[3] Inferences drawn from physicochemical studies of crystallogenesis and precrystalline state

Targeting Efficient Features of Urate Oxidase to Increase Its Solubility

With the demand for mass production of protein drugs, solubility has become a serious issue. Extrinsic and intrinsic factors both affect this property. A homotetrameric cofactor-free urate oxidase (UOX) is not sufficiently soluble. To engineer UOX for optimum solubility, it is important to identify the most effective factor that influences solubility. The most effective feature to target for protein engineering was determined by measuring various solubility-related factors of UOX. A large library of homologous sequences was obtained from the databases. The data was reduced to six enzymes from different organisms. On the basis of various sequence- and structure-derived elements, the most and the least soluble enzymes were defined. To determine the best protein engineering target for modification, features of the most and least soluble enzymes were compared. Metabacillus fastidiosus UOX was the most soluble enzyme, while Agrobacterium globiformis UOX was the least soluble. According to the comparison-constant method, positive surface patches caused by arginine residue distribution are appropriate targets for modification. Two Arg to Ala mutations were introduced to the least soluble enzyme to test this hypothesis. These mutations significantly enhanced the mutant's solubility. While different algorithms produced conflicting results, it was difficult to determine which proteins were most and least soluble. Solubility prediction requires multiple algorithms based on these controversies. Protein surfaces should be investigated regionally rather than globally, and both sequence and structural data should be considered. Several other biotechnological products could be engineered using the data reduction and comparison-constant methods used in this study.

Physicochemical properties of seed protein isolates extracted from pepper meal by pressure-assisted and conventional solvent defatting

Pepper seed is one by-product in pepper processing, rich in protein, fat, and fiber, and is a new plant-based protein source. In this paper, the physicochemical and functional properties of pepper seed protein isolates (PSPIs) extracted from pepper meal by pressure-assisted defatting (PAD) and conventional solvent defatting (CSD) were investigated. The yields of SPIs extracted by CSD and PAD were 22.8% and 20.5%, respectively. Compared with the PSPIs obtained by CSD, the solubility, water-holding and oil-holding capacities, and emulsifying and foaming abilities of the PSPIs obtained by PAD were significantly increased by 11.22%, 29.17%, 40%, 160%, and 100%, respectively. Additionally, UV-visible, intrinsic fluorescence and infrared spectroscopic characterization revealed the tertiary and secondary conformation changes of the PSPIs, which might contribute to the improvement of their functional properties. Overall, PAD significantly improved the functional properties of the PSPIs. The PSPIs extracted by this innovative technology would be a new plant protein alternative for food formulations with better functional properties.

Probing Interfacial Effects on Ionization Energies: The Surprising Banality of Anion-Water Hydrogen Bonding at the Air/Water Interface

Liquid microjet photoelectron spectroscopy is an increasingly common technique to measure vertical ionization energies (VIEs) of aqueous solutes, but the interpretation of these experiments is subject to questions regarding sensitivity to bulk versus interfacial solvation environments. We have computed aqueous-phase VIEs for a set of inorganic anions, using a combination of molecular dynamics simulations and electronic structure calculations, with results that are in excellent agreement with experiment regardless of whether the simulation data are restricted to ions at the air/water interface or to those in bulk aqueous solution. Although the computed VIEs are sensitive to ion-water hydrogen bonding, we find that the short-range solvation structure is sufficiently similar in both environments that it proves impossible to discriminate between the two on the basis of the VIE, a conclusion that has important implications for the interpretation of liquid-phase photoelectron spectroscopy. More generally, analysis of the simulation data suggests that the surface activity of soft anions is largely a second or third solvation shell effect, arising from disruption of water-water hydrogen bonds and not from significant changes in first-shell anion-water hydrogen bonding.

Activity profile of innate immune-related enzymes and bactericidal of freshwater fish epidermal mucus extract at different pH

The epidermal mucus of fish performs diverse functions from prevention of mechanical abrasion to limit pathogen invasions. The current experiment was designed to extract skin mucus proteins of three freshwater fish, i.e. common carp (Cyprinus carpio), mrigal (Cirrhinus mrigala) and rohu (Labeo rohita) with organic solvent (methanol) and dissolve in different pH of Tris-HCl buffers to examine the significance of pH in the solubilisation of skin mucus proteins. The protein profiles of different pH solubilised methanol fish skin mucus extracts were determined by SDS-PAGE. The non-specific immune enzymes, alkaline phosphatase, lysozyme and protease of fish skin mucus were compared and this present study demonstrated that these enzymes differed in their activity depending on pH buffers. The higher lysozyme and protease activity were observed at the pH of 8.0 and higher alkaline phosphatase activity in the pH 9.0 of C. mrigala fish skin mucus methanol extract. In addition, the bactericidal activity was evaluated against the pathogens Proteus vulgaris and Pseudomonas aeruginosa. The pH 8.0 of C. mrigala skin mucus extract revealed better bactericidal activity than other fish species mucus pH buffers against both P. vulgaris and P. aeruginosa. In the case of protein profile from SDS-PAGE, based on pH buffers and the solubilisation of proteins, differences in the resolution of bands were observed. The higher alkaline pH of 9.0 showed smeared gel bands in all the three fish skin mucus methanol extract. The present study suggests that methanol extracted C. mrigala fish skin mucus at pH 8.0 showed better innate immune enzymes and bactericidal activity. The additional examinations of C. mrigala skin mucus methanol extract in this pH aids in identifying novel bioactive molecules. This is the study of proteome of three fish species skin mucus in the effect of pH. Further analyses are required to evaluate proteins present in fish skin mucus extracted with methanol and the influence of pH on protein solubility. These findings could be helpful in exploring natural alternatives to antibiotics in aquaculture industry against infectious pathogens.

Anion binding to ubiquitin and its relevance to the Hofmeister effects

Although the non-covalent interactions between proteins and salts contributing to the Hofmeister effects have been generally mapped, there are many questions regarding the specifics of these interactions. We report here studies involving the small protein ubiquitin and salts of polarizable anions. These studies reveal a complex interplay between the reverse Hofmeister effect at low pH, the salting-in Hofmeister effect at higher pH, and six anion binding sites in ubiquitin at the root of these phenomena. These sites are all located at protuberances of preorganized secondary structure, and although stronger at low pH, are still apparent when ubiquitin possesses no net charge. These results demonstrate the traceability of these Hofmeister phenomena and suggest new strategies for understanding the supramolecular properties of proteins.

Studying the supramolecular properties of Ubiquitin reveals six anion binding sites that contribute to the reverse Hofmeister effect at low pH and the salting-in Hofmeister effect at higher pH.

Effect of pH and denaturants on the fold and metal status of anthrax lethal factor

Anthrax lethal factor (LF) is a critical component of the anthrax toxin, and functions intracellularly as a zinc-dependent endopeptidase targeting proteins involved in maintaining critical host signaling pathways. To reach the cytoplasm, LF requires to be unfolded and guided through the narrow protective antigen pore in a pH-dependent process. The current study sought to address the question as to whether LF is capable of retaining its metal ion when exposed to a low-pH environment (similar to that found in late endosomes) and an unfolding stress (induced by urea). Using a combination of tryptophan fluorescence spectroscopy and chelation studies, we show that a decrease in the pH value (from 7.0 to 5.0) leads to a pronounced shift in the onset of structural alterations in LF to lower urea concentrations. More importantly, the enzyme was found to retain its Zn²⁺ ion beyond the unfolding transitions monitored by Trp fluorescence, a finding indicative of tight metal binding to LF in a non-native state. In addition, an analysis of red-edge excitation shift (REES) spectra suggests the protein to maintain residual structure (a feature necessary for metal binding) even at very high denaturant concentrations. Furthermore, studies using the chromophoric chelator 4-(2-pyridylazo)resorcinol (PAR) revealed LF's Zn²⁺ ion to become accessible to complexation at urea concentrations in between those required to cause structural changes and metal dissociation. This phenomenon likely originates from the conversion of a PAR-inaccessible (closed) to a PAR-accessible (open) state of LF at intermediate denaturant concentrations.

Structure of odorant binding proteins and chemosensory proteins determined by X-ray crystallography

OBPs and CSPs are small soluble proteins used by organisms as shuttle to transport odorant molecules between air and the membrane-embedded receptors. Deciphering the interactions of these proteins with their ligands at a molecular level may give clue on the function and specificity of the olfactory chain. To reach this goal, protein crystallography is very helpful with more than hundred entries available in the protein data bank (PDB). In this chapter, we present the peculiarities of OBPs and CSPs concerning their crystallization and 3D structure determination by X-ray diffraction.

Exploration of Insulin Amyloid Polymorphism Using Raman Spectroscopy and Imaging

We aimed to investigate insulin amyloid fibril polymorphism caused by salt effects and heating temperature and to visualize the structural differences of the polymorphisms in situ using Raman imaging without labeling. The time course monitoring for amyloid formation was carried out in an acidic condition without any salts and with two species of salts (NaCl and Na₂SO₄) by heating at 60, 70, 80, and 90°C. The intensity ratio of two Raman bands at 1672 and 1657 cm^-1 due to antiparallel β-sheet and α-helix structures, respectively, was revealed to be an indicator of amyloid fibril formation, and the relative proportion of the β-sheet structure was higher in the case with salts, especially at a higher temperature with Na₂SO₄. In conjunction with the secondary structural changes of proteins, the S-S stretching vibrational mode of a disulfide bond (∼514 cm^-1) and the ratio of the tyrosine doublet I₈₅₀/I₈₂₆ were also found to be markers distinguishing polymorphisms of insulin amyloid fibrils by principal component analysis. Especially, amyloid fibrils with Na₂SO₄ media formed the gauche-gauche-gauche conformation of disulfide bond at a higher rate, but without any salts, the gauche-gauche-gauche conformation was partially transformed into the gauche-gauche-trans conformation at higher temperatures. The different environments of the hydroxyl groups of the tyrosine residue were assumed to be caused by fibril polymorphism. Raman imaging using these marker bands also successfully visualized the two- and three- dimensional structural differences of amyloid polymorphisms. These results demonstrate the potential of Raman imaging as a diagnostic tool for polymorphisms in tissues of amyloid-related diseases.

Investigation of the reversibility of freeze/thaw stress-induced protein instability using heat cycling as a function of different cryoprotectants

Formulation conditions have a significant influence on the degree of freeze/thaw (FT) stress-induced protein instabilities. Adding cryoprotectants might stabilize the induced FT stress instabilities. However, a simple preservation of protein stability might be insufficient and further methods are necessary. This study aims to evaluate the addition of a heat cycle following FT application as a function of different cryoprotectants with lysozyme as exemplary protein. Sucrose and glycerol were shown to be the most effective cryoprotectants when compared to PEG200 and Tween20. In terms of heat-induced reversibility of aggregates, glycerol showed the best performance followed by sucrose, NaCl and Tween20 systems. The analysis was performed using a novel approach to visualize complex interplays by a clustering and data reduction scheme. In addition, solubility and structural integrity were measured and confirmed the obtained results.

Apparent protein cloud point temperature determination using a low volume high-throughput cryogenic device in combination with automated imaging

Short-term parameters correlating to long-term protein stability, such as the protein cloud point temperature (T_cloud), are of interest to improve efficiency during protein product development. Such efficiency is reached if short-term parameters are obtained in a low volume and high-throughput (HT) manner. This study presents a low volume HT detection method for (sub-zero) T_cloud determination of lysozyme, as such an experimental method is not available yet. The setup consists of a cryogenic device with an automated imaging system. Measurement reproducibility (median absolute deviation of 0.2 °C) and literature-based parameter validation (Pearson correlation coefficient of 0.996) were shown by a robustness and validation study. The subsequent case study demonstrated a partial correlation between the obtained apparent T_cloud parameter and long-term protein stability as a function of lysozyme concentration, ion type, ionic strength, and freeze/thaw stress. The presented experimental setup demonstrates its ability to advance short-term strategies for efficient protein formulation development.

The behavior of ions in water is controlled by their water affinity

The strong, long-range electrostatic forces described by Coulomb's law disappear for ions in water, and the behavior of these ions is instead controlled by their water affinity – a weak, short-range force which arises from their charge density. This was established experimentally in the mid-1980s by size-exclusion chromatography on carefully calibrated Sephadex®G-10 (which measures the effective volume and thus the water affinity of an ion) and by neutron diffraction with isotopic substitution (which measures the density and orientation of water molecules near the diffracting ion and thus its water affinity). These conclusions have been confirmed more recently by molecular dynamics simulations, which explicitly model each individual water molecule. This surprising change in force regime occurs because the oppositely charged ions in aqueous salt solutions exist functionally as ion pairs (separated by 0, 1 or 2 water molecules) as has now been shown by dielectric relaxation spectroscopy; this cancels out the strong long-range electrostatic forces and allows the weak, short-range water affinity effects to come to the fore. This microscopic structure of aqueous salt solutions is not captured by models utilizing a macroscopic dielectric constant. Additionally, the Law of Matching Water Affinity, first described in 1997 and 2004, establishes that contact ion pair formation is controlled by water affinity and is a major determinant of the solubility of charged species since only a net neutral species can change phases.

Interactions between Hofmeister anions and the binding pocket of a protein

This paper uses the binding pocket of human carbonic anhydrase II (HCAII, EC 4.2.1.1) as a tool to examine the properties of Hofmeister anions that determine (i) where, and how strongly, they associate with concavities on the surfaces of proteins and (ii) how, upon binding, they alter the structure of water within those concavities. Results from X-ray crystallography and isothermal titration calorimetry show that most anions associate with the binding pocket of HCAII by forming inner-sphere ion pairs with the Zn(2+) cofactor. In these ion pairs, the free energy of anion-Zn(2+) association is inversely proportional to the free energetic cost of anion dehydration; this relationship is consistent with the mechanism of ion pair formation suggested by the "law of matching water affinities". Iodide and bromide anions also associate with a hydrophobic declivity in the wall of the binding pocket. Molecular dynamics simulations suggest that anions, upon associating with Zn(2+), trigger rearrangements of water that extend up to 8 Å away from their surfaces. These findings expand the range of interactions previously thought to occur between ions and proteins by suggesting that (i) weakly hydrated anions can bind complementarily shaped hydrophobic declivities, and that (ii) ion-induced rearrangements of water within protein concavities can (in contrast with similar rearrangements in bulk water) extend well beyond the first hydration shells of the ions that trigger them. This study paints a picture of Hofmeister anions as a set of structurally varied ligands that differ in size, shape, and affinity for water and, thus, in their ability to bind to—and to alter the charge and hydration structure of—polar, nonpolar, and topographically complex concavities on the surfaces of proteins.

Characterization of selective binding of biologically relevant inorganic ions with the proline zwitterion by 3D-RISM theory

The features of selective binding of several biologically relevant mono- and divalent inorganic ions with the proline zwitterion were studied over a wide range of electrolyte concentrations.

Weak protein-cationic co-ion interactions addressed by X-ray crystallography and mass spectrometry

The adsorption of Rb(+), Cs(+), Mn(2+), Co(2+) and Yb(3+) onto the positively charged hen egg-white lysozyme (HEWL) has been investigated by solving 13 X-ray structures of HEWL crystallized with their chlorides and by applying electrospray ionization mass spectrometry (ESI-MS) first to dissolved protein crystals and then to the protein in buffered salt solutions. The number of bound cations follows the order Cs(+) < Mn(2+) ≃ Co(2+) < Yb(3+) at 293 K. HEWL binds less Rb(+) (qtot = 0.7) than Cs(+) (qtot = 3.9) at 100 K. Crystal flash-cooling drastically increases the binding of Cs(+), but poorly affects that of Yb(3+), suggesting different interactions. The addition of glycerol increases the number of bound Yb(3+) cations, but only slightly increases that of Rb(+). HEWL titrations with the same chlorides, followed by ESI-MS analysis, show that only about 10% of HEWL binds Cs(+) and about 40% binds 1-2 Yb(3+) cations, while the highest binding reaches 60-70% for protein binding 1-3 Mn(2+) or Co(2+) cations. The binding sites identified by X-ray crystallography show that the monovalent Rb(+) and Cs(+) preferentially bind to carbonyl groups, whereas the multivalent Mn(2+), Co(2+) and Yb(3+) interact with carboxylic groups. This work elucidates the basis of the effect of the Hofmeister cation series on protein solubility.

Charged surfactants induce a non-fibrillar aggregation pathway of amyloid-beta peptide

The amyloid β-peptide with a sequence of 42 amino acids is the major constituent of extracellular amyloid deposits in Alzheimer's disease plaques. The control of the peptide self-assembly is difficult to achieve because the process is fast and is affected by many variables. In this paper, we describe the effect of different charged and non-charged surfactants on Aβ(₁₋₄₂) fibrillation to define common alternate aggregation pathways. The characterization of the peptide-surfactant interactions by ultra-structural analysis, thioflavin T assay and secondary structure analysis, suggested that charged surfactants interact with Aβ(₁₋₄₂) through electrostatic interactions. Charged micelles slow down the aggregation process and stabilize the peptide in the oligomeric state, whereas non-charged surfactants promote the Aβ(₁₋₄₂) fibril formation.

Application of a PEG precipitation method for solubility screening: a tool for developing high protein concentration formulations

Previous publications demonstrated that the extrapolated solubility by polyethylene glycol (PEG) precipitation method (Middaugh et al., J Biol Chem 1979; 254:367-370; Juckes, Biochim Biophys Acta 1971; 229:535-546; Foster et al., Biochim Biophys Acta 1973; 317:505; Mahadevan and Hall, AIChE J 1990; 36:1517-1528; Stevenson and Hageman, Pharm Res 1995; 12:1671-1676) has a strong correlation to experimentally measured solubility of proteins. Here, we explored the utility of extrapolated solubility as a method to compare multiple protein drug candidates when nonideality of a highly soluble protein prohibits accurate quantitative solubility prediction. To achieve high efficiency and reduce the amount of protein required, the method is miniaturized to microwell plate format for high-throughput screening application. In this simplified version of the method, comparative solubility of proteins can be obtained without the need of concentration measurement of the supernatant following the precipitation step in the conventional method. The monoclonal antibodies with the lowest apparent solubilities determined by this method are the most difficult to be concentrated, indicating a good correlation between the prediction and empirical observations. This study also shows that the PEG precipitation method gives results for opalescence prediction that favorably compares to experimentally determined opalescence levels at high concentration. This approach may be useful in detecting proteins with potential solubility and opalescence problems prior to the time-consuming and expensive development process of high concentration formulation.

Toward a molecular understanding of protein solubility: increased negative surface charge correlates with increased solubility

Protein solubility is a problem for many protein chemists, including structural biologists and developers of protein pharmaceuticals. Knowledge about how intrinsic factors influence solubility is limited due to the difficulty of obtaining quantitative solubility measurements. Solubility measurements in buffer alone are difficult to reproduce, because gels or supersaturated solutions often form, making it impossible to determine solubility values for many proteins. Protein precipitants can be used to obtain comparative solubility measurements and, in some cases, estimations of solubility in buffer alone. Protein precipitants fall into three broad classes: salts, long-chain polymers, and organic solvents. Here, we compare the use of representatives from two classes of precipitants, ammonium sulfate and polyethylene glycol 8000, by measuring the solubility of seven proteins. We find that increased negative surface charge correlates strongly with increased protein solubility and may be due to strong binding of water by the acidic amino acids. We also find that the solubility results obtained for the two different precipitants agree closely with each other, suggesting that the two precipitants probe similar properties that are relevant to solubility in buffer alone.

Specific anion effects on water structure adjacent to protein monolayers

Vibrational sum frequency spectroscopy (VSFS) was used to explore specific ion effects on interfacial water structure adjacent to a bovine serum albumin (BSA) monolayer adsorbed at the air/water interface. The subphase conditions were varied by the use of six different sodium salts and four different pH values. At pH 2 and 3, the protein layer was positively charged and it was found that the most chaotropic anions caused the greatest attenuation of water structure. The order of the salts followed an inverse Hofmeister series. On the other hand, when the protein layer was near its isoelectric point (pH 5), the most chaotropic anions caused the greatest increase in water structure, although the effect was weak. In this case, a direct Hofmeister series was obeyed. Finally, virtually no effect was observed when the protein layer was negatively charged with a subphase pH of 9. For comparison, similar experiments were run with positively charged, negatively charged, and zwitterionic surfactant monolayers. These experiments gave rise to nearly the identical results as the protein monolayer which suggested that specific anion effects are dominated by the charge state of the interfacial layer rather than its detailed chemical structure. In a final set of experiments, salt effects were examined with a monolayer made from an elastin-like polypeptide (ELP). The peptide consisted of 120 pentameric repeats of the sequence Val-Pro-Gly-Val-Gly. Data from this net neutral biopolymer followed a very weak, but direct Hofmeister series. This suggested that direct anion binding to the amide groups in the backbone of a polypeptide is quite weak in agreement with the BSA data. The results from the variously charged protein, surfactant, and polymer monolayers were compared with a modified Gouy-Chapman-Stern model. The agreement with this simple model was quite good.

Promoting crystallization of antibody-antigen complexes via microseed matrix screening

The application of microseed matrix screening to the crystallization of related antibodies in complex with IL-13 is described. Both self-seeding or cross-seeding helped promote nucleation and increase the hit rate.

The application of microseed matrix screening to the crystallization of antibody–antigen complexes is described for a set of antibodies that include mouse anti-IL-13 antibody C836, its humanized version H2L6 and an affinity-matured variant of H2L6, M1295. The Fab fragments of these antibodies were crystallized in complex with the antigen human IL-13. The initial crystallization screening for each of the three complexes included 192 conditions. Only one hit was observed for H2L6 and none were observed for the other two complexes. Matrix self-microseeding using these microcrystals yielded multiple hits under various conditions that were further optimized to grow diffraction-quality H2L6 crystals. The same H2L6 seeds were also successfully used to promote crystallization of the other two complexes. The M1295 crystals appeared to be isomorphous to those of H2L6, whereas the C836 crystals were in a different crystal form. These results are consistent with the concept that the conditions that are best for crystal growth may be different from those that favor nucleation. Microseed matrix screening using either a self-seeding or cross-seeding approach proved to be a fast, robust and reliable method not only for the refinement of crystallization conditions but also to promote crystal nucleation and increase the hit rate.

Chemistry of Hofmeister anions and osmolytes

The study of the interactions of salts and osmolytes with macromolecules in aqueous solution originated with experiments concerning protein precipitation more than 100 years ago. Today, these solutes are known to display recurring behavior for myriad biological and chemical processes. Such behavior depends both on the nature and concentration of the species in solution. Despite the generality of these effects, our understanding of the molecular-level details of ion and osmolyte specificity is still quite limited. Here, we review recent studies of the interactions between anions and urea with model macromolecular systems. A mechanism for specific ion effects is elucidated for aqueous systems containing charged and uncharged polymers, polypeptides, and proteins. The results clearly show that the effects of the anions are local and involve direct interactions with macromolecules and their first hydration shell. Also, a hydrogen-bonding mechanism is tested for the urea denaturation of proteins with some of these same systems. In that case, direct hydrogen bonding can be largely discounted as the key mechanism for urea stabilization of uncollapsed and/or unfolded structures.

The stabilities of protein crystals

We describe a model for protein crystallization equilibria. The model includes four terms, (1) protein translational entropy opposes crystallization, (2) proteins are attracted to each other by a nonelectrostatic contact free energy favoring crystallization, (3) proteins in the crystal repel each other but, to a greater extent, attract counterions sequestered in the crystal, which favors crystallization, and (4) the translational entropy of the counterions opposes their sequestration into the crystal, opposing crystallization. We treat the electrostatics using the nonlinear Poisson-Boltzmann equation, and we use unit cell information from native protein crystals to determine the boundary conditions. This model predicts the stabilities of protein crystals as functions of temperature, pH, and salt concentrations, in good agreement with the data of Pusey et al. on tetragonal and orthorhombic crystal forms of lysozyme. The experiments show a weak dependence of crystal solubility on pH. According to the model, this is because the entropic cost to neutralize the crystal is compensated by favorable protein-salt interactions. Experiments also show that adding salt stabilizes the crystal. Cohn's empirical law predicts that the logarithm of solubility should be a linear function of salt. The present theory predicts nonlinearity, in better agreement with the experiments. The model shows that the salting out phenomena is not due to more counterion shielding but to lowered counterion translational entropy. Models of this type may help guide faster and better ways to crystallize proteins.

The solubility of hen lysozyme in ethylammonium nitrate/H2O mixtures and a novel approach to protein crystallization

We report on the solubility of hen lysozyme (HEWL) in aqueous ethylammonium nitrate (EAN) as a function of water content. We find the solubility behavior to be complex, exhibiting both a maximum (400 mg/mL) at very high EAN content) and a minimum at intermediate EAN content. We exploit this solubility profile in a novel approach to generating crystals of hydrophilic proteins, based on rehydration of a high concentration protein solution. We describe the production of crystals of X-ray diffraction quality. Two related ionic liquid solvent systems, with the same solubility profiles but different effective pH characteristics, are identified for future evaluation.

The inverse and direct Hofmeister series for lysozyme

Anion effects on the cloud-point temperature for the liquid-liquid phase transition of lysozyme were investigated by temperature gradient microfluidics under a dark field microscope. It was found that protein aggregation in salt solutions followed 2 distinct Hofmeister series depending on salt concentration. Namely, under low salt conditions the association of anions with the positively charged lysozyme surface dominated the process and the phase transition temperature followed an inverse Hofmeister series. This inverse series could be directly correlated to the size and hydration thermodynamics of the anions. At higher salt concentrations, the liquid-liquid phase transition displayed a direct Hofmeister series that correlated with the polarizability of the anions. A simple model was derived to take both charge screening and surface tension effects into account at the protein/water interface. Fitting the thermodynamic data to this model equation demonstrated its validity in both the high and low salt regimes. These results suggest that in general positively charged macromolecular systems should show inverse Hofmeister behavior only at relatively low salt concentrations, but revert to a direct Hofmeister series as the salt concentration is increased.

Effect of Different Salt Ions on the Propensity of Aggregation and on the Structure of Alzheimer’s Aβ(1-40) Amyloid Fibrils

The formation of amyloid fibrils and other polypeptide aggregates depends strongly on the physico-chemical environment. One such factor affecting aggregation is the presence and concentration of salt ions. We have examined the effects of salt ions on the aggregation propensity of Alzheimer's Abeta(1-40) peptide and on the structure of the dissolved and of the fibrillar peptide. All salts examined promote aggregation strongly. The most pronounced effect is seen within the cationic series, i.e. for MgCl2. Evaluation of different possible explanations suggests that Abeta(1-40) aggregation depends on direct interaction between ions and Abeta(1-40) peptide, and correlates with ion-induced changes of the surface tension. Salts have profound effects on the fibril structure. In the presence of salts, fibrils are associated with smaller diameters, narrower crossover distances and lower amide I maxima. Since Abeta(1-40) aggregation responds to salts in a manner unlike that for other polypeptides, such as glucagon, beta2-microglobulin or alpha-synuclein; these data argue that there is no fully uniform way in which salts affect aggregation of different polypeptide chains. These observations are important for understanding and predicting aggregation on the basis of simple physico-chemical properties.

Ions in water: Characterizing the forces that control chemical processes and biological structure

The continuum electrostatics model of Debye and Hückel [P. Debye and E. Hückel, On the theory of electrolytes. I. Freezing point depression and related phenomena., Phys. Z. 24 (1923) 185-206.] and its successors utilize a macroscopic dielectric constant and assume that all interactions involving ions are strictly electrostatic, implying that simple ions in water generate electric fields strong enough to orient water dipoles over long distances. However, solution neutron and X-ray diffraction indicate that even di- and tri-valent ions do not significantly alter the density or orientation of water more than two water molecules (5 A) away. Therefore the long range electric fields (generated by simple ions) which can be detected by various resonance techniques such as fluorescence resonance energy transfer over distances of 30 A (about 11 water diameters) or more must be weak relative to the strength of water-water interactions. Two different techniques indicate that the interaction of water with anions is by an approximately linear hydrogen bond, suggesting that the dominant forces on ions in water are short range forces of a chemical nature.

Amino acid contribution to protein solubility: Asp, Glu, and Ser contribute more favorably than the other hydrophilic amino acids in RNase Sa

Poor protein solubility is a common problem in high-resolution structural studies, formulation of protein pharmaceuticals, and biochemical characterization of proteins. One popular strategy to improve protein solubility is to use site-directed mutagenesis to make hydrophobic to hydrophilic mutations on the protein surface. However, a systematic investigation of the relative contributions of all 20 amino acids to protein solubility has not been done. Here, 20 variants at the completely solvent-exposed position 76 of ribonuclease (RNase) Sa are made to compare the contributions of each amino acid. Stability measurements were also made for these variants, which occur at the i+1 position of a type II beta-turn. Solubility measurements in ammonium sulfate solutions were made at high positive net charge, low net charge, and high negative net charge. Surprisingly, there was a wide range of contributions to protein solubility even among the hydrophilic amino acids. The results suggest that aspartic acid, glutamic acid, and serine contribute significantly more favorably than the other hydrophilic amino acids especially at high net charge. Therefore, to increase protein solubility, asparagine, glutamine, or threonine should be replaced with aspartic acid, glutamic acid or serine.

Improving marginal crystals

The physical chemistry of crystal growth can help to identify directions in which to look for improved crystal properties. In this chapter, we summarize how crystal growth depends on parameters that can be controlled experimentally, and relate them to the tools available for optimizing a particular crystal form for crystal shape, volume, and diffraction quality. Our purpose is to sketch the conceptual basis of optimization and to provide sample protocols derived from those foundations. We hope to assist even those who chose not to use systematic methods by enabling them to carry out rudimentary optimization searches armed with a better understanding of how the underlying physical chemistry operates.

Hydrogen Bonding Markedly Reduces the pK of Buried Carboxyl Groups in Proteins

The ionizable groups in proteins with the lowest pKs are the carboxyl groups of aspartic acid side-chains. One of the lowest, pK=0.6, is observed for Asp76 in ribonuclease T1. This low pK appeared to result from hydrogen bonds to a water molecule and to the side-chains of Asn9, Tyr11, and Thr91. The results here confirm this by showing that the pK of Asp76 increases to 1.7 in N9A, to 4.0 in Y11F, to 4.2 in T91V, to 4.4 in N9A+Y11F, to 4.9 in N9A+T91V, to 5.9 in Y11F+T91V, and to 6.4 in the triple mutant: N9A+Y11F+T91V. In ribonuclease Sa, the lowest pK=2.4 for Asp33. This pK increases to 3.9 in T56A, which removes the hydrogen bond to Asp33, and to 4.4 in T56V, which removes the hydrogen bond and replaces the -OH group with a -CH(3) group. It is clear that hydrogen bonds are able to markedly lower the pK values of carboxyl groups in proteins. These same hydrogen bonds make large contributions to the conformational stability of the proteins. At pH 7, the stability of D76A ribonuclease T1 is 3.8 kcal mol(-1) less than wild-type, and the stability of D33A ribonuclease Sa is 4.1 kcal mol(-1) less than wild-type. There is a good correlation between the changes in the pK values and the changes in stability. The results suggest that the pK values for these buried carboxyl groups would be greater than 8 in the absence of hydrogen bonds, and that the hydrogen bonds and other interactions of the carboxyl groups contribute over 8 kcal mol(-1) to the stability.

pK values of the ionizable groups of proteins

We have used potentiometric titrations to measure the pK values of the ionizable groups of proteins in alanine pentapeptides with appropriately blocked termini. These pentapeptides provide an improved model for the pK values of the ionizable groups in proteins. Our pK values determined in 0.1 M KCl at 25 degrees C are: 3.67+/-0.03 (alpha-carboxyl), 3.67+/-0.04 (Asp), 4.25+/-0.05 (Glu), 6.54+/-0.04 (His), 8.00+/-0.03 (alpha-amino), 8.55+/-0.03 (Cys), 9.84+/-0.11 (Tyr), and 10.40+/-0.08 (Lys). The pK values of some groups differ from the Nozaki and Tanford (N & T) pK values often used in the literature: Asp (3.67 this work vs. 4.0 N & T); His (6.54 this work vs. 6.3 N & T); alpha-amino (8.00 this work vs. 7.5 N & T); Cys (8.55 this work vs. 9.5 N & T); and Tyr (9.84 this work vs. 9.6 N & T). Our pK values will be useful to those who study pK perturbations in folded and unfolded proteins, and to those who use theory to gain a better understanding of the factors that determine the pK values of the ionizable groups of proteins.

Structural details at active site of hen egg white lysozyme with di- and trivalent metal ions

Metal binding to lysozyme has received wide interest. In particular, it is interesting that Ni2+, Mn2+, Co2+, and Yb3+ chloride salts induce an increase in the solubility of the tetragonal form in crystals of hen egg white lysozyme at high salt concentration, but that Mg2+ and Ca2+ chloride salts do not. To investigate the interactions of the di- and trivalent metal ions with the active site of lysozyme and compare the effects of the di- and trivalent metal ions on molecular conformation of lysozyme based on the structural analysis, the crystal structures of hen egg white lysozyme grown at pH 4.6, in the presence of 0.5 M MgCl2, CaCl2, NiCl2, MnCl2, CoCl2, and YbCl3, have been determined by X-ray crystallography at 1.58 A resolution. The crystals grown in these salts have an identical space group, P4(3)2(1)2. The molecules show no conformational changes, irrespective of the salts used. Ni2+ and Co2+ binding to the Odelta atom of Asp52 in the active site at 1.98 and 2.02 A, respectively, and Yb3+ binding to both the Odelta atom of Asp52 and the Odelta1 atom of Asn46 at 2.25 A have been identified. The binding sites of Mn2+, Mg2+, and Ca2+ have not been found from different Fourier electron density maps. The Ni2+ and Co2+ ions bind to the Odelta atom of Asp52 at almost the same position, while the Yb3+ ion takes a different position from the Ni2+ and Co2+ ions. On the other hand, the anion Cl-, interacting with the Oeta atom of Tyr23 at a site of about 2.90 A, has also been determined for each crystal.