (ITC) measurements, we establish different binding affinities of cations to BSA with Ho3+ having the highest one. We propose that a combination of different cation features such as radius, polarisability and in particular hydration effects determine the protein-protein interaction induced by these cations. Our findings imply that subtle differences in cation properties can be a sensitive tool to fine-tune protein-protein interactions and phase behaviour in solution.

Dynamics of liquid-liquid phase separation of wheat gliadins

During wheat seeds development, storage proteins are synthetized and subsequently form dense protein phases, also called Protein Bodies (PBs). The mechanisms of PBs formation and the supramolecular assembly of storage proteins in PBs remain unclear. In particular, there is an apparent contradiction between the low solubility in water of storage proteins and their high local dynamics in dense PBs. Here, we probe the interplay between short-range attraction and long-range repulsion of a wheat gliadin isolate by investigating the dynamics of liquid-liquid phase separation after temperature quench. We do so using time-resolved small angle light scattering, phase contrast microscopy and rheology. We show that gliadins undergo liquid-liquid phase separation through Nucleation and Growth or Spinodal Decomposition depending on the quench depth. They assemble into dense phases but remain in a liquid-like state over an extended range of temperatures and concentrations. The analysis of phase separation kinetics reveals that the attraction strength of gliadins is in the same order of magnitude as other proteins. We discuss the respective role of competing interactions, protein intrinsic disorder, hydration and polydispersity in promoting local dynamics and providing this liquid-like behavior despite attractive forces.

Predicting the solubility of mixtures of sugars and their replacers using the Flory-Huggins theory

In this paper we investigate whether the Flory-Huggins theory can describe the thermodynamics of solutions of simple carbohydrates, like sugars and polyols. In particular, we focus on the description of the solubility of the carbohydrates in water. This is investigated for both binary and ternary mixtures, having two types of these carbohydrates. This research question arises especially in the case of bakery products, where one seeks to replace sucrose with other simple carbohydrates - which are often polyols. Based on the model parameters obtained from fitting the theory to the experimental data of binary solutions, we show that the theory can predict (a) solubility data for ternary mixtures, over a broad range of concentrations and temperatures, and (b) the deliquescence point of binary mixtures of carbohydrate crystals as a function of temperature. The theory can even be applied to carbohydrates, which form hydrate crystals. Together with our earlier theories on the thermodynamics of complex food mixtures, we have now a complete thermodynamic framework to describe the phase and state transitions of food materials as confectionery and bakery products, where the question of sucrose replacement is urgent.

Why Do Disordered and Structured Proteins Behave Differently in Phase Separation?

Intracellular membraneless organelles and their myriad cellular functions have garnered tremendous recent interest. It is becoming well accepted that they form via liquid-liquid phase separation (LLPS) of protein mixtures (often including RNA), where the organelles correspond to a protein-rich droplet phase coexisting with a protein-poor bulk phase. The major protein components contain disordered regions and often also RNA-binding domains, and the disordered fragments on their own easily undergo LLPS. By contrast, LLPS for structured proteins has been observed infrequently. The contrasting phase behaviors can be explained by modeling disordered and structured proteins, respectively, as polymers and colloids. These physical models also provide a better understanding of the regulation of droplet formation by cellular signals and its dysregulation leading to diseases.

Physical principles of intracellular organization via active and passive phase transitions

Exciting recent developments suggest that phase transitions represent an important and ubiquitous mechanism underlying intracellular organization. We describe key experimental findings in this area of study, as well as the application of classical theoretical approaches for quantitatively understanding these data. We also discuss the way in which equilibrium thermodynamic driving forces may interface with the fundamentally out-of-equilibrium nature of living cells. In particular, time and/or space-dependent concentration profiles may modulate the phase behavior of biomolecules in living cells. We suggest future directions for both theoretical and experimental work that will shed light on the way in which biological activity modulates the assembly, properties, and function of viscoelastic states of living matter.

Metastability Gap in the Phase Diagram of Monoclonal IgG Antibody

Crystallization of IgG antibodies has important applications in the fields of structural biology, biotechnology, and biopharmaceutics. However, a rational approach to crystallize antibodies is still lacking. In this work, we report a method to estimate the solubility of antibodies at various temperatures. We experimentally determined the full phase diagram of an IgG antibody. Using the full diagram, we examined the metastability gaps, i.e., the distance between the crystal solubility line and the liquid-liquid coexistence curve, of IgG antibodies. By comparing our results to the partial phase diagrams of other IgGs reported in literature, we found that IgG antibodies have similar metastability gaps. Thereby, we present an equation with two phenomenological parameters to predict the approximate location of the solubility line of IgG antibodies with respect to their liquid-liquid coexistence curves. We have previously shown that the coexistence curve of an antibody solution can be readily determined by the polyethylene glycol-induced liquid-liquid phase separation method. Combining the polyethylene glycol-induced liquid-liquid phase separation measurements and the phenomenological equation in this article, we provide a general and practical means to predict the thermodynamic conditions for crystallizing IgG antibodies in the solution environments of interest.

Nonclassical nucleation pathways in protein crystallization

Classical nucleation theory (CNT), which was established about 90 years ago, has been very successful in many research fields, and continues to be the most commonly used theory in describing the nucleation process. For a fluid-to-solid phase transition, CNT states that the solute molecules in a supersaturated solution reversibly form small clusters. Once the cluster size reaches a critical value, it becomes thermodynamically stable and 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 between the initial supersaturated solution and the final crystals. Depending on the exact free energy landscapes, the MIPs can be a high density liquid phase, mesoscopic clusters, or a pre-ordered state. In this review, we focus on the studies of nonclassical pathways in protein crystallization and discuss the applications of the various scenarios of two-step nucleation theory. In particular, we focus on protein solutions in the presence of multivalent salts, which serve as a model protein system to study the nucleation pathways. We wish to point out the unique features of proteins as model systems for further studies.

Nuclear Magnetic Resonance Structure of a Major Lens Protein, Human γC-Crystallin: Role of the Dipole Moment in Protein Solubility

A hallmark of the crystallin proteins is their exceptionally high solubility, which is vital for maintaining the high refractive index of the eye lens. Human γC-crystallin is a major γ-crystallin whose mutant forms are associated with congenital cataracts but whose three-dimensional structure is not known. An earlier study of a homology model concluded that human γC-crystallin has low intrinsic solubility, mainly because of the atypical magnitude and fluctuations of its dipole moment. On the contrary, the high-resolution tertiary structure of human γC-crystallin determined here shows unequivocally that it is a highly soluble, monomeric molecule in solution. Notable differences between the orientations and interactions of several side chains are observed upon comparison to those in the model. No evidence of the pivotal role ascribed to the effect of dipole moment on protein solubility was found. The nuclear magnetic resonance structure should facilitate a comprehensive understanding of the deleterious effects of cataract-associated mutations in human γC-crystallin.

Stable, metastable, and kinetically trapped amyloid aggregate phases

Self-assembly of proteins into amyloid fibrils plays a key role in a multitude of human disorders that range from Alzheimer's disease to type II diabetes. Compact oligomeric species, observed early during amyloid formation, are reported as the molecular entities responsible for the toxic effects of amyloid self-assembly. However, the relation between early-stage oligomeric aggregates and late-stage rigid fibrils, which are the hallmark structure of amyloid plaques, has remained unclear. We show that these different structures occupy well-defined regions in a peculiar phase diagram. Lysozyme amyloid oligomers and their curvilinear fibrils only form after they cross a salt and protein concentration-dependent threshold. We also determine a boundary for the onset of amyloid oligomer precipitation. The oligomeric aggregates are structurally distinct from rigid fibrils and are metastable against nucleation and growth of rigid fibrils. These experimentally determined boundaries match well with colloidal model predictions that account for salt-modulated charge repulsion. The model also incorporates the metastable and kinetic character of oligomer phases. Similarities and differences of amyloid oligomer assembly to metastable liquid-liquid phase separation of proteins and to surfactant aggregation are discussed.

Nucleation precursors in protein crystallization

Protein crystal nucleation is a central problem in biological crystallography and other areas of science, technology and medicine. Recent studies have demonstrated that protein crystal nuclei form within crucial precursors. Here, methods of detection and characterization of the precursors are reviewed: dynamic light scattering, atomic force microscopy and Brownian microscopy. Data for several proteins provided by these methods have demonstrated that the nucleation precursors are clusters consisting of protein-dense liquid, which are metastable with respect to the host protein solution. The clusters are several hundred nanometres in size, the cluster population occupies from 10(-7) to 10(-3) of the solution volume, and their properties in solutions supersaturated with respect to crystals are similar to those in homogeneous, i.e. undersaturated, solutions. The clusters exist owing to the conformation flexibility of the protein molecules, leading to exposure of hydrophobic surfaces and enhanced intermolecular binding. These results indicate that protein conformational flexibility might be the mechanism behind the metastable mesoscopic clusters and crystal nucleation. Investigations of the cluster properties are still in their infancy. Results on direct imaging of cluster behaviors and characterization of cluster mechanisms with a variety of proteins will soon lead to major breakthroughs in protein biophysics.

Reentrant condensation, liquid–liquid phase separation and crystallization in protein solutions induced by multivalent metal ions

We briefly summarize the recent progress in tuning protein interactions as well as phase behavior in protein solutions using multivalent metal ions. We focus on the influence of control parameters and the mechanism of reentrant condensation, the metastable liquid–liquid phase separation and classical vs. non-classical pathways of protein crystallization.

Structural fingerprints and their evolution during oligomeric vs. oligomer-free amyloid fibril growth

Deposits of fibrils formed by disease-specific proteins are the molecular hallmark of such diverse human disorders as Alzheimer's disease, type II diabetes, or rheumatoid arthritis. Amyloid fibril formation by structurally and functionally unrelated proteins exhibits many generic characteristics, most prominently the cross β-sheet structure of their mature fibrils. At the same time, amyloid formation tends to proceed along one of two separate assembly pathways yielding either stiff monomeric filaments or globular oligomers and curvilinear protofibrils. Given the focus on oligomers as major toxic species, the very existence of an oligomer-free assembly pathway is significant. Little is known, though, about the structure of the various intermediates emerging along different pathways and whether the pathways converge towards a common or distinct fibril structures. Using infrared spectroscopy we probed the structural evolution of intermediates and late-stage fibrils formed during in vitro lysozyme amyloid assembly along an oligomeric and oligomer-free pathway. Infrared spectroscopy confirmed that both pathways produced amyloid-specific β-sheet peaks, but at pathway-specific wavenumbers. We further found that the amyloid-specific dye thioflavin T responded to all intermediates along either pathway. The relative amplitudes of thioflavin T fluorescence responses displayed pathway-specific differences and could be utilized for monitoring the structural evolution of intermediates. Pathway-specific structural features obtained from infrared spectroscopy and Thioflavin T responses were identical for fibrils grown at highly acidic or at physiological pH values and showed no discernible effects of protein hydrolysis. Our results suggest that late-stage fibrils formed along either pathway are amyloidogenic in nature, but have distinguishable structural fingerprints. These pathway-specific fingerprints emerge during the earliest aggregation events and persist throughout the entire cascade of aggregation intermediates formed along each pathway.

The self-assembly, aggregation and phase transitions of food protein systems in one, two and three dimensions

The aggregation of proteins is of fundamental relevance in a number of daily phenomena, as important and diverse as blood coagulation, medical diseases, or cooking an egg in the kitchen. Colloidal food systems, in particular, are examples that have great significance for protein aggregation, not only for their importance and implications, which touches on everyday life, but also because they allow the limits of the colloidal science analogy to be tested in a much broader window of conditions, such as pH, ionic strength, concentration and temperature. Thus, studying the aggregation and self-assembly of proteins in foods challenges our understanding of these complex systems from both the molecular and statistical physics perspectives. Last but not least, food offers a unique playground to study the aggregation of proteins in three, two and one dimensions, that is to say, in the bulk, at air/water and oil/water interfaces and in protein fibrillation phenomena. In this review we will tackle this very ambitious task in order to discuss the current understanding of protein aggregation in the framework of foods, which is possibly one of the broadest contexts, yet is of tremendous daily relevance.

Phase diagrams and kinetics of phase transitions in protein solutions

The phase behavior of proteins is of interest for fundamental and practical reasons. The nucleation of new phases is one of the last major unresolved problems of nature. The formation of protein condensed phases (crystals, polymers, and other solid aggregates, as well as dense liquids and gels) underlies pathological conditions, plays a crucial role in the biological function of the respective protein, or is an essential part of laboratory and industrial processes. In this review, we focus on phase transitions of proteins in their properly folded state. We first summarize the recently acquired understanding of physical processes underlying the phase diagrams of the protein solutions and the thermodynamics of protein phase transitions. Then we review recent findings on the kinetics of nucleation of dense liquid droplets and crystals. We explore the transition from nucleation to spinodal decomposition for liquid-liquid separation and introduce the new concept of solution-to-crystal spinodal. We review the two-step mechanism of protein crystal nucleation, in which mesoscopic metastable protein clusters serve as precursors to the ordered crystal nuclei. The concepts and mechanisms reviewed here provide powerful tools for control of the nucleation process by varying the solution thermodynamic parameters.

The role of macromolecular crowding in the evolution of lens crystallins with high molecular refractive index

Crystallins are present in the lens at extremely high concentrations in order to provide transparency and generate a high refractive power of the lens. The crystallin families prevalent in the highest density lens tissues are γ-crystallins in vertebrates and S-crystallins in cephalopods. As shown elsewhere, in parallel evolution, both have evolved molecular refractive index increments 5-10% above those of most proteins. Although this is a small increase, it is statistically very significant and can be achieved only by very unusual amino acid compositions. In contrast, such a molecular adaptation to aid in the refractive function of the lens did not occur in crystallins that are preferentially located in lower density lens tissues, such as vertebrate α-crystallin and taxon-specific crystallins. In the current work, we apply a model of non-interacting hard spheres to examine the thermodynamic contributions of volume exclusion at lenticular protein concentrations. We show that the small concentration decrease afforded by the higher molecular refractive index increment of crystallins can amplify nonlinearly to produce order of magnitude differences in chemical activities, and lead to reduced osmotic pressure and the reduced propensity for protein aggregation. Quantitatively, this amplification sets in only at protein concentrations as high as those found in hard lenses or the nucleus of soft lenses, in good correspondence to the observed crystallin properties in different tissues and different species. This suggests that volume exclusion effects provide the evolutionary driving force for the unusual refractive properties and the unusual amino acid compositions of γ-crystallins and S-crystallins.

Mechanism of aggregation of UV-irradiated β(L)-crystallin

Thermal denaturation and aggregation of UV-irradiated β(L)-crystallin from eye lenses of steers have been studied. The data on size-exclusion chromatography and SDS-PAGE indicated that UV irradiation of β(L)-crystallin at 10 °С resulted in fragmentation of the protein molecule and formation of cross-linked aggregates. Fluorescence data showed that tryptophan fluorescence in the irradiated protein decreased exponentially with the UV dose. Decrease in tryptophan fluorescence is a result of photochemical destruction, but not of conformational changes of protein, because there is no red shift in the fluorescence maximum. The differential scanning calorimetry (DSC) profiles of the samples of UV-irradiated and wild type β(L)-crystallin were registered. The area under curves, which is proportional to the amount of the native protein, decreased exponentially with increasing the irradiation dose. The shape of the DSC profiles for the samples of UV-irradiated β(L)-crystallin was identical to that for wild type β(L)-crystallin. The DSC data allowed estimating the portion of UV-denatured β(L)-crystallin, which is not registered by DSC, and the portion of the combined fraction consisting of native and UV-damaged molecules retaining the native structure. A conclusion has been made that UV-induced denaturation of β(L)-crystallin follows the one-hit model. The study of the kinetics of thermal aggregation of UV-irradiated β(L)-crystallin at 37 °С using dynamic light scattering showed that the initial stage of aggregation was that of formation of the start aggregates with the hydrodynamic radius of 20 nm. Further sticking of the start aggregates proceeded in the regime of reaction-limited cluster-cluster aggregation. Splitting of the aggregate population into two components occurred above a definite point in time.

Nucleation

Crystallization starts with nucleation and control of nucleation is crucial for the control of the number, size, perfection, polymorphism and other characteristics of crystalline materials. This is particularly true for crystallization in solution, which is an essential part of processes in the chemical and pharmaceutical industries and a major step in physiological and pathological phenomena. There have been significant recent advances in the understanding of the mechanism of nucleation of crystals in solution. The foremost of these are the two-step mechanism of nucleation and the notion of the solution-crystal spinodal. According to the two-step mechanism, the crystalline nucleus appears inside pre-existing metastable clusters of size several hundred nanometers, which consist of dense liquid and are suspended in the solution. While initially proposed for protein crystals, the applicability of this mechanism has been demonstrated for small molecule organic materials, colloids, polymers, and biominerals. This mechanism helps to explain several long-standing puzzles of crystal nucleation in solution: nucleation rates which are many orders of magnitude lower than theoretical predictions, the significance of the dense protein liquid, and others. At high supersaturations typical of most crystallizing systems, the generation of crystal embryos occurs in the spinodal regime, where the nucleation barrier is negligible. The solution-crystal spinodal helps to understand the role of heterogeneous substrates in nucleation and the selection of crystalline polymorphs. Importantly, these ideas provide powerful tools for control of the nucleation process by varying the solution thermodynamic parameters.

The two-step mechanism of nucleation of crystals in solution

The formation of crystalline nanoparticles starts with nucleation and control of nucleation is crucial for the control of the number, size, perfection, polymorph modification and other characteristics of particles. Recently, there have been significant advances in the understanding of the mechanism of nucleation of crystals in solution. The most significant of these is the two-step mechanism of nucleation, according to which the crystalline nucleus appears inside pre-existing metastable clusters of size several hundred nanometers, which consist of dense liquid and are suspended in the solution. While initially proposed for protein crystals, the applicability of this mechanism has been demonstrated for small-molecule organic and inorganic materials, colloids, and biominerals. This mechanism helps to explain several long-standing puzzles of crystal nucleation in solution: nucleation rates which are many orders of magnitude lower than theoretical predictions, nucleation kinetic dependencies with steady or receding parts at increasing supersaturation, the role of heterogeneous substrates for polymorph selection, the significance of the dense protein liquid, and others. More importantly, this mechanism provides powerful tools for control of the nucleation process by varying the solution thermodynamic parameters so that the volume occupied by the dense liquid shrinks or expands.

Effects of ammonium sulfate and sodium chloride concentration on PEG/protein liquid-liquid phase separation

When added to protein solutions, poly(ethylene glycol) (PEG) creates an effective attraction between protein molecules due to depletion forces. This effect has been widely used to crystallize proteins, and PEG is among the most successful crystallization agents in current use. However, PEG is almost always used in combination with a salt at either low or relatively high concentrations. Here the effects of sodium chloride and ammonium sulfate concentration on PEG 8000/ovalbumin liquid-liquid (L-L) phase separation are investigated. At low salt the L-L phase separation occurs at decreasing protein concentration with increasing salt concentration, presumably due to repulsive electrostatic interactions between proteins. At high salt concentration, the behavior depends on the nature of the salt. Sodium chloride has little effect on the L-L phase separation, but ammonium sulfate decreases the protein concentration at which the L-L phase separation occurs. This trend is attributed to the effects of critical fluctuations on depletion forces. The implications of these results for designing solution conditions optimal for protein crystallization are discussed.

Shear effects on crystal nucleation in colloidal suspensions

Extensive two-dimensional Langevin dynamics simulations are used to determine the effect of steady shear flows on the crystal nucleation kinetics of charge stabilized colloids and colloids whose pair potential possess an attractive shallow well of a few k_{B}T 's (attractive colloids). Results show that in both types of systems small amounts of shear speeds up the crystallization process and enhances the quality of the growing crystal significantly. Moderate shear rates, on the other hand, destroy the ordering in the system. The very high shear rate regime where a reentering transition to the ordered state could exist is not considered in this work. In addition to the crystal nucleation phenomena, the analysis of the transport properties and the characterization of the steady state regime under shear are performed.

Fractal aggregates in protein crystal nucleation

Monte Carlo simulations of homogeneous nucleation for a protein model with an exceedingly short-ranged attractive potential yielded a nonconventional crystal nucleation mechanism, which proceeds by the formation of fractal, low-dimensional aggregates followed by a concurrent collapse and increase of the crystallinity of these aggregates to become compact ordered nuclei. This result corroborates a recently proposed two-step mechanism for protein crystal nucleation from solution.