Phase diagrams and kinetics of phase transitions in protein solutions

Molecular Serum Albumin Unmask Nanobio Properties of Molecular Graphenes in Shungite Carbon Nanoparticles

Serum albumin is a popular macromolecule for studying the effect of proteins on the colloidal stability of nanoparticle (NP) dispersions, as well as the protein-nanoparticle interaction and protein corona formation. In this work, we analyze the specific conformation-dependent phase, redox, and fatty acid delivery properties of bovine albumin in the presence of shungite carbon (ShC) molecular graphenes stabilized in aqueous dispersions in the form of NPs in order to reveal the features of NP bioactivity. The formation of NP complexes with proteins (protein corona around NP) affects the transport properties of albumin for the delivery of fatty acids. Being acceptors of electrons and ligands, ShC NPs are capable of exhibiting both their own biological activity and significantly affecting conformational and phase transformations in protein systems.

Pathologic polyglutamine aggregation begins with a self-poisoning polymer crystal

A long-standing goal of amyloid research has been to characterize the structural basis of the rate-determining nucleating event. However, the ephemeral nature of nucleation has made this goal unachievable with existing biochemistry, structural biology, and computational approaches. Here, we addressed that limitation for polyglutamine (polyQ), a polypeptide sequence that causes Huntington's and other amyloid-associated neurodegenerative diseases when its length exceeds a characteristic threshold. To identify essential features of the polyQ amyloid nucleus, we used a direct intracellular reporter of self-association to quantify frequencies of amyloid appearance as a function of concentration, conformational templates, and rational polyQ sequence permutations. We found that nucleation of pathologically expanded polyQ involves segments of three glutamine (Q) residues at every other position. We demonstrate using molecular simulations that this pattern encodes a four-stranded steric zipper with interdigitated Q side chains. Once formed, the zipper poisoned its own growth by engaging naive polypeptides on orthogonal faces, in a fashion characteristic of polymer crystals with intramolecular nuclei. We further show that self-poisoning can be exploited to block amyloid formation, by genetically oligomerizing polyQ prior to nucleation. By uncovering the physical nature of the rate-limiting event for polyQ aggregation in cells, our findings elucidate the molecular etiology of polyQ diseases.

Pathologic polyglutamine aggregation begins with a self-poisoning polymer crystal

A long-standing goal of amyloid research has been to characterize the structural basis of the rate-determining nucleating event. However, the ephemeral nature of nucleation has made this goal unachievable with existing biochemistry, structural biology, and computational approaches. Here, we addressed that limitation for polyglutamine (polyQ), a polypeptide sequence that causes Huntington's and other amyloid-associated neurodegenerative diseases when its length exceeds a characteristic threshold. To identify essential features of the polyQ amyloid nucleus, we used a direct intracellular reporter of self-association to quantify frequencies of amyloid appearance as a function of concentration, conformational templates, and rational polyQ sequence permutations. We found that nucleation of pathologically expanded polyQ involves segments of three glutamine (Q) residues at every other position. We demonstrate using molecular simulations that this pattern encodes a four-stranded steric zipper with interdigitated Q side chains. Once formed, the zipper poisoned its own growth by engaging naive polypeptides on orthogonal faces, in a fashion characteristic of polymer crystals with intramolecular nuclei. We further show that self-poisoning can be exploited to block amyloid formation, by genetically oligomerizing polyQ prior to nucleation. By uncovering the physical nature of the rate-limiting event for polyQ aggregation in cells, our findings elucidate the molecular etiology of polyQ diseases.

Polymorphic protein phase transitions driven by surface anisotropy

Phase transitions of proteins are strongly influenced by surface chemical modifications or mutations. Human γD-crystallin (HGD) single-mutants have been extensively studied because they are associated with the onset of juvenile cataract. However, they have also provided a rich library of molecules to examine how specific inter-protein interactions direct protein assembly, providing new insights and valuable experimental data for coarse-grained patchy-particle models. Here, we demonstrate that the addition of new inter-protein interactions by mutagenesis is additive and increases the number and variety of condensed phases formed by proteins. When double mutations incorporating two specific single point mutations are made, the properties of both single mutations are retained in addition to the formation of a new condensed phase. We find that the HGD double-mutant P23VC110M self-assembles into spherical particles with retrograde solubility, orthorhombic crystals, and needle/plate shape crystals, while retaining the ability to undergo liquid-liquid phase separation. This rich polymorphism is only partially predicted by the experimental data on the constituent single mutants. We also report a previously un-characterized amorphous protein particle, with unique properties that differ from those of protein spherulites, protein particulates previously described. The particles we observe are amorphous, reversible with temperature, tens of microns in size, and perfectly spherical. When they are grown on pristine surfaces, they appear to form by homogeneous nucleation, making them unique, and we believe a new form of protein condensate. This work highlights the challenges in predicting protein behavior, which has frustrated rational assembly and crystallization but also provides rich data to develop new coarse-grained models to explain the observed polymorphism.

A nucleation barrier spring-loads the CBM signalosome for binary activation

Immune cells activate in binary, switch-like fashion via large protein assemblies known as signalosomes, but the molecular mechanism of the switch is not yet understood. Here, we employed an in-cell biophysical approach to dissect the assembly mechanism of the CARD-BCL10-MALT1 (CBM) signalosome, which governs nuclear transcription factor-κB activation in both innate and adaptive immunity. We found that the switch consists of a sequence-encoded and deeply conserved nucleation barrier to ordered polymerization by the adaptor protein BCL10. The particular structure of the BCL10 polymers did not matter for activity. Using optogenetic tools and single-cell transcriptional reporters, we discovered that endogenous BCL10 is functionally supersaturated even in unstimulated human cells, and this results in a predetermined response to stimulation upon nucleation by activated CARD multimers. Our findings may inform on the progressive nature of age-associated inflammation, and suggest that signalosome structure has evolved via selection for kinetic rather than equilibrium properties of the proteins.

The innate immune system is the body’s first line of defence against pathogens. Although innate immune cells do not recognize specific disease-causing agents, they can detect extremely low levels of harmful organisms or substances. In response, they activate signals that lead to inflammation, which tells other cells that there is an infection. Innate immune cells are turned on in a switch-like fashion, becoming active very quickly after interacting with a pathogen. This is due to the action of signalosomes, large complexes made up of several proteins that clump together to form long chains that activate the cell.

But how do these large protein complexes assemble quick enough to create the switch-like activation observed in innate immune cells? To answer this question, Rodríguez Gama et al. focused on the CBM signalosome, which is involved in triggering inflammation through the activation of a protein called NF-kB.

First, Rodríguez Gama et al. used genetic tools to determine that activating the CBM signalosome drives a switch-like activation of NF-kB in cells. This means that individual cells in a population either become fully activated or not at all in response to minute amounts of harmful substances.

Once they had established this, Rodríguez Gama et al. wanted to know which protein in the CBM signalosome was responsible for the switch. They found that one of the proteins in the signalosome, called BCL10, has a ‘nucleation barrier’ encoded in its sequence. This means that it is very hard for BCL10 to start clumping together, but once it does, the clumps grow on their own. The nucleation barrier describes exactly how hard it is for these clumps to get started, and is determined by how disorganized the protein is.

When a pathogen ‘stimulates’ an immune cell, a tiny template is formed that lowers the nucleation barrier so that BCL10 can then aggregate itself together, leading to the switch-like behaviour observed. The nucleation barrier allows there to be more than enough BCL10 present in the cell at all times – ready to clump together at a moment’s notice – and this permits the cell to detect very low levels of a pathogen.

Rodríguez Gama et al. then tested whether BCL10 from other animals also has a nucleation barrier. They found that this feature is conserved from cnidarians, such as corals or jellyfish, to mammals, including humans. This suggests that the use of nucleation barriers to regulate innate immune signalling has existed for a long time throughout evolution.

The work by Rodríguez Gama et al. broadens our understanding of how the innate immune system senses and responds to extremely low levels of pathogens. That BCL10 is always ready to clump together suggests it may be a driving force for chronic and age-associated inflammation. Additionally, the findings of Rodríguez Gama et al. also offer insights into how other signalosomes may become activated, and offer the possibility of new drugs aimed at modifying nucleation barriers.

Reversible Kinetic Trapping of FUS Biomolecular Condensates

Formation of membrane-less organelles by self-assembly of disordered proteins can be triggered by external stimuli such as pH, salt, or temperature. These organelles, called biomolecular condensates, have traditionally been classified as liquids, gels, or solids with limited subclasses. Here, the authors show that a thermal trigger can lead to formation of at least two distinct liquid condensed phases of the fused in sarcoma low complexity (FUS LC) domain. Forming FUS LC condensates directly at low temperature leads to formation of metastable, kinetically trapped condensates that show arrested coalescence, escape from which to untrapped condensates can be achieved via thermal annealing. Using experimental and computational approaches, the authors find that molecular structure of interfacial FUS LC in kinetically trapped condensates is distinct (more β-sheet like) compared to untrapped FUS LC condensates. Moreover, molecular motion within kinetically trapped condensates is substantially slower compared to that in untrapped condensates thereby demonstrating two unique liquid FUS condensates. Controlling condensate thermodynamic state, stability, and structure with a simple thermal switch may contribute to pathological protein aggregate stability and provides a facile method to trigger condensate mixing for biotechnology applications.

Surface Exposed Free Cysteine Suppresses Crystallization of Human γD-Crystallin

Human γD-crystallin (HGD) has remarkable stability against condensation in the human lens, sometimes over a whole lifetime. The native protein has a surface exposed free cysteine that forms dimers (Benedek, 1997; Ramkumar et al., 1864)^1,2 without specific biological function and leads to further protein association and/or aggregation, which creates a paradox for understanding its stability. Previous work has demonstrated that chemical modification of the protein at the free cysteine (C110), increases the temperature at which liquid-liquid phase separation occurs (LLPS), lowers protein solubility and suggests an important role for this amino acid in maintaining its long-term resistance to condensation. Here we demonstrate that mutation of the cysteine does not alter the structure or solubility (liquidus) line for the protein, but dramatically increases the protein crystal nucleation rate following LLPS, suggesting that the free cysteine has a vital role in suppressing crystallization in the human lens.

Effect of a Good buffer on the fate of metastable protein-rich droplets near physiological composition

Metastable protein-rich microdroplets are produced from liquid-liquid phase separation (LLPS) of protein aqueous solutions. These globules can be intermediates for the formation of other protein-rich phases. Lysozyme aqueous solutions undergo LLPS around 0 °C in the presence of NaCl near physiological conditions. Here, it is shown that insertion of small amounts of 4-(2-hydroxyethyl)-1-piperazineethanesulfonate (HEPES, 0.1 M) as a second additive to lysozyme-NaCl-water solutions near physiological ionic strength (0.2 M) is an essential step for triggering conversion of protein-rich droplets into another phase. Specifically, LLPS induced by cooling reproducibly leads to a rapid and high-yield formation of compact tetragonal crystalline microparticles only in the presence of HEPES. These microcrystals exhibit small size (1-3 μm), narrow size distribution and guest-binding properties. The temperature-concentration phase diagram shows a characteristic topology with LLPS boundary metastable with respect to tetragonal microcrystals, which in turn become less stable than rod-shaped orthorhombic crystals above 40 °C. Interestingly, dynamic light scattering, hydrogen-ion titrations and isothermal titration calorimetry reveal that lysozyme-HEPES interactions were found to be weakly attractive and exothermic. Our findings indicate that additives of salting-in type can represent an important factor controlling the fate of metastable protein-rich microdroplets relevant to drug formulations, femtosecond crystallography, and potential implications in protein-driven cytoplasmic compartmentalization.

Iron Dysregulation and Inflammagens Related to Oral and Gut Health Are Central to the Development of Parkinson's Disease

Neuronal lesions in Parkinson's disease (PD) are commonly associated with α-synuclein (α-Syn)-induced cell damage that are present both in the central and peripheral nervous systems of patients, with the enteric nervous system also being especially vulnerable. Here, we bring together evidence that the development and presence of PD depends on specific sets of interlinking factors that include neuroinflammation, systemic inflammation, α-Syn-induced cell damage, vascular dysfunction, iron dysregulation, and gut and periodontal dysbiosis. We argue that there is significant evidence that bacterial inflammagens fuel this systemic inflammation, and might be central to the development of PD. We also discuss the processes whereby bacterial inflammagens may be involved in causing nucleation of proteins, including of α-Syn. Lastly, we review evidence that iron chelation, pre-and probiotics, as well as antibiotics and faecal transplant treatment might be valuable treatments in PD. A most important consideration, however, is that these therapeutic options need to be validated and tested in randomized controlled clinical trials. However, targeting underlying mechanisms of PD, including gut dysbiosis and iron toxicity, have potentially opened up possibilities of a wide variety of novel treatments, which may relieve the characteristic motor and nonmotor deficits of PD, and may even slow the progression and/or accompanying gut-related conditions of the disease.

Optimization of crystallization of biological macromolecules using dialysis combined with temperature control

A rational way to find the appropriate conditions to grow crystal samples for bio-crystallography is to determine the crystallization phase diagram, which allows precise control of the parameters affecting the crystal growth process. First, the nucleation is induced at supersaturated conditions close to the solubility boundary between the nucleation and metastable regions. Then, crystal growth is further achieved in the metastable zone - which is the optimal location for slow and ordered crystal expansion - by modulation of specific physical parameters. Recently, a prototype of an integrated apparatus for the rational optimization of crystal growth by mapping and manipulating temperature-precipitant-concentration phase diagrams has been constructed. Here, it is demonstrated that a thorough knowledge of the phase diagram is vital in any crystallization experiment. The relevance of the selection of the starting position and the kinetic pathway undertaken in controlling most of the final properties of the synthesized crystals is shown. The rational crystallization optimization strategies developed and presented here allow tailoring of crystal size and diffraction quality, significantly reducing the time, effort and amount of expensive protein material required for structure determination.

A stepwise mechanism for aqueous two-phase system formation in concentrated antibody solutions

Aqueous two-phase system (ATPS) formation is the macroscopic completion of liquid-liquid phase separation (LLPS), a process by which aqueous solutions demix into 2 distinct phases. We report the temperature-dependent kinetics of ATPS formation for solutions containing a monoclonal antibody and polyethylene glycol. Measurements are made by capturing dark-field images of protein-rich droplet suspensions as a function of time along a linear temperature gradient. The rate constants for ATPS formation fall into 3 kinetically distinct categories that are directly visualized along the temperature gradient. In the metastable region, just below the phase separation temperature, T _ph , ATPS formation is slow and has a large negative apparent activation energy. By contrast, ATPS formation proceeds more rapidly in the spinodal region, below the metastable temperature, T _meta , and a small positive apparent activation energy is observed. These region-specific apparent activation energies suggest that ATPS formation involves 2 steps with opposite temperature dependencies. Droplet growth is the first step, which accelerates with decreasing temperature as the solution becomes increasingly supersaturated. The second step, however, involves droplet coalescence and is proportional to temperature. It becomes the rate-limiting step in the spinodal region. At even colder temperatures, below a gelation temperature, T _gel , the proteins assemble into a kinetically trapped gel state that arrests ATPS formation. The kinetics of ATPS formation near T _gel is associated with a remarkably fragile solid-like gel structure, which can form below either the metastable or the spinodal region of the phase diagram.

Self-organization across scales: from molecules to organisms

Creating ordered structures from chaotic environments is at the core of biological processes at the subcellular, cellular and organismic level. In this perspective, we explore the physical as well as biological features of two prominent concepts driving self-organization, namely phase transition and reaction-diffusion, before closing with a discussion on open questions and future challenges associated with studying self-organizing systems.This article is part of the theme issue 'Self-organization in cell biology'.

Quantifying Nucleation In Vivo Reveals the Physical Basis of Prion-like Phase Behavior

Protein self-assemblies modulate protein activities over biological timescales that can exceed the lifetimes of the proteins or even the cells that harbor them. We hypothesized that these timescales relate to kinetic barriers inherent to the nucleation of ordered phases. To investigate nucleation barriers in living cells, we developed distributed amphifluoric FRET (DAmFRET). DAmFRET exploits a photoconvertible fluorophore, heterogeneous expression, and large cell numbers to quantify via flow cytometry the extent of a protein's self-assembly as a function of cellular concentration. We show that kinetic barriers limit the nucleation of ordered self-assemblies and that the persistence of the barriers with respect to concentration relates to structure. Supersaturation resulting from sequence-encoded nucleation barriers gave rise to prion behavior and enabled a prion-forming protein, Sup35 PrD, to partition into dynamic intracellular condensates or to form toxic aggregates. Our results suggest that nucleation barriers govern cytoplasmic inheritance, subcellular organization, and proteotoxicity.

Observable Two-Step Nucleation Mechanism in Solid-State Formation of Tungsten Carbide

The nucleation of crystals from ubiquitous solid-state reactions impacts a wide range of natural and synthetic processes and is fundamental to physical and chemical synthesis. However, the microscopic organization mechanism of amorphous precursors to nanoscale clusters of ordered atoms (nucleus) in an all-solid environment is inaccessible by common experimental probes. Here, by using in situ transmission electron microscopy in combination with theoretical simulations, we show in the reactive formation of a metal carbide that nucleation actually occurs via a two-step mechanism, in which a spinodal-structured amorphous intermediate reorganizes from an amorphous precursor and precedes the emergence of a crystalline nucleus, rather than direct one-step nucleation from classical consideration. We further isolated a series of sophisticated dynamics during formation and development of the nucleus in real-space and interpreted them by thermodynamic favorability. We anticipate that such an indirect organization mechanism which contains a metastable intermedium among the free energy gap between precursors and nanocrystals has its chance in underlying most solid-state crystallizations, whereas the as-established experimental method represents a step forward in exploring fundamentals in chemical reaction, material engineering, etc.

Quantitative Evaluation of Protein Solubility in Aqueous Solutions by PEG-Induced Liquid-Liquid Phase Separation

This chapter describes an experimental method to quantitatively evaluate the solubility of proteins in aqueous solutions. Measurement of protein solubility can be challenging because low solubility can be manifested through various pathways (e.g., crystallization, aggregation, gelation, and liquid-liquid phase separation), some of which may occur over long periods of time. In the method described here, a nonionic polymer, polyethylene glycol (PEG), is added to a protein solution of interest to induce instantaneous formation of protein-rich liquid droplets. After incubation at a given temperature, the samples are centrifuged. The protein concentration in the supernatant is measured at various PEG concentrations to calculate an equilibrium binding free energy, which provides a measure of protein solubility. Based on the first principles of thermodynamics, this method is highly reproducible and applicable to various proteins and buffer conditions.

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.

Physico-chemical characteristics of evaporating respiratory fluid droplets

The detailed physico-chemical characteristics of respiratory droplets in ambient air, where they are subject to evaporation, are poorly understood. Changes in the concentration and phase of major components in a droplet-salt (NaCl), protein (mucin) and surfactant (dipalmitoylphosphatidylcholine)-may affect the viability of any pathogens contained within it and thus may affect the efficiency of transmission of infectious disease by droplets and aerosols. The objective of this study is to investigate the effect of relative humidity (RH) on the physico-chemical characteristics of evaporating droplets of model respiratory fluids. We labelled these components in model respiratory fluids and observed evaporating droplets suspended on a superhydrophobic surface using optical and fluorescence microscopy. When exposed to continuously decreasing RH, droplets of different model respiratory fluids assumed different morphologies. Loss of water induced phase separation as well as indication of a decrease in pH. The presence of surfactant inhibited the rapid rehydration of the non-volatile components. An enveloped virus, ϕ6, that has been proposed as a surrogate for influenza virus appeared to be homogeneously distributed throughout the dried droplet. We hypothesize that the increasing acidity and salinity in evaporating respiratory droplets may affect the structure of the virus, although at low enough RH, crystallization of the droplet components may eliminate their harmful effects.

Octamer formation in lysozyme solutions at the initial crystallization stage detected by small-angle neutron scattering

Solutions of lysozyme in heavy water were studied by small-angle neutron scattering (SANS) at concentrations of 40, 20 and 10 mg ml^-1 with and without the addition of precipitant, and at temperatures of 10, 20 and 30°C. In addition to the expected protein monomers, dimeric and octameric species were identified in solutions at the maximum concentration and close to the optimal conditions for crystallization. An optimal temperature for octamer formation was identified and both deviation from this temperature and a reduction in protein concentration led to a significant decrease in the volume fractions of octamers detected. In the absence of precipitant, only monomers and a minor fraction of dimers are present in solution.

Nucleation and growth of a core-shell composite nucleus by diffusion

The critical radius of a core-shell-type nucleus grown by diffusion in a phase-separated solution is studied. A kinetic critical radius rather than the thermodynamic critical radius of standard classical nucleation theory can be defined from the diffusional growth equations. It is shown that there exist two kinetic critical radii for the core-shell-type nucleus, for which both the inner-core radius and the outer-shell radius will be stationary. Therefore, these two critical radii correspond to a single critical point of the nucleation path with a single energy barrier even though the nucleation looks like a two-step process. The two radii are given by formulas similar to that of classical nucleation theory if the Ostwald-Freundlich boundary condition is imposed at the surface of the inner nucleus and that of the outer shell. The subsequent growth of a core-shell-type postcritical nucleus follows the classical picture of Ostwald's step rule. Our result is consistent with some of the experimental and numerical results which suggest the core-shell-type critical nucleus.

Second Virial Coefficient As Determined from Protein Phase Behavior

We quantitatively link the macroscopic phase behavior of protein solutions to protein-protein interactions based on a coarse-grained colloidal approach. We exploit the extended law of corresponding states and apply the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory in order to infer the second virial coefficient b₂, an integral measure of the interaction potential, from the phase behavior, namely, cloud-point temperature (CPT) measurements under conditions favoring protein crystallization. This determination of b₂ yields values that quantitatively agree with the results of static light scattering (SLS) experiments. The strength of the attractions is quantified in terms of an effective Hamaker constant, which accounts for van der Waals attractions as well as non-DLVO forces, such as hydration and hydrophobic interactions. Our approach based on simple lab experiments to determine the CPT in combination with the DLVO theory is expected to facilitate further biophysical research on protein-protein interactions in complex solution environments.

Multistep nucleation of nanocrystals in aqueous solution

The nucleation and growth of solids from solutions impacts many natural processes and is fundamental to applications in materials engineering and medicine. For a crystalline solid, the nucleus is a nanoscale cluster of ordered atoms that forms through mechanisms still poorly understood. In particular, it is unclear whether a nucleus forms spontaneously from solution via a single- or multiple-step process. Here, using in situ electron microscopy, we show how gold and silver nanocrystals nucleate from supersaturated aqueous solutions in three distinct steps: spinodal decomposition into solute-rich and solute-poor liquid phases, nucleation of amorphous nanoclusters within the metal-rich liquid phase, followed by crystallization of these amorphous clusters. Our ab initio calculations on gold nucleation suggest that these steps might be associated with strong gold-gold atom coupling and water-mediated metastable gold complexes. The understanding of intermediate steps in nuclei formation has important implications for the formation and growth of both crystalline and amorphous materials.

Self-crowding induced phase separation in protein dispersions

The coupling between protein conformation, molecular volume, and solution phase behaviour is studied theoretically for a two-state, coarse-grained protein model in which protein molecules can reversibly switch between a native and a non-native excited state. In the model, native and non-native conformers are represented by perfect spheres with different hard-core diameters. We presume the larger, non-native species to attract each other through some unspecified potential. We find that at low concentrations the native state is stabilised energetically and that at high concentrations the native state is again stabilised but this time by self-crowding, i.e., a lack of free volume. These two regimes are separated by two first-order transitions from a region where the non-native conformational state is prevalent, stabilised by attractive interactions between the proteins. The calculated phase diagram is very sensitive to even quite small differences in particle volumes and has unusual features, including the loss of a critical point if the size difference is sufficiently large.

Amorphous Aggregation of Cytochrome c with Inherently Low Amyloidogenicity Is Characterized by the Metastability of Supersaturation and the Phase Diagram

Despite extensive studies on the folding and function of cytochrome c, the mechanisms underlying its aggregation remain largely unknown. We herein examined the aggregation behavior of the physiologically relevant two types of cytochrome c, metal-bound cytochrome c, and its fragment with high amyloidogenicity as predicted in alcohol/water mixtures. Although the aggregation propensity of holo cytochrome c was low due to high solubility, markedly unfolded apo cytochrome c, lacking the heme prosthetic group, strongly promoted the propensity for amorphous aggregation with increases in hydrophobicity. Silver-bound apo cytochrome c increased the capacity of fibrillar aggregation (i.e., protofibrils or immature fibrils) due to subtle structural changes of apo cytochrome c by strong binding of silver. However, mature amyloid fibrils were not detected for any of the cytochrome c variants or its fragment, even with extensive ultrasonication, which is a powerful amyloid inducer. These results revealed the intrinsically low amyloidogenicity of cytochrome c, which is beneficial for its homeostasis and function by facilitating the folding and minimizing irreversible amyloid formation. We propose that intrinsically low amyloidogenicity of cytochrome c is attributed to the low metastability of supersaturation. The phase diagram constructed based on solubility and aggregate type is useful for a comprehensive understanding of protein aggregation. Furthermore, amorphous aggregation, which is also viewed as a generic property of proteins, and amyloid fibrillation can be distinguished from each other by the metastability of supersaturation.

Oligomers of Heat-Shock Proteins: Structures That Don't Imply Function

Most proteins must remain soluble in the cytosol in order to perform their biological functions. To protect against undesired protein aggregation, living cells maintain a population of molecular chaperones that ensure the solubility of the proteome. Here we report simulations of a lattice model of interacting proteins to understand how low concentrations of passive molecular chaperones, such as small heat-shock proteins, suppress thermodynamic instabilities in protein solutions. Given fixed concentrations of chaperones and client proteins, the solubility of the proteome can be increased by tuning the chaperone-client binding strength. Surprisingly, we find that the binding strength that optimizes solubility while preventing irreversible chaperone binding also promotes the formation of weakly bound chaperone oligomers, although the presence of these oligomers does not significantly affect the thermodynamic stability of the solution. Such oligomers are commonly observed in experiments on small heat-shock proteins, but their connection to the biological function of these chaperones has remained unclear. Our simulations suggest that this clustering may not have any essential biological function, but rather emerges as a natural side-effect of optimizing the thermodynamic stability of the proteome.

Effect of Excipients on Liquid-Liquid Phase Separation and Aggregation in Dual Variable Domain Immunoglobulin Protein Solutions

Liquid-liquid phase separation (LLPS) and aggregation can reduce the physical stability of therapeutic protein formulations. On undergoing LLPS, the protein-rich phase can promote aggregation during storage due to high concentration of the protein. Effect of different excipients on aggregation in protein solution is well documented; however data on the effect of excipients on LLPS is scarce in the literature. In this study, the effect of four excipients (PEG 400, Tween 80, sucrose, and hydroxypropyl beta-cyclodextrin (HPβCD)) on liquid-liquid phase separation and aggregation in a dual variable domain immunoglobulin protein solution was investigated. Sucrose suppressed both LLPS and aggregation, Tween 80 had no effect on either, and PEG 400 increased LLPS and aggregation. Attractive protein-protein interactions and liquid-liquid phase separation decreased with increasing concentration of HPβCD, indicating its specific binding to the protein. However, HPβCD had no effect on the formation of soluble aggregates and fragments in this study. LLPS and aggregation are highly temperature dependent; at low temperature protein exhibits LLPS, at high temperature protein exhibits aggregation, and at an intermediate temperature both phenomena occur simultaneously depending on the solution conditions.

Protein collapse driven against solvation free energy without H-bonds

Proteins collapse and fold because intramolecular interactions and solvent entropy, which favor collapse, outweigh solute-solvent interactions that favor expansion. Since the protein backbone actively participates in protein folding and some intrinsically disordered proteins are glycine rich, oligoglycines are good models to study the protein backbone as it collapses, both during conformational changes in disordered proteins and during folding. The solvation free energies of short glycine oligomers become increasingly favorable as chain length increases. In contrast, the solubility limits of glycine oligomers decrease with increasing chain length, indicating that peptide-peptide, and potentially solvent-solvent interactions, overcome peptide-solvent interactions to favor aggregation at finite concentrations of glycine oligomers. We have recently shown that hydrogen- (H-) bonds do not contribute significantly to the concentration-based aggregation of pentaglycines but that dipole-dipole (CO) interactions between the amide groups on the backbone do. Here we demonstrate for the collapse of oligoglycines ranging in length from 15 to 25 residues similarly that H-bonds do not contribute significantly to collapse but that CO dipole interactions do. These results illustrate that some intrapeptide interactions that determine the solubility limit of short glycine oligomers are similar to those that drive the collapse of longer glycine peptides.

Phase separation in solutions with specific and nonspecific interactions

Protein solutions, which tend to be thermodynamically stable under physiological conditions, can demix into protein-enriched and protein-depleted phases when stressed. Using a lattice-gas model of proteins with both isotropic and specific, directional interactions, we calculate the critical conditions for phase separation for model proteins with up to four patches via Monte Carlo simulations and statistical associating fluid theory. Given a fixed specific interaction strength, the critical value of the isotropic energy, which accounts for dispersion forces and nonspecific interactions, measures the stability of the solution with respect to nonspecific interactions. Phase separation is suppressed by the formation of protein complexes, which effectively passivate the strongly associating sites on the monomers. Nevertheless, we find that protein models with three or more patches can form extended aggregates that phase separate despite the assembly of passivated complexes, even in the absence of nonspecific interactions. We present a unified view of the critical behavior of model fluids with anisotropic interactions, and we discuss the implications of these results for the thermodynamic stability of protein solutions.

The role of flexibility and molecular shape in the crystallization of proteins by surface mutagenesis

Proteins are dynamic systems and interact with their environment. The analysis of crystal contacts in the most accurately determined protein structures (d < 1.5 Å) reveals that in contrast to current views, static disorder and high side-chain entropy are common in the crystal contact area. These observations challenge the validity of the theory that presumes that the occurrence of well ordered patches of side chains at the surface is an essential prerequisite for a successful crystallization event. The present paper provides evidence in support of the approach for understanding protein crystallization as a process dependent on multiple factors, each with its relative contribution, rather than a phenomenon driven by a few dominant physicochemical characteristics. The role of the molecular shape as a factor in the crystallization of proteins by surface mutagenesis is discussed.

Opalescence in monoclonal antibody solutions and its correlation with intermolecular interactions in dilute and concentrated solutions

Opalescence indicates physical instability of a formulation because of the presence of aggregates or liquid-liquid phase separation in solution and has been reported for monoclonal antibody (mAb) formulations. Increased solution opalescence can be attributed to attractive protein-protein interactions (PPIs). Techniques including light scattering, AUC, or membrane osmometry are routinely employed to measure PPIs in dilute solutions, whereas opalescence is seen at relatively higher concentrations, where both long- and short-range forces contribute to overall PPIs. The mAb molecule studied here shows a unique property of high opalescence because of liquid-liquid phase separation. In this study, opalescence measurements are correlated to PPIs measured in diluted and concentrated solutions using light scattering (kD ) and high-frequency rheology (G'), respectively. Charges on the molecules were calculated using zeta potential measurements. Results indicate that high opalescence and phase separation are a result of the attractive interactions in solution; however, the presence of attractive interactions do not always imply phase separation. Temperature dependence of opalescence suggests that thermodynamic contribution to opalescence is significant and Tcloud can be utilized as a potential tool to assess attractive interactions in solution.

Solubility and aggregation of Gly(5) in water

Experimentally, the solubility of oligoglycines in water decreases as its length increases. Computationally, the free energy of solvation becomes more favorable with chain length for short (n = 1–5) oligoglycines. We present results of large scale simulations with over 600 pentaglycines at varying concentrations in explicit solvent to consider the mechanism of aggregation. The solubility limit of Gly₅ for the force field used was calculated and compared with experimental values. We find that intermolecular interactions between pentaglycines are favored over interactions between glycine and water, leading to their aggregation. However, the interaction driving peptide associations, liquid–liquid phase separation, are not predominantly hydrogen bonding. Instead, non-hydrogen bonding interactions between partially charged atoms on the peptide backbone allow the formation of dipole–dipole and charge layering correlations that mechanistically stabilize the formation of large, stable peptide clusters.

Multiphase water-in-oil emulsion droplets for cell-free transcription-translation

The construction of genetically encoded cellular mimics in compartments containing organized synthetic cytosols is desirable for the development of artificial cells. Phase separated aqueous domains were placed within water-in-oil emulsion droplets in a manner compatible with transcription and translation machinery. Aqueous two-phase and three-phase systems (ATPS and A3PS) were assembled with dextran, poly(ethylene glycol), and Ficoll. Aqueous two-phase systems were capable of supporting the cell-free expression of protein within water droplets, whereas the aqueous three-phase-based system did not give rise to detectable protein synthesis. The expressed protein preferentially partitioned to the dextran-enriched phase. The system could serve as a foundation for building cellular mimics with liquid organelles.

Nucleation and growth by diffusion under Ostwald-Freundlich boundary condition

The critical radius of a nucleus grown by diffusion in a solution is studied thermodynamically as well as kinetically. The thermodynamic growth equation called Zeldovich equation of classical nucleation theory and the kinetic diffusional growth equation combined with the Ostwald-Freundlich boundary condition lead to the same critical radius. However, it should be pointed out that the diffusional equation may lead to a kinetic critical radius that is different from the thermodynamic critical radius, thus indicating the possibility of kinetically controlling the critical radius of a nucleus.

Phase separation as a possible means of nuclear compartmentalization

The nucleus is perhaps the most familiar organelle within eukaryotic cells, serving as a compartment to house the genetic material. The nuclear volume is subdivided into a variety of functional and dynamic nuclear bodies not separated from the nucleoplasm by membranes. It has been hypothesized that aqueous phase separation brought about by macromolecular crowding may be in part responsible for these intranuclear compartments. This chapter discusses macromolecular solution chemistry with regard to several common types of phase separation in polymer solutions as well as to recent evidence that suggests that cytoplasmic and nuclear bodies may exist as liquid phases. We then examine the functional significance of phase separation and how it may serve as a means of compartmentalizing various nuclear activities, and describe recent studies that have used simple model systems to generate coexisting aqueous phase compartments, concentrate molecules within them, and perform localized biochemical reactions.

Nucleation pathway of core-shell composite nucleus in size and composition space and in component space

The kinetics of nucleation of a core-shell composite nucleus that consists of a core of stable final phase surrounded by a wetting layer of intermediate metastable phase is studied using the kinetic theory of binary nucleation not only in the size and composition space but also in the component space. The steady-state solution of the Fokker-Planck equation is considered. Various formulas for the critical nucleus at the saddle point as well as for the postcritical nucleus are derived. The kinetics of nucleation at the saddle point is more appropriately characterized in the size and composition space, while the kinetics of the postcritical nucleus is more appropriately described in the component space. Although both the free-energy landscape and the reaction rates play decisive role to determine the kinetics of nucleation at the saddle point, the details of the free-energy landscape are irrelevant to the kinetics of the postcritical nucleus.