Patterns of protein protein interactions in salt solutions and implications for protein crystallization

Understanding of formation, gastrointestinal breakdown, and application of whey protein emulsion gels: Insights from intermolecular interactions

Whey protein emulsion gel is an ideal model food for revealing how the multilength scale food structures affect food digestion, as their structure and mechanical properties can be precisely manipulated by controlling the type and intensity of intermolecular interactions between protein molecules. However, there are still significant understanding gaps among intermolecular interactions, protein aggregation and gelation, emulsion gel formation, gel breakdown in the gastrointestinal tract (GIT), and the practical use of whey protein emulsion gels, which limits their GIT-targeted applications. In this regard, the relationship between the structure and digestion behavior of heat-set whey protein emulsion gels is reviewed and discussed mainly from the following aspects: (1) structural characteristics of whey protein molecules; (2) how different types of intermolecular interactions influence heat-induced aggregation and gelation of whey protein in the aqueous solutions and the oil-in-water emulsions, and the mechanical properties of the final gels; (3) functions of the mouth, the stomach, and the small intestine in processing of solid foods, and how different types of intermolecular interactions influence the breakdown properties of heat-set whey protein emulsion gels in GIT (i.e., their respective role in controlling gel digestion). Finally, the implications of knowledge derived from the formation and gastrointestinal breakdown of heat-set whey protein emulsion gels for developing controlled delivery vehicles, human satiety enhancers, and sensory modifiers are highlighted.

Scattering approaches to unravel protein solution behaviors in ionic liquids and deep eutectic solvents: From basic principles to recent developments

Proteins in ionic liquids (ILs) and deep eutectic solvents (DESs) have gained significant attention due to their potential applications in various fields, including biocatalysis, bioseparation, biomolecular delivery, and structural biology. Scattering approaches including dynamic light scattering (DLS) and small-angle X-ray and neutron scattering (SAXS and SANS) have been used to understand the solution behavior of proteins at the nanoscale and microscale. This review provides a thorough exploration of the application of these scattering techniques to elucidate protein properties in ILs and DESs. Specifically, the review begins with the theoretical foundations of the relevant scattering approaches and describes the essential solvent properties of ILs and DESs linked to scattering such as refractive index, scattering length density, ion-pairs, liquid nanostructure, solvent aggregation, and specific ion effects. Next, a detailed introduction is provided on protein properties such as type, concentration, size, flexibility and structure as observed through scattering methodologies. This is followed by a review of the literature on the use of scattering for proteins in ILs and DESs. It is highlighted that enhanced data analysis and modeling tools are necessary for assessing protein flexibility and structure, and for understanding protein hydration, aggregation and specific ion effects. It is also noted that complementary approaches are recommended for comprehensively understanding the behavior of proteins in solution due to the complex interplay of factors, including ion-binding, dynamic hydration, intermolecular interactions, and specific ion effects. Finally, the challenges and potential research directions for this field are proposed, including experimental design, data analysis approaches, and supporting methods to obtain fundamental understandings of complex protein behavior and protein systems in solution. We envisage that this review will support further studies of protein interface science, and in particular studies on solvent and ion effects on proteins.

Online Mixed-Bed Ion Exchange Chromatography for Native Top-Down Proteomics of Complex Mixtures

Native top-down mass spectrometry (nTDMS) allows characterization of protein structure and noncovalent interactions with simultaneous sequence mapping and proteoform characterization. The majority of nTDMS studies utilize purified recombinant proteins, with significant challenges hindering application to endogenous systems. To perform native top-down proteomics (nTDP), where endogenous proteins from complex biological systems are analyzed by nTDMS, it is essential to separate proteins under nondenaturing conditions. However, it remains difficult to achieve high resolution with MS-compatible online chromatography while preserving protein tertiary structure and noncovalent interactions. Herein, we report the use of online mixed-bed ion exchange chromatography (IEC) to enable separation of endogenous proteins from complex mixtures under nondenaturing conditions, preserving noncovalent interactions for nTDP analysis. We have successfully detected large proteins (>146 kDa) and identified endogenous metal-binding and oligomeric protein complexes in human heart tissue lysate. The use of a mixed-bed stationary phase allowed retention and elution of proteins over a wide range of isoelectric points without altering the sample or mobile phase pH. Overall, our method provides a simple online IEC-MS platform that can effectively separate proteins from complex mixtures under nondenaturing conditions and preserve higher-order structure for nTDP applications.

Addition of sodium malonate alters the morphology and increases the critical flux during tangential flow filtration of precipitated immunoglobulins

Recent studies have demonstrated that one can control the packing density, and in turn the filterability, of protein precipitates by changing the pH and buffer composition of the precipitating solution to increase the structure/order within the precipitate. The objective of this study was to examine the effect of sodium malonate, which is known to enhance protein crystallizability, on the morphology of immunoglobulin precipitates formed using a combination of ZnCl2 and polyethylene glycol. The addition of sodium malonate significantly stabilized the precipitate particles as shown by an increase in melting temperature, as determined by differential scanning calorimetry, and an increase in the enthalpy of interaction, as determined by isothermal titration calorimetry. The sodium malonate also increased the selectivity of the precipitation, significantly reducing the coprecipitation of DNA from a clarified cell culture fluid. The resulting precipitate had a greater packing density and improved filterability, enabling continuous tangential flow filtration with minimal membrane fouling relative to precipitates formed under otherwise identical conditions but in the absence of sodium malonate. These results provide important insights into strategies for controlling precipitate morphology to enhance the performance of precipitation-filtration processes for the purification of therapeutic proteins.

Protein extraction from chlorella pyrenoidosa microalgae: Green methodologies, functional assessment, and waste stream valorization for bioenergy production

C. pyrenoidosa, a species of microalgae, has been recognized as a viable protein source for human consumption. The primary challenges in this context are the development of an efficient extraction process and the valorization of the resultant waste streams. This study, situated within the paradigm of circular economy, presents an innovative extraction approach that achieved a protein extraction efficiency of 62 %. The extracted protein exhibited remarkable oil-water emulsifying performances, such as uniform morphology with high creaming stability, suggesting a sustainable alternative to conventional emulsifiers. Additionally, hydrothermal liquefaction technique was employed for converting the residual biomass and waste solution from the extraction process into biocrude. A biocrude yield exceeding 40 wt%, characterized by a carbon content of 73 % and a higher heating value of 36 MJ/kg, were obtained. These findings demonstrate the promising potential of microalgae biorefinery, which is significant for paving toward circular economy and zero-waste society.

Molecular Crowding Alters the Interactions of Polymyxin Lipopeptides within the Periplasm of E. coli: Insights from Molecular Dynamics

The cell envelope of Gram-negative bacteria is a crowded tripartite architecture that separates the cell interior from the external environment. Two membranes encapsulate the aqueous periplasm, which contains the cell wall. Little is known about the mechanisms via which antimicrobial peptides move through the periplasm from the outer membrane to their site of action, the inner membrane. We utilize all-atom molecular dynamics to study two antimicrobial peptides, polymyxins B1 and E, within models of the E. coli periplasm crowded to different extents. In a simple chemical environment, both PMB1 and PME bind irreversibly to the cell wall. The presence of specific macromolecules leads to competition with the polymyxins for cell wall interaction sites, resulting in polymyxin dissociation from the cell wall. Chemical complexity also impacts interactions between polymyxins and Braun's lipoprotein; thus, the interaction modes of lipoprotein antibiotics within the periplasm are dependent upon the nature of the other species present.

Combined Effects of Pressure and Ionic Strength on Protein-Protein Interactions: An Empirical Approach

Proteins are exposed to hydrostatic pressure (HP) in a variety of ecosystems as well as in processing steps such as freeze-thaw, cell disruption, sterilization, and homogenization, yet pressure effects on protein-protein interactions (PPIs) remain underexplored. With the goal of contributing toward the expanded use of HP as a fundamental control parameter in protein research, processing, and engineering, small-angle X-ray scattering was used to examine the effects of HP and ionic strength on ovalbumin, a model protein. Based on an extensive data set, we develop an empirical method for scaling PPIs to a master curve by combining HP and osmotic effects. We define an effective pressure parameter that has been shown to successfully apply to other model protein data available in the literature, with deviations evident for proteins that do not follow the apparent Hofmeister series. The limitations of the empirical scaling are discussed in the context of the hypothesized underlying mechanisms.

Probing ion-binding at a protein interface: Modulation of protein properties by ionic liquids

Ions are important to modulate protein properties, including solubility and stability, through specific ion effects. Ionic liquids (ILs) are designer salts with versatile ion combinations with great potential to control protein properties. Although protein-ion binding of common metals is well-known, the IL effect on proteins is not well understood. Here, we employ the model protein lysozyme in dilute and concentrated IL solutions to determine the specific ion binding effect on protein phase behaviour, activity, size and conformational change, aggregation and intermolecular interactions. A combination of spectroscopic techniques, activity assays, small-angle X-ray scattering, and crystallography highlights that ILs, particularly their anions, bind to specific sites in the protein hydration layer via polar contacts on charged, polar and aromatic residues. The specific ion binding can induce more flexible loop regions in lysozyme, while the ion binding in the bulk phase can be more dynamic in solution. Overall, the protein behaviour in ILs depends on the net effect of nonspecific interactions and specific ion binding. Compared to formate, the nitrate anion induced high protein solubility, low activity, elongated shape and aggregation, which is largely owing to its higher propensity for ion binding. These findings provide new insights into protein-IL binding interactions and using ILs to modulate protein properties.

Nonlinear dielectric response of dilute protein solutions

A theory for the nonlinear dielectric response of dilute protein solutions is presented. The field-dependent dielectric function of the protein solution changes linearly with the electric field squared in the lowest order. The slope of this dependence is expressed in terms of the protein dipole moment M0, its volume fraction in solution η0, and the second osmotic virial coefficient. For practical conditions, the nonlinear dielectric response scales as η03M08. This strong dependence on the protein dipole moment and concentration establishes a sharp contrast between the nonlinear response of solvated proteins relative to the surrounding polar solvent. Nonlinear dielectric response can serve as a sensitive tool for monitoring protein conformations and physiological activity.

Decoupling of Interactions between Model-Charged Peptides Reveals Key Factors Responsible for Liquid-Liquid Phase Separation

Liquid-liquid phase separation (LLPS) by disordered proteins has been shown to govern biological processes and cause numerous diseases. Therefore, a deeper understanding of the interactions and their variation with external factors is key to modulating the LLPS behavior of different systems and protecting proteins from pathological aggregation. In this context, we have looked at interactions between similarly charged peptides to understand the molecular features that may drive or prevent condensate formation under various conditions. We have studied dimer formation for model peptides where charged and noncharged amino acids have been placed alternatively. Using arginine and glutamic acid as the charged residues and varying the other residues with glycine, alanine, and proline to alter hydrophobicity, we have obtained the free-energy surface (FES) for the dimer formation for these systems under high salt concentration at two different temperatures using all-atom molecular dynamics simulations and the well-tempered metadynamics method. Our results indicate that a combination of effects such as hydrophobicity, arginine-arginine interactions, or water release from the solvation shell makes dimerization free energy more favorable for the positively charged peptides with lower flexibility. For the negatively charged peptides, the crucial role of water has been found in governing the FES. Systems having charged residues and phenylalanine in the peptide sequence also have been studied at high salt concentrations using unbiased simulations. In this case, only the positively charged peptides were found to aggregate through temperature-dependent hydrophobic and cation-π interactions. Overall, our study indicates that the negatively charged peptides are more likely to remain in the dilute phase under various conditions compared to the positively charged systems. The findings from our study would be helpful in designing and controlling systems to obtain LLPS behavior for therapeutic usage.

Prevalence and mechanism of synergistic carboxylate-cation-water interactions in halophilic proteins

The cytoplasmic proteins of some halophilic organisms remain stable and functional at multimolar concentrations of KCl, i.e., under conditions that most mesophilic proteins cannot withstand. Their stability arises from their unusual amino acid composition. The most dramatic difference between halophilic and mesophilic proteins is that the former are rich in acidic amino acids. It has been proposed that one of the evolutionary driving forces for this difference is the occurrence of synergistic interactions between multiple acidic amino acids at the surface of the protein, the potassium cations in solution, and water. We investigate this possibility with molecular dynamics simulations, using high-quality force fields for the protein-water, protein-ion, and ion-ion interactions. We create a rigorous thermodynamic definition of interactions between acidic amino acids on proteins that can be used to distinguish between synergistic, noninteracting and interfering interactions. Our results demonstrate that synergistic interactions between neighboring acidic amino acids in halophilic proteins are frequent at multimolar KCl concentration. Synergistic interactions have an electrostatic origin, and are associated with stronger water-to-carboxylate hydrogen bonds than for acidic amino acids without synergistic interactions. Synergistic interactions are not observed in minimal systems of carboxylates, indicating that the protein environment is critical for their emergence. Our results demonstrate that synergistic interactions are neither associated with rigid amino acid orientations nor with highly structured and slow moving water networks, as had been originally proposed. Moreover, synergistic interactions can also be found in unfolded protein conformations. However, because these conformations are only a small subset of the unfolded state ensemble, synergistic interactions should contribute to the net stabilization of the folded state.

Solution characterization of the dynamic conjugative entry exclusion protein TraG

The R100 plasmid and the secretion system it encodes are representative of F-like conjugative type IV secretion systems for the transmission of mobile DNA elements in gram-negative bacteria, serving as a major contributor to the spread of antibiotic resistance in bacterial pathogens. The TraG protein of F-like systems consists of a membrane-bound N-terminal domain and a periplasmic C-terminal domain, denoted TraG*. TraG* is essential in preventing redundant DNA transfer through a process termed entry exclusion. In the donor cell, it interacts with TraN to facilitate mating pair stabilization; however, if a mating pore forms between bacteria with identical plasmids, TraG* interacts with its cognate TraS in the inner membrane of the recipient bacterium to prevent redundant donor-donor conjugation. Structural studies of TraG* from the R100 plasmid have revealed the presence of a dynamic region between the N- and C-terminal domains of TraG. Thermofluor, circular dichroism, collision-induced unfolding-mass spectrometry, and size exclusion chromatography linked to multiangle light scattering and small angle x-ray scattering experiments indicated an N-terminal truncation mutant displayed higher stability and less disordered content relative to full-length TraG*. The 45 N-terminal residues of TraG* are hypothesized to serve as part of a flexible linker between the two independently functioning domains.

A method for quantifying how the activity of an enzyme is affected by the net charge of its nearest crowded neighbor

The electrostatic effects of protein crowding have not been systematically explored. Rather, protein crowding is generally studied with co‐solvents or crowders that are electrostatically neutral, with no methods to measure how the net charge (Z) of a crowder affects protein function. For example, can the activity of an enzyme be affected electrostatically by the net charge of its neighbor in crowded milieu? This paper reports a method for crowding proteins of different net charge to an enzyme via semi‐random chemical crosslinking. As a proof of concept, RNase A was crowded (at distances ≤ the Debye length) via crosslinking to different heme proteins with Z = +8.50 ± 0.04, Z = +6.39 ± 0.12, or Z = −10.30 ± 1.32. Crosslinking did not disrupt the structure of proteins, according to amide H/D exchange, and did not inhibit RNase A activity. For RNase A, we found that the electrostatic environment of each crowded neighbor had significant effects on rates of RNA hydrolysis. Crowding with cationic cytochrome c led to increases in activity, while crowding with anionic “supercharged” cytochrome c or myoglobin diminished activity. Surprisingly, electrostatic crowding effects were amplified at high ionic strength (I = 0.201 M) and attenuated at low ionic strength (I = 0.011 M). This salt dependence might be caused by a unique set of electric double layers at the dimer interspace (maximum distance of 8 Å, which cannot accommodate four layers). This new method of crowding via crosslinking can be used to search for electrostatic effects in protein crowding.

Phase stability of aqueous mixtures of bovine serum albumin with low molecular mass salts in presence of polyethylene glycol

The stability of bovine serum albumin (BSA) solutions against phase separation caused by cooling the system is studied under the combined influence of added poly(ethylene glycol) (PEG) and alkali halide salts in water as solvent. The phase stability of the system depends on the concentration of the added PEG and its molecular mass, the concentration of the low molecular mass electrolyte and its nature, as also on the pH of the solution. More specifically, the addition of NaCl to the BSA-PEG mixture promotes phase separation at pH = 4.0, where BSA carries the net positive charge in aqueous solution, and it increases the stability of the solution at pH=4.6, i.e., near the isoionic point of the protein. Moreover, at pH = 4.6, the cloud-point temperature decreases in the order from NaF to NaI and from LiCl to CsCl. The order of the salts at pH = 4.0 is exactly reversed: LiCl and NaF show the weakest effect on the cloud-point temperature and the strongest decrease in stability is caused by RbCl and NaNO3. An attempt is made to correlate these observations with the free energies of hydration of the added salt ions and with the effect of adsorption of salt ions on the protein surface on the protein-protein interactions. Kosmotropic salt ions decrease the phase stability of BSA-PEG-salt solutions at pH < pI, while exactly the opposite is true at pH = pI.

A General Small-Angle X-ray Scattering-Based Screening Protocol for Studying Physical Stability of Protein Formulations

A fundamental step in developing a protein drug is the selection of a stable storage formulation that ensures efficacy of the drug and inhibits physiochemical degradation or aggregation. Here, we designed and evaluated a general workflow for screening of protein formulations based on small-angle X-ray scattering (SAXS). Our SAXS pipeline combines automated sample handling, temperature control, and fast data analysis and provides protein particle interaction information. SAXS, together with different methods including turbidity analysis, dynamic light scattering (DLS), and SDS-PAGE measurements, were used to obtain different parameters to provide high throughput screenings. Using a set of model proteins and biopharmaceuticals, we show that SAXS is complementary to dynamic light scattering (DLS), which is widely used in biopharmaceutical research and industry. We found that, compared to DLS, SAXS can provide a more sensitive measure for protein particle interactions, such as protein aggregation and repulsion. Moreover, we show that SAXS is compatible with a broader range of buffers, excipients, and protein concentrations and that in situ SAXS provides a sensitive measure for long-term protein stability. This workflow can enable future high-throughput analysis of proteins and biopharmaceuticals and can be integrated with well-established complementary physicochemical analysis pipelines in (biopharmaceutical) research and industry.

The citron homology domain as a scaffold for Rho1 signaling

Aspergillus fumigatus gives rise to invasive aspergillosis in immunocompromised individuals. The rise of A. fumigatus antifungal resistance threatens a limited arsenal of treatment options. Here, we use genetic and molecular approaches to dissect the contribution of the citron homology (CNH) domain of the guanine nucleotide exchange factor Rom2 in regulating the biosynthesis of the essential and unique fungal cell wall, an important target of antifungal compounds. The CNH domain plays an essential role as a stabilizer for the small GTPase Rho1, a key regulator of glucan biosynthesis. This work provides a model for their interaction, revealing a promising molecular mechanism to explore in the quest for novel antifungal compounds.

Aspergillus fumigatus is a human opportunistic pathogen showing emerging resistance against a limited repertoire of antifungal agents available. The GTPase Rho1 has been identified as an important regulator of the cell wall integrity signaling pathway that regulates the composition of the cell wall, a structure that is unique to fungi and serves as a target for antifungal compounds. Rom2, the guanine nucleotide exchange factor to Rho1, contains a C-terminal citron homology (CNH) domain of unknown function that is found in many other eukaryotic genes. Here, we show that the Rom2 CNH domain interacts directly with Rho1 to modulate β-glucan and chitin synthesis. We report the structure of the Rom2 CNH domain, revealing that it adopts a seven-bladed β-propeller fold containing three unusual loops. A model of the Rho1–Rom2 CNH complex suggests that the Rom2 CNH domain interacts with the Rho1 Switch II motif. This work uncovers the role of the Rom2 CNH domain as a scaffold for Rho1 signaling in fungal cell wall biosynthesis.

Quantifying the Separation of Positive and Negative Areas in Electrostatic Potential for Predicting Feasibility of Ammonium Sulfate for Protein Crystallization

Ammonium sulfate (AS) and poly(ethylene glycol) (PEG) are the most popular precipitants in protein crystallization. Some proteins are preferably crystallized by AS, while some are by PEG. The electrostatic potential is related to the preference of the precipitant agents. The iso-surfaces of the electrostatic potentials for the AS-crystallized proteins display a common shape and a distinct separation between the positive and negative areas. In contrast, the PEG-crystallized proteins show unclear positive and negative separation. In this work, we propose schemes to quantitatively evaluate the separation for predicting which precipitant is favorable for crystal growth between AS or PEG. Three methods were attempted to quantify the amplitude of the separation, separation distance, dipole moment, and shape regularity. The positive and negative areas are approximated to the spherical potentials caused by point charges. The first method is a measurement of the distance between the positive and negative point charges. The second one is an assessment including the quantity of electric charge into the distance. The last one is an approach monitoring the clarity of the positive and negative separation. The average value for 25 kinds of AS-preferring proteins was higher than that for the PEG-preferring ones in all three methods. Therefore, every method can distinguish the proteins preferring AS for crystal growth from those preferring PEG. These methods require an iso-surface of the electrostatic potential depicted at a certain contouring value. The shape of the iso-surface depends on the contouring value. The dependency on contour was examined by depicting the iso-surfaces of electrostatic potential with three values at ±0.8, ±0.5, and ±0.2 kT/e. While reducing the contouring value leads to the increase in separation distance and the decrease in shape regularity, dipole moment is independent of the alteration of contouring value. While the AS-preferring proteins are distinguishable from the PEG-preferring ones in any contouring values, the iso-surface at ±0.5 kT/e seems adequate for regular use. The dipole moment assessment is feasible for the choice of potent precipitants for crystal growth in experiments.

The Development of the Innovative Synthesis Methodology of Albumin Nanoparticles Supported by Their Physicochemical, Cytotoxic and Hemolytic Evaluation

Many studies are being performed to develop effective carriers for controlled cytostatic delivery wherein albumin is a promising material due to its tendency to accumulate near cancer cells. The novelty of this work involves the development of the synthesis methodology of albumin nanoparticles and their biological and physicochemical evaluation. Albumin particles were obtained via the salt-induced precipitation and K3PO4 was used as a salting-out agent. Various concentrations of protein and salting-out agent solutions were mixed using a burette or a syringe system. It was proved that the size of the particles depended on the concentrations of the reagents and the methodology applied. As a result of a process performed using a burette and 2 M K3PO4, albumin spheres having a size 5-25 nm were obtained. The size of nanospheres and their spherical shape was confirmed via TEM analysis. The use of a syringe system led to preparation of particles of large polydispersity. The highest albumin concentration allowing for synthesis of homogeneous particles was 2 g/L. The presence of albumin in spheres was confirmed via the FT-IR technique and UV-Vis spectroscopy. All samples showed no cytotoxicity towards normal human dermal fibroblasts and no hemolytic properties against human erythrocytes (the hemolysis did not exceed 2.5%).

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.

Proteins maintain hydration at high [KCl] concentration regardless of content in acidic amino acids

Proteins of halophilic organisms, which accumulate molar concentrations of KCl in their cytoplasm, have a much higher content in acidic amino acids than proteins of mesophilic organisms. It has been proposed that this excess is necessary to maintain proteins hydrated in an environment with low water activity, either via direct interactions between water and the carboxylate groups of acidic amino acids or via cooperative interactions between acidic amino acids and hydrated cations. Our simulation study of five halophilic proteins and five mesophilic counterparts does not support either possibility. The simulations use the AMBER ff14SB force field with newly optimized Lennard-Jones parameters for the interactions between carboxylate groups and potassium ions. We find that proteins with a larger fraction of acidic amino acids indeed have higher hydration levels, as measured by the concentration of water in their hydration shell and the number of water/protein hydrogen bonds. However, the hydration level of each protein is identical at low (b_KCl = 0.15 mol/kg) and high (b_KCl = 2 mol/kg) KCl concentrations; excess acidic amino acids are clearly not necessary to maintain proteins hydrated at high salt concentration. It has also been proposed that cooperative interactions between acidic amino acids in halophilic proteins and hydrated cations stabilize the folded protein structure and would lead to slower dynamics of the solvation shell. We find that the translational dynamics of the solvation shell is barely distinguishable between halophilic and mesophilic proteins; if such a cooperative effect exists, it does not have that entropic signature.

Crystallization of nanoparticles induced by precipitation of trace polymeric additives

Orthogonal to guided growth of nanoparticle (NP) crystals using DNA or supramolecules, a trace amount of polymeric impurities (<0.1 wt.%) leads to reproducible, rapid growth of 3D NP crystals in solution and on patterned substrates with high yield. When polymers preferentially precipitate on the NP surfaces, small NP clusters form and serve as nuclei for NP crystal growth in dilute solutions. This precipitation-induced NP crystallization process is applicable for a range of polymers, and the resultant 3-D NP crystals are tunable by varying polymeric additives loading, solvent evaporation rate, and NP size. The present study elucidates how to balance cohesive energy density and NP diffusivity to simultaneously favor nuclei formation energetically and kinetic growth in dilute solutions to rapidly crystalize NPs over multiple length scales. Furthermore, the amount of impurities needed to grow NP crystals (<0.1%) reminds us the importance of fine details to interpret experimental observations in nanoscience.

Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions

Liquid-liquid phase separation of proteins underpins the formation of membraneless compartments in living cells. Elucidating the molecular driving forces underlying protein phase transitions is therefore a key objective for understanding biological function and malfunction. Here we show that cellular proteins, which form condensates at low salt concentrations, including FUS, TDP-43, Brd4, Sox2, and Annexin A11, can reenter a phase-separated regime at high salt concentrations. By bringing together experiments and simulations, we demonstrate that this reentrant phase transition in the high-salt regime is driven by hydrophobic and non-ionic interactions, and is mechanistically distinct from the low-salt regime, where condensates are additionally stabilized by electrostatic forces. Our work thus sheds light on the cooperation of hydrophobic and non-ionic interactions as general driving forces in the condensation process, with important implications for aberrant function, druggability, and material properties of biomolecular condensates.

Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions

Liquid-liquid phase separation of proteins underpins the formation of membraneless compartments in living cells. Elucidating the molecular driving forces underlying protein phase transitions is therefore a key objective for understanding biological function and malfunction. Here we show that cellular proteins, which form condensates at low salt concentrations, including FUS, TDP-43, Brd4, Sox2, and Annexin A11, can reenter a phase-separated regime at high salt concentrations. By bringing together experiments and simulations, we demonstrate that this reentrant phase transition in the high-salt regime is driven by hydrophobic and non-ionic interactions, and is mechanistically distinct from the low-salt regime, where condensates are additionally stabilized by electrostatic forces. Our work thus sheds light on the cooperation of hydrophobic and non-ionic interactions as general driving forces in the condensation process, with important implications for aberrant function, druggability, and material properties of biomolecular condensates.

Homogeneous batch micro-crystallization of proteins from ammonium sulfate

The emergence of X-ray free-electron lasers has led to the development of serial macromolecular crystallography techniques, making it possible to study smaller and more challenging crystal systems and to perform time-resolved studies on fast time scales. For most of these studies the desired crystal size is limited to a few micrometres, and the generation of large amounts of nanocrystals or microcrystals of defined size has become a bottleneck for the wider implementation of these techniques. Despite this, methods to reliably generate microcrystals and fine-tune their size have been poorly explored. Working with three different enzymes, L-aspartate α-decarboxylase, copper nitrite reductase and copper amine oxidase, the precipitating properties of ammonium sulfate were exploited to quickly transition from known vapour-diffusion conditions to reproducible, large-scale batch crystallization, circumventing the tedious determination of phase diagrams. Furthermore, the specific ammonium sulfate concentration was used to fine-tune the crystal size and size distribution. Ammonium sulfate is a common precipitant in protein crystallography, making these findings applicable to many crystallization systems to facilitate the production of large amounts of microcrystals for serial macromolecular crystallography experiments.

A review of solvent freeze-out technology for protein crystallization

In this review, we summarize important advances in solvent freeze-out (SFO) technology for protein crystallization, including the background of SFO, its fundamental principle, and some crucial conditions and factors for optimizing SFO technology.

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.

The effect of monovalent (Na+, K+) and divalent (Ca2+, Mg2+) cations on rapeseed oleosome (oil body) extraction and stability at pH 7

Oleosomes are storage vehicles of TAGs in plant seeds. They are protected with a phospholipid-protein monolayer and extracted with alkaline aqueous media; however, pH adjustment intensifies the extraction process. Therefore, the aim of this work was to investigate the extraction mechanism of rapeseed oleosomes at pH 7 and at the presence of monovalent and divalent cations (Na⁺, K⁺, Mg²⁺_, and Ca⁺²). The oleosome yield at pH 9.5 was 64 wt%, while the yield at pH 7 with H₂O was just 43 wt.%. The presence of cations at pH 7, significantly enhanced the yield, with K⁺ giving the highest yield (64 wt.%). The cations affected the oleosome interface and their interactions. The presence of monovalent cations resulted in aggregation and minor coalescence, while divalent cations resulted in extensive coalescence. These results help to understand the interactions of oleosomes in their native matrix and design simple extraction processes at neutral conditions.

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.

Evolution of Interactions in the Protein Solution As Induced by Mono and Multivalent Ions

The evolution of interactions in the bovine serum albumin (BSA) protein solution on addition of mono and multivalent (di, tri and tetra) counterions has been studied using small-angle neutron scattering (SANS), dynamic light scattering (DLS) and ζ-potential measurements. It is found that in the presence of mono and divalent counterions, protein behavior can be well explained by DLVO theory, combining the contributions of screened Coulomb repulsion with the van der Waals attraction. The addition of mono or divalent salts in protein solution reduces the repulsive barrier and hence the overall interaction becomes attractive, but the system remains in one-phase for the entire concentration range of the salts, added in the system. However, contrary to DLVO theory, the protein solution undergoes a reentrant phase transition from one-phase to a two-phase system and then back to the one-phase system in the presence of tri and tetravalent counterions. The results show that tri and tetravalent (unlike mono and divalent) counterions induce short-range attraction between the protein molecules, leading to the transformation from one-phase to two-phase system. The two-phase is characterized by the fractal structure of protein aggregates. The excess condensation of these higher-valent counterions in the double layer around the BSA causes the reversal of charge of the protein molecules resulting into reentrant of the one-phase, at higher salt concentrations. The complete phase behavior with mono and multivalent ions has been explained in terms of the interplay of electrostatic repulsion and ion-induced short-range attraction between the protein molecules.

Co-immunoprecipitation Assay Using Endogenous Nuclear Proteins from Cells Cultured Under Hypoxic Conditions

Low oxygen levels (hypoxia) trigger a variety of adaptive responses with the Hypoxia-inducible factor 1 (HIF-1) complex acting as a master regulator. HIF-1 consists of a heterodimeric oxygen-regulated α subunit (HIF-1α) and constitutively expressed β subunit (HIF-1β) also known as aryl hydrocarbon receptor nuclear translocator (ARNT), regulating genes involved in diverse processes including angiogenesis, erythropoiesis and glycolysis. The identification of HIF-1 interacting proteins is key to the understanding of the hypoxia signaling pathway. Besides the regulation of HIF-1α stability, hypoxia also triggers the nuclear translocation of many transcription factors including HIF-1α and ARNT. Notably, most of the current methods used to study such protein-protein interactions (PPIs) are based on systems where protein levels are artificially increased through protein overexpression. Protein overexpression often leads to non-physiological results arising from temporal and spatial artifacts. Here we describe a modified co-immunoprecipitation protocol following hypoxia treatment using endogenous nuclear proteins, and as a proof of concept, to show the interaction between HIF-1α and ARNT. In this protocol, the hypoxic cells were harvested under hypoxic conditions and the Dulbecco's Phosphate-Buffered Saline (DPBS) wash buffer was also pre-equilibrated to hypoxic conditions before usage to mitigate protein degradation or protein complex dissociation during reoxygenation. In addition, the nuclear fractions were subsequently extracted to concentrate and stabilize endogenous nuclear proteins and avoid possible spurious results often seen during protein overexpression. This protocol can be used to demonstrate endogenous and native interactions between transcription factors and transcriptional co-regulators under hypoxic conditions.

Super-Temporal-Resolved Microscopy Reveals Multistep Desorption Kinetics of α-Lactalbumin from Nylon

Insight into the mechanisms driving protein-polymer interactions is constantly improving due to advances in experimental and computational methods. In this study, we used super-temporal-resolved microscopy (STReM) to study the interfacial kinetics of a globular protein, α-lactalbumin (α-LA), adsorbing at the water-nylon 6,6 interface. The improved temporal resolution of STReM revealed that residence time distributions involve an additional step in the desorption process. Increasing the ionic strength in the bulk solution accelerated the desorption rate of α-LA, attributed to adsorption-induced conformational changes. Ensemble circular dichroism measurements were used to support a consecutive reaction mechanism. Without the improved temporal resolution of STReM, the desorption intermediate was not resolvable, highlighting both STReM's potential to uncover new kinetic mechanisms and the continuing need to push for better time and space resolution.

Dominant Albumin-Surface Interactions under Independent Control of Surface Charge and Wettability

Understanding protein adsorption behaviors on solid surfaces constitutes an important step toward development of efficacious and biocompatible medical devices. Both surface charge and wettability have been shown to influence protein adsorption attributes, including kinetics, quantities, deformation, and reversibility. However, determining the dominant interaction in these surface-induced phenomena is challenging because of the complexity of inter-related mechanisms at the liquid/solid interface. Herein, we reveal the dominant interfacial forces in these essential protein adsorption attributes under the influence of a combination of surface charge and wettability, using quartz crystal microbalance with dissipation monitoring and atomic force microscopy-based force spectroscopy on a series of model surfaces. These surfaces were fabricated via layer-by-layer assembly, which allowed two-dimensional control of surface charge and wettability with minimal cross-parameter dependency. We focused on a soft globular protein, bovine serum albumin (BSA), which is prone to conformational changes during adsorption. The information obtained from the two techniques shows that both surface charge and hydrophobicity can increase the protein-surface interaction forces and the adsorbed amount. However, surface hydrophobicity triggered a greater extent of deformation in the adsorbed BSA molecules, leading to more dehydration, spreading, and resistance to elution by ionic strength changes regardless of the surface charge. The role played by the surface charge in the adsorbed protein conformation and extent of desorption induced by changes in the ionic strength is secondary to that of surface hydrophobicity. These findings advance the understanding of how surface chemistry and properties can be tailored for directing protein-substrate interactions.

The Influence of Differently Shaped Gold Nanoparticles Functionalized with NIPAM-Based Hydrogels on the Release of Cytochrome C

Here, we report the synthesis and functionalization of five different shapes of Au nanoparticles (NPs), namely nanorods, tetrahexahedral, bipyramids, nanomakura, and spheres with PEG and poly (N-isopropylacrylamide)-acrylic acid (pNIPAm-AAc) hydrogels. The anisotropic NPs are synthesized using seed-mediated growth in the presence of silver. The NPs have been characterized using Dynamic Light Scattering (DLS), zeta potential measurements, UV-Visible spectrophotometry (UV-Vis), and Scanning Transmission Electron Microscopy (S(T)EM). Cyt C was loaded into the PEG-hydrogel-coated AuNPs using a modified breathing-in method. Loading efficiencies (up to 80%), dependent on particle geometry, concentration, and hydrogel content, were obtained. Release experiments conducted at high temperature (40 °C) and acidic pH (3) showed higher release for larger sizes of PEG-hydrogel-coated AuNPs, with temporal transition from spherical to thin film release geometry. AuNP shape, size, number density, and hydrogel content are found to influence the loading as well as release kinetics of Cyt C from these systems.

Strong attractions and repulsions mediated by monovalent salts

Controlling interactions between proteins and nanoparticles in electrolyte solutions is crucial for advancing biological sciences and biotechnology. The assembly of charged nanoparticles (NPs) and proteins in aqueous solutions can be directed by modifying the salt concentration. High concentrations of monovalent salt can induce the solubilization or crystallization of NPs and proteins. By using a multiscale coarse-grained molecular dynamics approach, we show that, due to ionic correlations in the electrolyte, NPs pairs at high monovalent salt concentrations interact via remarkably strong long-range attractions or repulsions, which can be split into three regimes depending on the surface charge densities of the NPs. NPs with zero-to-low surface charge densities interact via a long-range attraction that is stronger and has a similar range to the depletion attraction induced by polymers with radius of gyrations comparable to the NP diameter. On the other hand, moderately charged NPs with smooth surfaces as well as DNA-functionalized NPs with no possibility of hybridization between them interact via a strong repulsion of range and strength larger than the repulsion predicted by models that neglect ionic correlations, including the Derjaguin-Landau-Vervey-Overbeek (DLVO) model. Interactions between strongly charged NPs (>2 e/nm²), both types smooth and DNA-functionalized NPs, show an attractive potential well at intermediate-to-high salt concentrations, which demonstrates that electrolytes can induce aggregation of strongly charged NPs. Our work provides an improved understanding of the role of ionic correlations in NP assembly and design rules to utilize the salting-out process to crystallize NPs.

Self-association of a highly charged arginine-rich cell-penetrating peptide

Small-angle X-ray scattering (SAXS) measurements reveal a striking difference in intermolecular interactions between two short highly charged peptides-deca-arginine (R10) and deca-lysine (K10). Comparison of SAXS curves at high and low salt concentration shows that R10 self-associates, while interactions between K10 chains are purely repulsive. The self-association of R10 is stronger at lower ionic strengths, indicating that the attraction between R10 molecules has an important electrostatic component. SAXS data are complemented by NMR measurements and potentials of mean force between the peptides, calculated by means of umbrella-sampling molecular dynamics (MD) simulations. All-atom MD simulations elucidate the origin of the R10-R10 attraction by providing structural information on the dimeric state. The last two C-terminal residues of R10 constitute an adhesive patch formed by stacking of the side chains of two arginine residues and by salt bridges formed between the like-charge ion pair and the C-terminal carboxyl groups. A statistical analysis of the Protein Data Bank reveals that this mode of interaction is a common feature in proteins.

Investigation of host-pathogen interaction between Burkholderia pseudomallei and autophagy-related protein LC3 using hydrophobic chromatography-based technique

BACKGROUND

Burkholderia pseudomallei is an intracellular bacteria causing Melioidosis, the disease widely disseminates in Southeast Asia and Northern Australia. B. pseudomallei has ability to invade various types of host cell and to interfere with host defense mechanisms, such as nitric oxide (NO). Due to the cross-talk among alternative killing mechanisms in host immune response against invading microbes, autophagy is the molecular mechanism belonging to intracellular elimination of eukaryotic cells that has been widely discussed. However, bacterial evasion strategy of B. pseudomallei and host-bacterial protein-protein interaction within autophagic machinery remain unknown.

METHODS

Here, we demonstrated the protein-protein interaction study between different strains of B. pseudomallei, including wild type PP844 and rpoS mutant, with autophagy-related protein LC3 that has been constructed, using the modified immunoaffinity hydrophobic chromatography based-technique. Liquid chromatography tandem-mass spectrometry (LC-MS/MS) analysis was utilized for identifying the eluted proteins obtained from the established column. In addition, the expression level of gene encoding candidate protein was predicted prior to verification using real-time quantitative reverse transcription PCR assay (RT-qPCR).

RESULTS

LC3 recombinant proteins could be entrapped inside the column before encountering their bacterial interacting partners. Based on affinity interaction, the binding capacity of LC3 with antibody displayed over 50% readily for hydrophobically binding with bacterial proteins. Following protein identification, bacterial ATP-binding cassette (ABC) transporter periplasmic substrate-binding protein (BPSL2203) was identified as a candidate LC3-interacting protein, which was found only in B. pseudomallei wild type. Gene expression analysis and bioinformatics of BPSL2203 were validated the proteomic result which are suggesting the role of RpoS-dependent gene regulation.

CONCLUSIONS

Remarkably, utilization of the modified immunoaffinity hydrophobic chromatography with LC-MS/MS is a convenient and reliable approach to a study in B. pseudomallei-LC3 protein-protein interaction.

Prediction and characterization of the stability enhancing effect of the Cherry-Tag™ in highly concentrated protein solutions by complex rheological measurements and MD simulations

Solution stability attributes are one of the key parameters within the production and launching phase of new biopharmaceuticals. Instabilities of active biological compounds can reduce the yield of biopharmaceutical productions, and may induce undesired reactions in patients, such as immunogenic rejections. Protein solution stability thus needs to be engineered and monitored throughout production and storage. In contrast to the gold standard of long-term storage experiments applied in industry, novel experimental and in silico molecular dynamics tools for predicting protein solution stability can be applied within several minutes or hours. Here, a rheological approach in combination with molecular dynamics simulations are presented, for determining and predicting long-term phase behavior of highly concentrated protein solutions. A diversity of liquid phase conditions, including salt type, ionic strength, pH and protein concentration are tested in a Glutathione-S-Transferase (GST) case study, in combination with the enzyme with and without solubility-enhancing Cherry-Tag™. The rheological characterization of GST and Cherry-GST solutions enabled a fast and efficient prediction of protein instabilities without the need of long-term protein phase diagrams. Finally, the strong solubility enhancing properties of the Cherry-Tag™ were revealed by investigating protein surface properties in MD simulations. The tag highly altered the overall surface charge and hydrophobicity of GST, making it less accessible to alteration by the chemical surrounding.

Scaffold requirements for periodontal regeneration with enamel matrix derivative proteins

Periodontitis affects the attachment of natural teeth, and infection or inflammation associated with periodontitis may affect peri-implant tissues. Enamel matrix derivative (EMD) proteins provide stimulation for self-regeneration of the damaged tissue when applied to wide intrabony defects as part of a mixture with bone graft material. As a first step of the process enhancing cell proliferation and ligament formation, we demonstrated that EMD protein precipitation depends strongly on the physical and chemical characteristics of the bone grafts used in the mixture. To guarantee optimum protein-stimulated self-regulation, the pH of the initial EMD formulation must therefore be adjusted between 3.9 and 4.2 in order to compensate the change in pH induced by the bone graft. Moreover, the interaction between the two components resulted in precipitates of different shape and size differently covering the grafts. This outcome might potentially have clinical implications on cell attachment and periodontal ligament extension, which deserve further in vitro and in vivo tests.

The urea carboxylase and allophanate hydrolase activities of urea amidolyase are functionally independent

Urea amidolyase (UAL) is a multifunctional biotin-dependent enzyme that contributes to both bacterial and fungal pathogenicity by catalyzing the ATP-dependent cleavage of urea into ammonia and CO2 . UAL is comprised of two enzymatic components: urea carboxylase (UC) and allophanate hydrolase (AH). These enzyme activities are encoded on separate but proximally related genes in prokaryotes while, in most fungi, they are encoded by a single gene that produces a fusion enzyme on a single polypeptide chain. It is unclear whether the UC and AH activities are connected through substrate channeling or other forms of direct communication. Here, we use multiple biochemical approaches to demonstrate that there is no substrate channeling or interdomain/intersubunit communication between UC and AH. Neither stable nor transient interactions can be detected between prokaryotic UC and AH and the catalytic efficiencies of UC and AH are independent of one another. Furthermore, an artificial fusion of UC and AH does not significantly alter the AH enzyme activity or catalytic efficiency. These results support the surprising functional independence of AH from UC in both the prokaryotic and fungal UAL enzymes and serve as an important reminder that the evolution of multifunctional enzymes through gene fusion events does not always correlate with enhanced catalytic function.