Protein crystallization

Supersaturation, a Critical Factor Underlying Proteostasis of Amyloid Fibril Formation

From a physicochemical viewpoint, amyloid fibril formation is a phase transition from soluble to crystal-like sates limited by supersaturation. It occurs only above solubility (i.e., the solubility limit) coupled with a breakdown of supersaturation. Although many studies have examined the role of molecular chaperones in the context of proteostasis, the role of supersaturation has not been addressed. Moreover, although molecular chaperone-dependent disaggregations have been reported for preformed amyloid fibrils, amyloid fibrils will not dissolve above the solubility of monomers, even if agitations fragment long fibrils to shorter amyloid particles. On the other hand, on considering a reversible and coupled equilibrium of interactions, folding/unfolding and amyloid formation/disaggregation, molecules stabilizing native states can work as a disaggregase reversing the amyloid fibrils to monomers. It is likely that the proteostasis network has various intra- and extracellular components which disaggregate preformed amyloid fibrils as well as prevent amyloid formation. Further studies with a view of solubility and supersaturation will be essential for comprehensive understanding of proteostasis.

Protecting Proteins from Desiccation Stress Using Molecular Glasses and Gels

Faced with desiccation stress, many organisms deploy strategies to maintain the integrity of their cellular components. Amorphous glassy media composed of small molecular solutes or protein gels present general strategies for protecting against drying. We review these strategies and the proposed molecular mechanisms to explain protein protection in a vitreous matrix under conditions of low hydration. We also describe efforts to exploit similar strategies in technological applications for protecting proteins in dry or highly desiccated states. Finally, we outline open questions and possibilities for future explorations.

Bridging attraction of condensed bovine serum albumin solution in the presence of trivalent ions: A SANS study

The bridging attraction of condensed bovine serum albumin (BSA) solution (D2O) in the presence of yttrium chloride (YCl3) was studied by small angle neutron scattering (SANS). With increasing the concentration of YCl3 (cY) from 3 to 15 mM and from 15 to 100 mM, the intensity in low-q region increases and then decreases. Combining the tri-axial ellipsoid (TaE) geometry and the multi-component sticky hard sphere (SHS) potential, a SHS-TaE model was established to quantitatively determine the size and distribution of particles. In this way, the structural mechanism of the aggregation-redissolution process in protein solution was demonstrated and discussed. As cY increases from 3 to 100 mM, the SHS radius rL decreases from ca. 2.97 to 2.50 nm, suggesting that the relatively well dispersed BSAs may form aggregates with various polydispersities. The axis a increases from 1.88 to 2.30 nm, while b and c decrease from 3.53 to 3.23 nm and from 4.12 to 3.55 nm, respectively. (RgTaE decreases from ca. 2.57 to 2.38 nm). Moreover, the scattering length density (SLD) of BSA decreases from 3.67 to 1.56 × 10-6 Å-2. All these results consistently indicate a strengthened attraction and the BSA molecules might shrink and tune out to be more like of oblate ellipsoid with increasing the amount of YCl3.

In Situ Kinetic Observations on Crystal Nucleation and Growth

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

Calibration-free PAT: Locating selective crystallization or precipitation sweet spot in screenings with multi-way PARAFAC models

When developping selective crystallization or precipitation processes, biopharmaceutical modalities require empirical screenings and analytics tailored to the specific needs of the target molecule. The multi-way chemometric approach called parallel factor analysis (PARAFAC) coupled with ultraviolet visible light (UV/Vis) spectroscopy is able to predict specific concentrations and spectra from highly structured data sets without the need for calibration samples and reference analytics. These calculated models can provide exploratory information on pure species spectra and concentrations in all analyzed samples by representing one model component with one species. In this work, protein mixtures, monoclonal antibodies, and virus-like particles in chemically defined and complex solutions were investigated in three high-throughput crystallization or precipitation screenings with the aim to construct one PARAFAC model per case. Spectroscopic data sets of samples after the selective crystallization or precipitation, washing, and redissolution were recorded and arranged into a four-dimensional data set per case study. Different reference analytics and pure species spectra served as validation. Appropriate spectral preprocessing parameters were found for all case studies allowing even the application of this approach to the third case study in which quantitative concentration analytics are missing. Regardless of the modality or the number of species present in complex solutions, all models were able to estimate the specific concentration and find the optimal process condition regarding yield and product purity. It was shown that in complex solutions, species demonstrating similar phase behavior can be clustered as one component and described in the model. PARAFAC as a calibration-free approach coupled with UV/Vis spectroscopy provides a fast overview of species present in complex solution and of their concentration during selective crystallization or precipitation, washing, and redissolution.

Supersaturation-Dependent Formation of Amyloid Fibrils

The supersaturation of a solution refers to a non-equilibrium phase in which the solution is trapped in a soluble state, even though the solute’s concentration is greater than its thermodynamic solubility. Upon breaking supersaturation, crystals form and the concentration of the solute decreases to its thermodynamic solubility. Soon after the discovery of the prion phenomena, it was recognized that prion disease transmission and propagation share some similarities with the process of crystallization. Subsequent studies exploring the structural and functional association between amyloid fibrils and amyloidoses solidified this paradigm. However, recent studies have not necessarily focused on supersaturation, possibly because of marked advancements in structural studies clarifying the atomic structures of amyloid fibrils. On the other hand, there is increasing evidence that supersaturation plays a critical role in the formation of amyloid fibrils and the onset of amyloidosis. Here, we review the recent evidence that supersaturation plays a role in linking unfolding/folding and amyloid fibril formation. We also introduce the HANABI (HANdai Amyloid Burst Inducer) system, which enables high-throughput analysis of amyloid fibril formation by the ultrasonication-triggered breakdown of supersaturation. In addition to structural studies, studies based on solubility and supersaturation are essential both to developing a comprehensive understanding of amyloid fibrils and their roles in amyloidosis, and to developing therapeutic strategies.

Reverse-engineering method for XPCS studies of non-equilibrium dynamics

X-ray photon correlation spectroscopy (XPCS) is a powerful tool in the investigation of dynamics covering a broad time and length scale. It has been widely used to probe dynamics for systems in both equilibrium and non-equilibrium states; in particular, for systems undergoing a phase transition where the structural growth kinetics and the microscopic dynamics are strongly intertwined. The resulting time-dependent dynamic behavior can be described using the two-time correlation function (TTC), which, however, often contains more interesting features than the component along the diagonal, and cannot be easily interpreted via the classical simulation methods. Here, a reverse engineering (RE) approach is proposed based on particle-based heuristic simulations. This approach is applied to an XPCS measurement on a protein solution undergoing a liquid-liquid phase separation. It is demonstrated that the rich features of experimental TTCs can be well connected with the key control parameters including size distribution, concentration, viscosity and mobility of domains. The dynamic information obtained from this RE analysis goes beyond the existing theory. The RE approach established in this work is applicable for other processes such as film growth, coarsening or evolving systems.

Aerospace Technology Improves Fermentation Potential of Microorganisms

It is highly possible to obtain high-quality microbial products in appreciable amounts, as aerospace technology is advancing continuously. Genome-wide genetic variations in microorganisms can be triggered by space microgravity and radiation. Mutation rate is high, mutant range is wide, and final mutant character is stable. Therefore, space microorganism breeding is growing to be a new and promising area in microbial science and has greatly propelled the development of fermentation technology. Numerous studies have discovered the following improvements of fermentation potential in microorganisms after exposure to space: (1) reduction in fermentation cycle and increase in growth rate; (2) improvement of mixed fermentation species; (3) increase in bacterial conjugation efficiency and motility; (4) improvement of the bioactivity of various key enzymes and product quality; (5) enhancement of multiple adverse stress resistance; (6) improvement of fermentation metabolites, flavor, appearance, and stability. Aerospace fermentation technology predominantly contributes to bioprocessing in a microgravity environment. Unlike terrestrial fermentation, aerospace fermentation keeps cells suspended in the fluid medium without significant shear forces. Space radiation and microgravity have physical, chemical, and biological effects on mutant microorganisms by causing alternation in fluid dynamics and genome, transcriptome, proteome, and metabolome levels.

Tracing transport of protein aggregates in microgravity versus unit gravity crystallization

Microgravity conditions have been used to improve protein crystallization from the early 1980s using advanced crystallization apparatuses and methods. Early microgravity crystallization experiments confirmed that minimal convection and a sedimentation-free environment is beneficial for growth of crystals with higher internal order and in some cases, larger volume. It was however realized that crystal growth in microgravity requires additional time due to slower growth rates. The progress in space research via the International Space Station (ISS) provides a laboratory-like environment to perform convection-free crystallization experiments for an extended time. To obtain detailed insights in macromolecular transport phenomena under microgravity and the assumed reduction of unfavorable impurity incorporation in growing crystals, microgravity and unit gravity control experiments for three different proteins were designed. To determine the quantity of impurity incorporated into crystals, fluorescence-tagged aggregates of the proteins (acting as impurities) were prepared. The recorded fluorescence intensities of the respective crystals reveal reduction in the incorporation of aggregates under microgravity for different aggregate quantities. The experiments and data obtained, provide insights about macromolecular transport in relation to molecular weight of the target proteins, as well as information about associated diffusion behavior and crystal lattice formation. Results suggest one explanation why microgravity-grown protein crystals often exhibit higher quality. Furthermore, results from these experiments can be used to predict which proteins may benefit more from microgravity crystallization.

Probabilistic Nucleation and Crystal Growth in Porous Medium: New Insights from Calcium Carbonate Precipitation on Primary and Secondary Substrates

Knowledge of crystal nucleation and growth is paramount in understanding the geometry evolution of porous medium during reactive transport processes in geo-environmental studies. To predict transport properties precisely, it is necessary to delineate both the amount and location of nucleation and precipitation events in the spatiotemporal domain. This study investigates the precipitation of calcium carbonate crystals on a heterogeneous sandstone substrate as a function of chemical supersaturation, temperature, and time. The main objective was to evaluate solid formation under different boundary conditions when the solid-liquid interface plays a key role. New observations were made on the effect of primary and secondary substrates and the role of preferential precipitation locations on the rock surfaces. The results indicate that supersaturation and temperature determine the amount, distribution pattern, and growth rate of crystals. Substrate characteristics governed the nucleation, growth location, and evolution probability across time and space. Moreover, substrate surface properties introduced preferential sites that were occupied and covered with solids first. Our results highlight the complex dynamics induced by substrate surface properties on the spatial and temporal solute distribution, transport, and deposition. We accentuate the great potentials of the probabilistic nucleation model to describe mineral formation in a porous medium during reactive transport.

Protein-polymer mixtures in the colloid limit: Aggregation, sedimentation, and crystallization

While proteins have been treated as particles with a spherically symmetric interaction, of course in reality, the situation is rather more complex. A simple step toward higher complexity is to treat the proteins as non-spherical particles and that is the approach we pursue here. We investigate the phase behavior of the enhanced green fluorescent protein (eGFP) under the addition of a non-adsorbing polymer, polyethylene glycol. From small angle x-ray scattering, we infer that the eGFP undergoes dimerization and we treat the dimers as spherocylinders with aspect ratio L/D - 1 = 1.05. Despite the complex nature of the proteins, we find that the phase behavior is similar to that of hard spherocylinders with an ideal polymer depletant, exhibiting aggregation and, in a small region of the phase diagram, crystallization. By comparing our measurements of the onset of aggregation with predictions for hard colloids and ideal polymers [S. V. Savenko and M. Dijkstra, J. Chem. Phys. 124, 234902 (2006) and Lo Verso et al., Phys. Rev. E 73, 061407 (2006)], we find good agreement, which suggests that the behavior of the eGFP is consistent with that of hard spherocylinders and ideal polymers.

Interplay between Kinetics and Dynamics of Liquid-Liquid Phase Separation in a Protein Solution Revealed by Coherent X-ray Spectroscopy

Microscopic dynamics of complex fluids in the early stage of spinodal decomposition (SD) is strongly intertwined with the kinetics of structural evolution, which makes a quantitative characterization challenging. In this work, we use X-ray photon correlation spectroscopy to study the dynamics and kinetics of a protein solution undergoing liquid-liquid phase separation (LLPS). We demonstrate that in the early stage of SD, the kinetics relaxation is up to 40 times slower than the dynamics and thus can be decoupled. The microscopic dynamics can be well described by hyper-diffusive ballistic motions with a relaxation time exponentially growing with time in the early stage followed by a power-law increase with fluctuations. These experimental results are further supported by simulations based on the Cahn-Hilliard equation. The established framework is applicable to other condensed matter and biological systems undergoing phase transitions and may also inspire further theoretical work.

A coarse-grained xDLVO model for colloidal protein-protein interactions

Colloidal protein-protein interactions (PPIs) of attractive and repulsive nature modulate the solubility of proteins, their aggregation, precipitation and crystallization. Such interactions are very important for many biotechnological processes, but are complex and hard to control, therefore, difficult to be understood in terms of measurements alone. In diluted protein solutions, PPIs can be estimated from the osmotic second virial coefficient, B22, which has been calculated using different methods and levels of theory. The most popular approach is based on the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory and its extended versions, i.e. xDLVO. Despite much efforts, these models are not fully quantitative and must be fitted to experiments, which limits their predictive value. Here, we report an extended xDLVO-CG model, which extends existing models by a coarse-grained representation of proteins and the inclusion of an additional ion-protein dispersion interaction term. We demonstrate for four proteins, i.e. lysozyme (LYZ), subtilisin (Subs), bovine serum albumin (BSA) and immunoglobulin (IgG1), that semi-quantitative agreement with experimental values without the need to fit to experimental B22 values. While most likely not the final step in the nearly hundred years of research in PPIs, xDLVO-CG is a step towards predictive PPIs calculations that are transferable to different proteins.

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

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

Two-step crystallization and solid-solid transitions in binary colloidal mixtures

Crystallization is fundamental to materials science and is central to a variety of applications, ranging from the fabrication of silicon wafers for microelectronics to the determination of protein structures. The basic picture is that a crystal nucleates from a homogeneous fluid by a spontaneous fluctuation that kicks the system over a single free-energy barrier. However, it is becoming apparent that nucleation is often more complicated than this simple picture and, instead, can proceed via multiple transformations of metastable structures along the pathway to the thermodynamic minimum. In this article, we observe, characterize, and model crystallization pathways using DNA-coated colloids. We use optical microscopy to investigate the crystallization of a binary colloidal mixture with single-particle resolution. We observe classical one-step pathways and nonclassical two-step pathways that proceed via a solid-solid transformation of a crystal intermediate. We also use enhanced sampling to compute the free-energy landscapes corresponding to our experiments and show that both one- and two-step pathways are driven by thermodynamics alone. Specifically, the two-step solid-solid transition is governed by a competition between two different crystal phases with free energies that depend on the crystal size. These results extend our understanding of available pathways to crystallization, by showing that size-dependent thermodynamic forces can produce pathways with multiple crystal phases that interconvert without free-energy barriers and could provide approaches to controlling the self-assembly of materials made from colloids.

Microalgae proteins: production, separation, isolation, quantification, and application in food and feed

Many countries have been experienced an increase in protein consumption due to the population growth and adoption of protein-rich dietaries. Unfortunately, conventional-based protein agroindustry is associated with environmental impacts that might aggravate as the humankind increase. Thus, it is important to screen for novel protein sources that are environmentally friendly. Microalgae farming is a promising alternative to couple the anthropic emissions with the production of food and feed. Some microalgae show protein contents two times higher than conventional protein sources. The use of whole microalgae biomass as a protein source in food and feed is simple and well-established. Conversely, the production of microalgae protein supplements and isolates requires the development of feasible and robust processes able to fractionate the microalgae biomass in different value-added products. Since most of the proteins are inside the microalgae cells, several techniques of disruption have been proposed to increase the efficiency to extract them. After the disruption of the microalgae cells, the proteins can be extracted, concentrated, isolated or purified allowing the development of different products. This critical review addresses the current state of the production of microalgae proteins for multifarious applications, and possibilities to concatenate the production of proteins and advanced biofuels.

DNA-Directed Protein Packing within Single Crystals

Designed DNA-DNA interactions are investigated for their ability to modulate protein packing within single crystals of mutant green fluorescent proteins (mGFPs) functionalized with a single DNA strand (mGFP-DNA). We probe the effects of DNA sequence, length, and protein-attachment position on the formation and protein packing of mGFP-DNA crystals. Notably, when complementary mGFP-DNA conjugates are introduced to one another, crystals form with nearly identical packing parameters, regardless of sequence if the number of bases is equivalent. DNA complementarity is essential, because experiments with non-complementary sequences produce crystals with different protein arrangements. Importantly, the DNA length and its position of attachment on the protein markedly influence the formation of and protein packing within single crystals. This work shows how designed DNA interactions can be used to influence the growth and packing in X-ray diffraction quality protein single crystals and is thus an important step forward in protein crystal engineering.

Induction of crystal nucleation by orientation-controlled binding of His6-tagged proteins to functionalized gold nanoparticles

Functionalized gold nanoparticles can induce crystal nucleation by orientation-controlled NTA–Ni²⁺– His₆-tagged protein binding.

Catalystlike role of impurities in speeding layer-by-layer growth

Molecular self-assembly is usually done at low supersaturation, leading to low rates of growth, in order to allow time for binding mistakes to anneal. However, such conditions can lead to prohibitively long assembly times where growth proceeds by the slow nucleation of successive layers. Here we use a lattice model of molecular self-assembly to show that growth in this regime can be sped up by impurities, which lower the free-energy cost of layer nucleation. Under certain conditions impurities behave almost as a catalyst in that they are present at high concentration at the surface of the assembling structure, but at low concentration in the bulk of the assembled structure. Extrapolation of our numerics using simple analytic arguments suggests that this mechanism can reduce growth times by orders of magnitude in parameter regimes applicable to molecular systems.

X-ray photon correlation spectroscopy of protein dynamics at nearly diffraction-limited storage rings

This study explores the possibility of measuring the dynamics of proteins in solution using X-ray photon correlation spectroscopy (XPCS) at nearly diffraction-limited storage rings (DLSRs). We calculate the signal-to-noise ratio (SNR) of XPCS experiments from a concentrated lysozyme solution at the length scale of the hydrodynamic radius of the protein molecule. We take into account limitations given by the critical X-ray dose and find expressions for the SNR as a function of beam size, sample-to-detector distance and photon energy. Specifically, we show that the combined increase in coherent flux and coherence lengths at the DLSR PETRA IV yields an increase in SNR of more than one order of magnitude. The resulting SNR values indicate that XPCS experiments of biological macromolecules on nanometre length scales will become feasible with the advent of a new generation of synchrotron sources. Our findings provide valuable input for the design and construction of future XPCS beamlines at DLSRs.

Improved adsorption reactions, kinetics and stability for model and therapeutic proteins immobilised on affinity resins

Protein adsorption on solid state media is important for the industrial affinity chromatography of biotherapeutics and for preparing materials for self-interaction chromatography where fundamental protein solution thermodynamic properties are measured. The adsorption of three model proteins (lysozyme, catalase and BSA) and two antibodies (a monoclonal and a polyclonal antibody) have been investigated on commercial affinity chromatography media with different surface functionalities (Formyl, Tresyl and Amino). Both the extent of protein immobilised (mg protein/ml media) and the reaction kinetics are reported for a range of reaction conditions, including pH, differing buffers as well as the presence of secondary reactants (glutaraldehyde, sodium cyanoborohydride, EDC and NHS). Compared to the reaction conditions recommended by manufacturers as well as those reported in previous published work, significant increases in the extent of protein immobilisation and reaction kinetics are reported here. The addition of glutaraldehyde or sodium cyanoborohydride was found to be especially effective even when not directly needed for the adsorption to happen. For mAb and pIgG, immobilisation levels of 50 and 31 mg of protein/ml of resin respectively were achieved, which are 100% or more than previously reported. Enhanced levels were achieved for lysozyme of 120 mg/ml with very rapid reaction kinetics (< 1 h) with sodium cyanoborohydride. It can be concluded that specific chromatography resins with Tresyl activated support offered enhanced levels of protein immobilisation due to their ability to react to form amine or thio-ether linkages with proteins. Additionally, glutaraldehyde can result in higher immobilisation levels whilst it can also accelerate immobilisation reaction kinetics.

Unit-cell response of tetragonal hen egg white lysozyme upon controlled relative humidity variation

Variation of relative humidity (rH) greatly affects the internal order of solvent-based protein crystals, and the rearrangement of molecules can be efficiently recorded in distinct diffraction patterns. This study focuses on this topic, reporting the effect of rH variation experiments on hen egg white lysozyme (HEWL) polycrystalline precipitates of tetragonal symmetry using X-ray powder diffraction (XRPD). In situ XRPD data were collected on HEWL specimens during dehydration and rehydration processes using laboratory instrumentation. A known polymorph [space group P43212, a = 79.07181 (1), c = 38.0776 (1) Å] was identified during gradual dehydration from 95 to 63% rH and vice versa. Pawley analysis of collected data sets and accurate extraction of unit-cell parameters indicated a characteristic evolution of the tetragonal axes with rH. In addition, there is a low humidity level below which samples do not retain their crystallinity. This work illustrates the accuracy of laboratory XRPD as a probe for time-resolved studies of proteins and in situ investigations of gradual structural modifications upon rH variation. These experiments provide essential information for improving production and post-production practices of microcrystalline protein-based pharmaceuticals.

Microfluidic triple-gradient generator for efficient screening of chemical space

Generation of a combinatorial gradient for multiple chemicals is essential for studies of biochemical stimuli, chemoattraction, protein crystallization and others. While currently available platforms require complex design/settings to obtain a double-gradient chemical matrix, we herein report for the first time a simple triple-gradient matrix (TGM) device for efficient screening of chemical space. The TGM device is composed of two glass slides and works following the concept of SlipChip. The device utilizes XYZ space to distribute three chemicals and establishes a chemical gradient matrix within 5 min. The established matrix contains 24 or 104 screening conditions depending on the device used, which covers a concentration range of [0.117-1, 0.117-1 and 0.686-1] and [0.0830-1, 0.0830-1, 0.686-1] respectively for the three chemicals. With the triple gradients built simultaneously, this TGM device provides order-of-magnitude improvement in screening efficiency over existing single- or double-gradient generators. As a proof of concept, we applied the device to screen the crystallization conditions for two model proteins of lysozyme and trypsin and confirmed the crystal structures using X-ray diffraction. Furthermore, we successfully obtained the crystallization condition of adhesin competence repressor, a protein that senses the alterations in intracellular zinc concentrations. We expect the TGM system to be widely used as an analytical platform for material synthesis and chemical screening beyond for protein crystallization.

The mechanism of eutectic modification by trace impurities

In the quest toward rational design of materials, establishing direct links between the attributes of microscopic building blocks and the macroscopic performance limits of the bulk structures they comprise is essential. Building blocks of concern to the field of crystallization are the impurities, foreign ingredients that are either deliberately added to or naturally present in the growth medium. While the role of impurities has been studied extensively in various materials systems, the inherent complexity of eutectic crystallization in the presence of trace, often metallic impurities ('eutectic modification') remains poorly understood. In particular, the origins behind the drastic microstructural changes observed upon modification are elusive. Herein, we employ an integrated imaging approach to shed light on the influence of trace metal impurities during the growth of an irregular (faceted-non-faceted) eutectic. Our dynamic and 3D synchrotron-based X-ray imaging results reveal the markedly different microstructural and, for the first time, topological properties of the eutectic constituents that arise upon modification, not fully predicted by the existing theories. Together with ex situ crystallographic characterization of the fully-solidified specimen, our multi-modal study provides a unified picture of eutectic modification: The impurities selectively alter the stacking sequence of the faceted phase, thereby inhibiting its steady-state growth. Consequently, the non-faceted phase advances deeper into the melt, eventually engulfing the faceted phase in its wake. We present a quantitative topological framework to rationalize these experimental observations.

Correlating multidimensional short-term empirical protein properties to long-term protein physical stability data via empirical phase diagrams

Identification of long-term stable biopharmaceutical formulations is essential for biopharmaceutical product development. Reduction of the number of long-term storage experiments and a well-defined formulation search space requires knowledge-based formulation screenings and a detailed protein phase behavior understanding. To achieve this, short-term analytical techniques can serve as predictors for long-term protein phase behavior. Protein phase behavior studies that investigate this concept commonly display shortcomings such as limited and small datasets, sample adjustments, or simplistic data analysis. To overcome these shortcomings, 150 unique lysozyme solutions were analyzed using six different short-term analytical techniques. Lysozyme's structural properties, conformational stability, colloidal stability, surface charge, and surface hydrophobicity were obtained directly after formulation preparation. Employing the empirical phase diagram method, this short-term data was correlated to long-term physical stability data obtained during 40 days of storage. Short-term protein properties showed partial correlation to long-term phase behavior. Structural differences, changing surface properties, colloidal stability, and conformation stability as a function of formulation conditions were observed. This study contributes to long-term protein phase behavior research by presenting a systematic, data-dependent, and multidimensional data evaluation workflow to create a comprehensive overview of short-term protein analytics in relation to long-term protein phase behavior.

Reentrant Phase Behavior in Protein Solutions Induced by Multivalent Salts: Strong Effect of Anions Cl- Versus NO3

In this work, the effects of the two anions Cl^- and NO₃^- on the phase behavior of bovine serum albumin (BSA) in solution with trivalent salts are compared systematically. In the presence of trivalent metal salts, negatively charged proteins such as BSA in solution undergo a reentrant condensation (RC) phase behavior, which has been established for several proteins with chlorides of trivalent salts. Here, we show that replacing Cl^- by NO₃^- leads to a marked change in the phase behavior. The effect is investigated for the two different cations Y³⁺ and La³⁺. The salts are thus YCl₃, Y(NO₃)₃, LaCl₃, and La(NO₃)₃. The experimental phase behavior shows that while the chloride salts induce both liquid-liquid phase separation (LLPS) and RC, the nitrate salts also induce LLPS, but RC becomes partial with La(NO₃)₃ and disappears with Y(NO₃)₃. The observed phase behavior is rationalized by effective protein-protein interactions which are characterized using small-angle X-ray scattering. The results based on the reduced second virial coefficients B₂/ B₂^HS and 1/ I( q → 0) demonstrate that the NO₃^- salts induce a stronger attraction than the Cl^- salts. Overall, the effective attraction, the width of the condensed regime in the RC phase diagram, and the nature of LLPS follow the order LaCl₃ < YCl₃ < La(NO₃)₃ < Y(NO₃)₃. Despite the decisive role of cations in RC phase behavior, isothermal titration calorimetry measurements indicate that replacing anions does not significantly influence the cation binding to proteins. The experimental results observed are discussed based on an "enhanced Hofmeister effect" including electrostatic and hydrophobic interactions between protein-cation complexes.

The "speed limit" for macromolecular crystal growth

A simple “diffusion‐to‐capture” model is used to estimate the upper limit to the growth rate of macromolecular crystals under conditions when the rate limiting process is the mass transfer of sample from solution to the crystal. Under diffusion‐limited crystal growth conditions, this model predicts that the cross‐sectional area of a crystal will increase linearly with time; this prediction is validated by monitoring the growth rate of lysozyme crystals. A consequence of this analysis is that when crystal growth is diffusion‐limited, micron‐sized crystals can be produced in ~1 s, which would be compatible with the turnover time of many enzymes. Consequently, the ability to record diffraction patterns from sub‐micron sized crystals by X‐ray Free Electron Lasers and micro‐electron diffraction technologies opens the possibility of trapping intermediate enzyme states by crystallization.

Polyoxometalates: more than a phasing tool in protein crystallography

Protein crystallography is the most widely used method for determining the molecular structure of proteins and obtaining structural information on protein–ligand complexes at the atomic level. As the structure determines the functions and properties of a protein, crystallography is of immense importance for nearly all research fields related to biochemistry. However, protein crystallography suffers from some major drawbacks, whereby the unpredictability of the crystallization process represents the main bottleneck. Crystallization is still more or less a ‘trial and error’ based procedure, and therefore, very time and resource consuming. Many strategies  have been developed in the past decades to improve or enable the crystallization of proteins, whereby the use of so-called additives, which are mostly small molecules that make proteins more amenable to crystallization, is one of the most convenient and successful methods. Most of the commonly used additives are, however, restricted to particular crystallization conditions or groups of proteins. Therefore, a more universal additive addressing a wider range of proteins and being applicable to a broad spectrum of crystallization conditions would represent a significant advance in the field of protein crystallography. In recent years, polyoxometalates (POMs) emerged as a promising group of crystallization additives due to their unique structures and properties. In this regard, the tellurium-centered Anderson–Evans polyoxotungstate [TeW₆O₂₄]⁶⁻ (TEW) showed its high potential as crystallization additive. In this lecture text, the development of POMs as tools in protein crystallography are discussed with a special focus on the so far most successful cluster TEW.

Supramolecular polymer formation by a de novo hemoprotein with a synthetic diheme compound

Proteins are attractive materials for supramolecular chemistry due to their multifunctionality and self‐organization ability. In this work, we synthesized a diheme compound, in which two iron‐protoporphyrin IX molecules are associated via a linker chain, and introduced it into a de novo designed four‐helix bundle protein with two heme‐binding sites. The protein gradually bound the diheme compound by bis‐histidyl ligation and formed supramolecular polymers. Polymer formation was observed by atomic force microscopy (AFM), which revealed the highly branched, dendritic forms of the fibrous architecture. The present results may open a pathway toward nanowire construction with de novo heme‐proteins.

Application of Empirical Phase Diagrams for Multidimensional Data Visualization of High-Throughput Microbatch Crystallization Experiments

Protein phase diagrams are a tool to investigate the cause and consequence of solution conditions on protein phase behavior. The effects are scored according to aggregation morphologies such as crystals or amorphous precipitates. Solution conditions affect morphologic features, such as crystal size, as well as kinetic features, such as crystal growth time. Commonly used data visualization techniques include individual line graphs or phase diagrams based on symbols. These techniques have limitations in terms of handling large data sets, comprehensiveness or completeness. To eliminate these limitations, morphologic and kinetic features obtained from crystallization images generated with high throughput microbatch experiments have been visualized with radar charts in combination with the empirical phase diagram method. Morphologic features (crystal size, shape, and number, as well as precipitate size) and kinetic features (crystal and precipitate onset and growth time) are extracted for 768 solutions with varying chicken egg white lysozyme concentration, salt type, ionic strength, and pH. Image-based aggregation morphology and kinetic features were compiled into a single and easily interpretable figure, thereby showing that the empirical phase diagram method can support high-throughput crystallization experiments in its data amount as well as its data complexity.

Liquid phase condensation in cell physiology and disease

Phase transitions are ubiquitous in nonliving matter, and recent discoveries have shown that they also play a key role within living cells. Intracellular liquid-liquid phase separation is thought to drive the formation of condensed liquid-like droplets of protein, RNA, and other biomolecules, which form in the absence of a delimiting membrane. Recent studies have elucidated many aspects of the molecular interactions underlying the formation of these remarkable and ubiquitous droplets and the way in which such interactions dictate their material properties, composition, and phase behavior. Here, we review these exciting developments and highlight key remaining challenges, particularly the ability of liquid condensates to both facilitate and respond to biological function and how their metastability may underlie devastating protein aggregation diseases.

Automation aided optimization of cloning, expression and purification of enzymes of the bacterial sialic acid catabolic and sialylation pathways enzymes for structural studies

The process of obtaining a well-expressing, soluble and correctly folded constructs can be made easier and quicker by automating the optimization of cloning, expression and purification. While there are many semiautomated pipelines available for cloning, expression and purification, there is hardly any pipeline that involves complete automation. Here, we achieve complete automation of all the steps involved in cloning and in vivo expression screening. This is demonstrated using 18 genes involved in sialic acid catabolism and the surface sialylation pathway. Our main objective was to clone these genes into a His-tagged Gateway vector, followed by their small-scale expression optimization in vivo. The constructs that showed best soluble expression were then selected for purification studies and scaled up for crystallization studies. Our technique allowed us to quickly find conditions for producing significant quantities of soluble proteins in Escherichia coli, their large-scale purification and successful crystallization of a number of these proteins. The method can be implemented in other cases where one needs to screen a large number of constructs, clones and expression vectors for successful recombinant production of functional proteins.

Application of protein crystallization methodologies to enhance the solubility, stability and monodispersity of proteins

Application of protein crystallization methodologies to screen optimal solution formulations for proteins prone to aggregation.

Protein Crystallizability

Obtaining diffracting quality crystals remains a major challenge in protein structure research. We summarize and compare methods for selecting the best protein targets for crystallization, construct optimization and crystallization condition design. Target selection methods are divided into algorithms predicting the chance of successful progression through all stages of structural determination (from cloning to solving the structure) and those focusing only on the crystallization step. We tried to highlight pros and cons of different approaches examining the following aspects: data size, redundancy and representativeness, overfitting during model construction, and results evaluation. In summary, although in recent years progress was made and several sequence properties were reported to be relevant for crystallization, the successful prediction of protein crystallization behavior and selection of corresponding crystallization conditions continue to challenge structural researchers.

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.

Can the propensity of protein crystallization be increased by using systematic screening with metals?

Protein crystallization is one of the major bottlenecks in protein structure elucidation with new strategies being constantly developed to improve the chances of crystallization. Generally, well-ordered epitopes possessing complementary surface and capable of producing stable inter-protein interactions generate a regular three-dimensional arrangement of protein molecules which eventually results in a crystal lattice. Metals, when used for crystallization, with their various coordination numbers and geometries, can generate such epitopes mediating protein oligomerization and/or establish crystal contacts. Some examples of metal-mediated oligomerization and crystallization together with our experience on metal-mediated crystallization of a putative rRNA methyltransferase from Sinorhizobium meliloti are presented. Analysis of crystal structures from protein data bank (PDB) using a non-redundant data set with a 90% identity cutoff, reveals that around 67% of proteins contain at least one metal ion, with ∼14% containing combination of metal ions. Interestingly, metal containing conditions in most commercially available and popular crystallization kits generally contain only a single metal ion, with combinations of metals only in a very few conditions. Based on the results presented in this review, it appears that the crystallization screens need expansion with systematic screening of metal ions that could be crucial for stabilizing the protein structure or for establishing crystal contact and thereby aiding protein crystallization.

Protein Crystallization

Protein crystallization was discovered by chance nearly 200 years ago and was developed in the late nineteenth century as a powerful purification tool, and a demonstration of chemical purity. The crystallization of proteins, nucleic acids, and large biological complexes, such as viruses, depends on the creation of a solution that is supersaturated in the macromolecule, but exhibits conditions that do not significantly perturb its natural state. Supersaturation is produced through the addition of mild precipitating agents such as neutral salts or polymers, and by manipulation of various parameters that include temperature, ionic strength, and pH. Also important in the crystallization process are factors that can affect the structural state of the macromolecule, such as metal ions, inhibitors, cofactors, or other conventional small molecules. A variety of approaches have been developed that combine the spectrum of factors that effect and promote crystallization, and among the most widely used are vapor diffusion, dialysis, batch, and liquid-liquid diffusion. Successes in macromolecular crystallization have multiplied rapidly in recent years due to the advent of practical, easy-to-use screening kits, and the application of laboratory robotics.

From globules to crystals: a spectral study of poly(2-isopropyl-2-oxazoline) crystallization in hot water

One easy strategy to comprehend the complex folding/crystallization behaviors of proteins is to study the self-assembly process of their synthetic polymeric analogues with similar properties owing to their simple structures and easy access to molecular design. Poly(2-isopropyl-2-oxazoline) (PIPOZ) is often regarded as an ideal pseudopeptide with similar two-step crystallization behavior to proteins, whose aqueous solution experiences successive lower critical solution temperature (LCST)-type liquid-liquid phase separation upon heating and irreversible crystallization when annealed above LCST for several hours. In this paper, by microscopic observations, IR and Raman spectroscopy in combination with 2D correlation analysis, we show that the second step of PIPOZ crystallization in hot water can be further divided into two apparent stages, i.e., nucleation and crystal growth, and perfect crystalline PIPOZ chains are found to only develop in the second stage. While all the groups exhibit changes in initial nucleation, only methylene groups on the backbone participate in the crystal growth stage. During nucleation, a group motion transfer is found from the side chain to the backbone, and nucleation is assumed to be mainly driven by the cleavage of bridging C=O···D-O-D···O=C hydrogen bonds followed by chain arrangement due to amide dipolar orientation. Nevertheless, during crystal growth, a further chain ordering process occurs resulting in the final formation of crystalline PIPOZ chains with partial trans conformation of backbones and alternative side chains on the two sides. The underlying crystallization mechanism of PIPOZ in hot water we present here may provide very useful information for understanding the crystallization of biomacromolecules in biological systems.

Heterogeneous nucleation of Al melt in symmetrical or asymmetrical confined nanoslits

MD simulations are performed to study the solidification of Al melt in confined nanoslits (NSs) constructed by identical or different substrates, as well as on Fe substrates. Compared to the single substrate, the confined NS could promote the crystallization of Al melt, and its size has a significant impact on the solidified structure. In symmetrical NSs, liquid Al atoms would stack based on the atomic arrangement mode of the substrate, however in asymmetrical confined NSs, the atomic arrangement mode of liquid Al is governed by the constitution of asymmetrical substrates. Specifically, for the NS formed by Fe(110) and Fe(111) substrates, the induced region from the Fe(110) substrate is much bigger than that from Fe(111). Moreover, the freezing of liquid Al in asymmetrical NSs constructed from copper and iron has also been studied. These results throw light on heterogeneous nucleation in confined space.

Prediction of salt effects on protein phase behavior by HIC retention and thermal stability

In the biopharmaceutical industry it is mandatory to know and ensure the correct protein phase state as a critical quality attribute in every process step. Unwanted protein precipitation or crystallization can lead to column, pipe or filter blocking. In formulation, the formation of aggregates can even be lethal when injected into the patient. The typical methodology to illustrate protein phase states is the generation of protein phase diagrams. Commonly, protein phase behavior is shown in dependence of protein and precipitant concentration. Despite using high-throughput methods for the generation of phase diagrams, the time necessary to reach equilibrium is the bottleneck. Faster methods to predict protein phase behavior are desirable. In this study, hydrophobic interaction chromatography retention times were correlated to crystal size and form. High-throughput thermal stability measurements (melting and aggregation temperatures), using an Optim(®)2 system, were successfully correlated to glucose isomerase stability. By using hydrophobic interaction chromatography and thermal stability determinations, glucose isomerase conformational and colloidal stability were successfully predicted for different salts in a specific pH range.