Protein desalting by isoelectric focusing in a segmented immobilized pH gradient

We have recently described an apparatus for protein purification based on a segmented Immobiline gel, having one or more liquid interlayers in between. The principle is entirely new, as it is based on keeping the protein of interest isoelectric, in a flow chamber, and focusing the impurities in an Immobiline gel. For this, a hydraulic flow is coupled orthogonally to an electric flow, sweeping away the non-isoelectric impurities from the recycling chamber. We now demonstrate that the present apparatus can be efficiently used for protein desalting. Hemoglobin A samples, containing 50 mM NaCl or 50 mM ammonium acetate, could be efficiently desalted in 2 h of recycling, after which the total salt content had decreased to less than 0.005 mM (a salt decrement of more than 10,000 fold the initial input). However, with polyprotic buffers (sulphate, citrate, phosphate, oligoamines) the desalting process was much slower, typically of the order of 20 h, possibly due to interaction of these species with the surrounding Immobiline matrix. In this last case, outside pH control (e.g. with a pH-stat) is necessary during protein purification, as, due to the faster removal of the monovalent counterion, the solution in the recycling chamber can become rather acidic or alkaline. It is demonstrated that the 2 extremities of the Immobiline segments facing the sample recycling chamber act indeed as isoelectric membranes, having a good buffering capacity, preventing the protein macroion from leaving the chamber by continuously titrating it to its isoelectric point.     

Aluminum modifies the viscosity of filamentous actin solutions as measured by optical displacement microviscometry

Two-dimensional electrophoresis (2-DE) is a highly resolving technique for arraying proteins by isoelectric point and molecular mass. To date, the resolving ability of 2-DE for protein separation is unsurpassed, thus ensuring its use as the fundamental separation method for proteomics. When immobilized pH gradients (IPGs) are used for isoelectric focusing in the first dimension, excellent reproducibility and high protein load capacity can be achieved. While this has been beneficial for separations of soluble and mildly hydrophobic proteins, separations of membrane proteins and other hydrophobic proteins with IPGs have often been poor. Stimulated by the growing interest in proteomics, recent developments in 2-DE methodology have been aimed at rectifying this situation. Improvements have been made in the area of protein solubilization and sample fractionation, leading to a revamp of traditional approaches for 2-DE of membrane proteins. This review explores these developments.     

Isoelectric focusing and 2D electrophoresis of the human androgen receptor.

Nuclear androgen receptors from cultured genital skin fibroblasts were analyzed by non-denaturing isoelectric focusing (IEF) in ultrathin polyacrylamide gels before and after photoaffinity labeling with [3H]methyltrienolone. Both reversibly and covalently labeled receptors focused at pH 5.28 +/- 0.20 when extracted from nuclei with high salt. Lowering of the salt concentration yielded, in both cases, a second species which focused at pH 7.16. This species became predominant when nuclei were sonicated in IEF sample buffer containing no salt, even after extensive nucleic acid digestion. Low salt cytosols from both prostate and foreskin focused as a single peak of pI: 4.93 +/- 0.31 which remained unchanged when KCl was added to the cytosol up to a concentration of 0.6 M. SDS-polyacrylamide gel electrophoresis of photoaffinity labeled receptors revealed labeled proteins with Mw 90-95 kDa. Two-dimensional electrophoresis of photoaffinity labeled nuclear receptors, extracted in low or high salt, showed that the two isoforms (pI 5.28 and 7.16) contain the same steroid-binding subunit with Mw 90-95 kDa. Nuclear receptors from 4 patients with the receptor positive form of the Complete Androgen Insensitivity Syndrome (CAIS, Rc+) were analyzed by non-denaturing IEF: a single species was observed, focusing at pH 6.0 whether in high or low salt conditions. These results indicate that the nuclear androgen receptor is an acidic protein with pI 5.28 and Mw 90-95 kDa under maximum protein dissociation conditions. When extracted under low salt conditions, it can be isolated in a neutral form (pI 7.16) suggesting its association with a nuclear protein. Receptors of (CAIS, Rc+) patients have an abnormal charge and show no pI shift upon lowering of the salt concentration suggesting that this shift could be a significant step in the mechanism of action of androgens.     

Identification of guttation fluid proteins: the presence of pathogenesis-related proteins in non-infected barley plants

The main driving force behind water transport in plants is the air's low water potential. In the presence of high humidity, the transpiration process is halted and water transport is mainly sustained by the root pressure. The surplus of water following the removal of essential components (e.g. salts) is excreted by the plant via guttation through the hydathodes. When guttation occurs, the plant surface is wetted. These are the conditions that will allow epiphytic living, motile bacteria to move and to eventually enter the plant's interior via the hydathodes. The question arose as to whether the plant has developed a protection mechanism against motile bacteria in the vicinity of the hydathodes. Such a protection mechanism could use the well known pathogenesis-related (PR) proteins. Indeed, an analysis of the guttation fluid using one- and two-dimensional electrophoresis showed a clustering of approximately 200 proteins, primarily with isoelectric points in the acidic pH. Proteins identified using electrospray ionization mass spectroscopic analysis and western blot analysis belong mostly to the family of PR-proteins suggesting a role in plant protection against invaders. The protein profile of the guttation fluid was remarkably modified by treating plants with methyl jasmonic acid suggesting that the protein composition of the guttation fluid is controlled by internal and/or external stimuli.     

Identification of protein carbonyls after two-dimensional electrophoresis

The oxidative modification of proteins plays a major role in a number of human diseases, but identity of the specific proteins that are most susceptible to oxidation has posed a difficult problem. Protein carbonyls are increased after oxidative stress, and after derivatization with 2,4-dinitrophenyl hydrazine (DNP) they can be detected by various analytical and immunological methods. Although high resolution two-dimensional electrophoresis (2-DE) can resolve virtually all proteins present in a cell or tissue it has been difficult to determine the oxidized proteins because the DNP-derivatization process alters the isoelectric points of proteins, and additional procedures must be utilized to remove reaction byproducts. These additional procedures can lead to loss of sample, and poor isoelectric resolution on immobilized pH gradient (IPG) strips. We have developed a method that allows the IPG strips to be derivatized with DNP directly following isoelectric focusing of the proteins. This method allows the visualization of oxidized proteins by 2-DE with high reproducibility.     

High resolution two-dimensional electrophoresis of basic as well as acidic proteins.

A previously described two-dimensional electrophoresis procedure (O'Farrell, 1975) combined isoelectric focusing and sodium dodecylsulfate slab gel electrophoresis to give high resolution of proteins with isoelectric points in the range of pH 4–7. This paper describes an alternate procedure for the first dimension which, unlike isoelectric focusing, resolves basic as well as acidic proteins. This method, referred to as nonequilibrium pH gradient electrophoresis (NEPHGE), involves a short time of electrophoresis toward the cathode and separates most proteins according to their isoelectric points. Ampholines of different pH ranges are used to optimize separation of proteins with different isoelectric points. The method is applied to the resolution of basic proteins with pH 7–10 Ampholines, and to the resolution of total cellular proteins with pH 3.5–10 Ampholines. Histones and ribosomal proteins can be readily resolved even though most have isoelectric points beyond the maximum pH attained in these gels. The separation obtained by NEPHGE with pH 3.5–10 Ampholines was compared to that obtained when isoelectric focusing was used in the first dimension. The protein spot size and resolution are similar (each method resolving more than 1000 proteins), but there is less resolution of acidic proteins in this NEPHGE gel due to compression of the pattern. On the other hand, NEPHGE gels extend the range of analysis to include the 15–30% of the proteins which are excluded from isoelectric focusing gels. The distribution of cell proteins according to isoelectric point and molecular weight for a procaryote (E. coli) was compared to that of a eucaryote (African green monkey kidney); the eucaryotic cell proteins are, on the average, larger and more basic.     

Effects of pH on protein-protein interactions and implications for protein phase behavior

The effects of pH on protein interactions and protein phase behavior were investigated by measuring the reduced second osmotic virial coefficient (b2) for ovalbumin and catalase, and the aggregate and crystal solubilities for ovalbumin, beta-lactoglobulin A and B, ribonuclease A and lysozyme. The b2 trends observed for ovalbumin and catalase show that protein interactions become increasingly attractive with decreasing pH. This trend is in good agreement with ovalbumin phase behavior, which was observed to evolve progressively with decreasing pH, leading to formation of amorphous aggregates instead of gel bead-like aggregates, and spherulites instead of needle-like crystals. For both acidic and basic proteins, the aggregate solubility during protein salting-out decreased with decreasing pH, and contrary to what is commonly believed, neither aggregate nor crystal solubility had a minimum at the isoelectric point. beta-Lactoglobulin B was the only protein investigated to show salting-in behavior, and crystals were obtained at low salt concentrations in the vicinity of its isoelectric point. The physical origin of the different trends observed during protein salting-in and salting-out is discussed, and the implications for protein crystallization are emphasized.     

Optimizing pKa computation in proteins with pH adapted conformations

pK(A) in proteins are determined by electrostatic energy computations using a small number of optimized protein conformations derived from crystal structures. In these protein conformations hydrogen positions and geometries of salt bridges on the protein surface were determined self-consistently with the protonation pattern at three pHs (low, ambient, and high). Considering salt bridges at protein surfaces is most relevant, since they open at low and high pH. In the absence of these conformational changes, computed pK(A)(comp) of acidic (basic) groups in salt bridges underestimate (overestimate) experimental pK(A)(exp), dramatically. The pK(A)(comp) for 15 different proteins with 185 known pK(A)(exp) yield an RMSD of 1.12, comparable with two other methods. One of these methods is fully empirical with many adjustable parameters. The other is also based on electrostatic energy computations using many non-optimized side chain conformers but employs larger dielectric constants at short distances of charge pairs that diminish their electrostatic interactions. These empirical corrections that account implicitly for additional conformational flexibility were needed to describe the energetics of salt bridges appropriately. This is not needed in the present approach. The RMSD of the present approach improves if one considers only strongly shifted pK(A)(exp) in contrast to the other methods under these conditions. Our method allows interpreting pK(A)(comp) in terms of pH dependent hydrogen bonding pattern and salt bridge geometries. A web service is provided to perform pK(A) computations.     

Improvement of the two-dimensional gel electrophoresis analysis for the proteome study of Halobacterium salinarum

Inherent problems exist in the use of two-dimensional gel electrophoresis (2-DE) for sample preparation and separation of proteins from Halobacterium salinarum. In particular, proteins from cells grown in 25% NaCl are difficult to resolve by 2-DE due to the abundance of salt. To remove salts, a 3 kDa molecular weight cut-off column was used. When soluble proteins were separated by 2-DE, most of the proteins were concentrated in the acidic range. For separation of proteins in the pH 3-6 range, ultrazoom immobilized pH gradient strips were used. In addition, sample separation using a IPGphor/Multiphor combined system was a more effective method for the proteome analysis of acidic proteins than using IPGphor for the isoelectric focusing step.     

Effect of divalent ions on protein precipitation with polyethylene glycol: mechanism of action and applications.

Polyethylene glycol (PEG) is extensively employed for protein purification by fractional precipitation. Efficiency of precipitation is highest when the solution pH is near the isoelectric point of the target protein. At pH values far from the isoelectric point of the target protein, proteins develop a net positive or negative charge and are not more resistant to precipitation. We have found that divalent cations (Ba2+, Sr2+, and Ca2+) or divalent anions (SO4(2-)) significantly change the pattern of PEG precipitation when the ion is chosen so as to counteract the expected net charge on the target protein. At moderate (5-50 mM) concentrations of Ba2+, negatively charged proteins can be precipitated from solution at pH values as high as 10 with efficiency unchanged from precipitation at pH values near their isoelectric point values. The mechanism of PEG precipitation of protein at these high pH values appears to be unchanged from the mechanism operative at the protein isoelectric point. Precipitation is rapid and the capacity for protein precipitation is high. There is no detectable coprecipitation of small molecules (AMP, ATP, and NADH) or soluble proteins (carbonic anhydrase) induced when large quantities of protein are precipitated by this method. The purification of bovine carbonic anhydrase from erythrocyte lysate is more efficient at pH 10 in the presence of Ba2+ than is conventional PEG precipitation carried out at the isoelectric point of carbonic anhydrase. Application of these observations should broaden the utility of protein purification by fractional precipitation with PEG.     

Salting the charged surface: pH and salt dependence of protein G B1 stability

This study shows significant effects of protein surface charges on stability and these effects are not eliminated by salt screening. The stability for a variant of protein G B1 domain was studied in the pH-range of 1.5-11 at low, 0.15 M, and 2 M salt. The variant has three mutations, T2Q, N8D, and N37D, to guarantee an intact covalent chain at all pH values. The stability of the protein shows distinct pH dependence with the highest stability close to the isoelectric point. The stability is pH-dependent at all three NaCl concentrations, indicating that interactions involving charged residues are important at all three conditions. We find that 2 M salt stabilizes the protein at low pH (protein net charge is +6 and total number of charges is 6) but not at high pH (net charge is or=18). Furthermore, 0.15 M salt slightly decreases the stability of the protein over the pH range. The results show that a net charge of the protein is destabilizing and indicate that proteins contain charges for reasons other than improved stability. Salt seems to reduce the electrostatic contributions to stability under conditions with few total charges, but cannot eliminate electrostatic effects in highly charged systems.     

Comparison of Emulsifying Properties of Plant and Animal Proteins in Oil-in-Water Emulsions: Whey,Soy, and RuBisCo Proteins

There is increasing interest within the food industry in replacing animal-derived ingredients with plant-derived alternatives. In this study, we compared the emulsifying properties of an emerging plant protein (RuBisCo protein) with those of a well-established plant (soy protein) and animal (whey protein) protein. The RuBisCo protein (ribulose 1,5-bisphosphate carboxylase) was isolated from duckweed (lemna minor), which is an abundant plant material with a higher protein yield and biomass per unit area than most other plant protein sources. The ability of the three proteins to form and stabilize 10 wt% soybean oil-in-water emulsions was examined. The minimum amount of protein required to produce small droplets (d <?350 nm) decreased in the following order: RuBisCo > soy > whey protein. This effect was mainly attributed to the fact that the molar mass of the proteins decreased in the same order. Even so, the RuBisCo proteins were able to form stable emulsions when used at sufficiently high concentrations (≥ 1%). All three types of protein-coated oil droplets aggregated at pH values near their isoelectric points and at high ionic strengths but there were differences between them. In the absence of added salt, extensive droplet aggregation occurred from pH 4 to 5 for whey protein, from pH 2 to 5 for soy protein, and from pH 2 to 6 for RuBisCo protein. The isoelectric points of all three protein-coated droplets were around pH 5, but the magnitude of the surface potential at low and high pH values was higher for whey protein than for the two plant proteins. At pH 7, extensive droplet aggregation occurred at ≥100 mM NaCl for RuBisCo- and soy protein-coated droplets, but only at ≥400 mM NaCl for whey protein-coated ones. The RuBisCo-coated oil droplets were more prone to flocculation when heated, especially in the presence of salt (100 mM NaCl). Overall, these results show that RuBisCo protein can be used to form and stabilize oil-in-water emulsions, but the pH, salt, and temperature conditions must be carefully controlled to avoid droplet aggregation. We should note that droplet aggregation is advantageous in some applications because it leads to an increase in emulsion viscosity or gelation.

     

Preparative two-dimensional gel electrophoresis at alkaline pH using narrow range immobilized pH gradients

A reproducible high-resolution protein separation method is the basis for a successful differential proteome analysis. Of the techniques currently available, two-dimensional gel electrophoresis is most widely used, because of its robustness under various experimental conditions. With the introduction of narrow range immobilized pH gradient (IPG) strips (also referred to as ultra-zoom gels) in the first dimension, the depth of analysis, i.e. the number of proteins that can be resolved, has increased substantially. However, for poorly understood reasons isoelectric focusing on ultra-zoom gels in the alkaline region above pH 7 has suffered from problems with resolution and reproducibility. To tackle these difficulties we have optimized the separation of semipreparative amounts of proteins on alkaline IPG strips by focusing on two important phenomena: counteracting water transport during isoelectric focusing and migration of dithiothreitol (DTT) in alkaline pH gradients. The first problem was alleviated by the addition of glycerol and isopropanol to the focusing medium, leading to a significant improvement in the resolution above pH 7. Even better results were obtained by the introduction of excess of the reducing agent DTT at the cathode. With these adaptations together with an optimized composition of the IPG strip, separation efficiency in the pH 6.2-8.2 range is now comparable to the widely used acidic ultra-zoom gels. We further demonstrated the usefulness of these modifications up to pH 9.5, although further improvements are still needed in that range. Thus, by extending the range covered by conventional ultra-zoom gels, the depth of analysis of two-dimensional gel electrophoresis can be significantly increased, underlining the importance of this method in differential proteomics.     

Setting up standards and a reference map for the alkaline proteome of the Gram-positive bacterium Lactococcus lactis

Despite the fact that almost 39% of the theoretical expressed proteins of Lactococcus lactis have a predicted isoelectric point above 7, these proteins have not been studied in previous proteome analyses. In the present study, we set up a reference map of alkaline lactococcal proteins by using immobilized pH gradients (IPG) spanning pH 6 to 12 and 9 to 12, and protein identification by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). Different electrophoresis systems for isoelectric focusing were evaluated to optimize the first dimension. Best results were obtained by sample application using cup-loading at the anodic side and increasing the final voltage up to 8000 V for IPGs, using N,N-dimethylacrylamide as monomer. After two-dimensional gel electrophoresis of extracts obtained from exponentially growing cells, about 200 protein spots were selected for identification by peptide mass fingerprinting. With MALDI-TOF MS, 153 proteins were identified that were the products of 85 different genes. Their predicted isoelectric points range from as high as 11.31 to as low as 6.34. Ribosomal proteins, hypothetical proteins and proteins with unknown function represent the largest groups of identified proteins. For further classification, the codon adaptation index (CAI) and grand average of hydropathicity (GRAVY) for each lactococcal protein were calculated. The protein with the lowest CAI identified in this study is the manganese ABC transporter ATP-binding protein. Less than 10% of the alkaline lactococcal proteins have a smaller CAI. The highest GRAVY for an identified protein is 0.26. The complete in silico data of Lactococcus lactis as well as clickable reference maps are available at www.wzw.tum.de/proteomik/lactis.     

Isoelectric focusing of complex protein mixtures in the nanogram range in microgels (author's transl)]

A method is described for isolectric focusing of complex protein mixtures in 2, 5 or 10 mul capillaries. For one separation only 15- 50 ng of a protein mixture is needed. Isoelectric focusing is finished after 10 min, staining takes 20 min and destaining approximately 30 min. Using defined mixtures of Servalyt from different pH ranges, isoelectric focusing can be adapted to the protein sample to be fractionated. Protein peaks separated by isoelectric focusing can be electrophoretically eluted and for further analysis refractionated directly in a microgradient gel. The resolution power of microisoelectric focusing is as good as that of the wellknown macroprocedure, as is demonstrated by isoelectric focusing of the water soluble proteins from cerebellum and heart, of rat and human serum and of a human oncocytoma of the thyroid gland.     

Isoelectric protein purification by orthogonally coupled hydraulic and electric transports in a segmented immobilized pH gradient

A new method is described for preparative protein purification, based on isoelectric focusing on immobilized pH gradients. The principle is entirely new, as it is based on keeping the protein of interest isoelectric, in a flow-chamber, and focusing the impurities in the Immobiline gel. For this, a hydraulic flow is coupled orthogonally to an electric flow, sweeping away the non-isoelectric impurities from the recycling chamber. The sample flow-chamber is built in the centre of the apparatus, and is coupled to an upper and lower segment of an immobilized pH gradient. The protein to be purified is kept isoelectric in the flow-chamber and prevented from leaving it by arranging for the extremities of the immobilized pH gradient, forming the ceiling and the floor of this chamber, to have isoelectric points just higher (e.g. +0.05 pH units, on the cathodic side) and just lower (e.g. -0.05 pH units, on the anodic side) than the known pI of the species of interest. Macromolecules and small ions leave the flow chamber at a rate corresponding to a first order reaction kinetics (the plot of log C vs. time being linear). In general, for macromolecules, 12 h of recycling under current allow removal of 95% impurities. After 24 h of recycling, the protein of interest is more than 99.5% pure. The recoveries are very high (approaching 100%) as the sample under purification never enters the Immobiline gel and thus does not have to be extracted from a hydrophilic matrix, as typical of preparative gel electrophoresis.     

Fluorescence of eosinophil leucocyte granules induced by 1-hydroxy-3,6,8-pyrenetrisulfonate. Visualization of differences in protein isoelectric points

After treatment of horse, rat and human blood smears with alkaline solutions of 1-hydroxy-3,6,8-pyrenetrisulfonate (HPTS), eosinophil leucocyte granules were the unique cell components which showed a bright green fluorescence. When stained with HPTS at pH 10, the whole granule of horse eosinophils showed high emission which strongly diminished after washing or staining in salt solutions or by using blocking methods for amino groups. Using HPTS at pH 12, the fluorescence reaction of house granules was specifically located in the peripheral region, appearing as fluorescent rings. These microscopic observations, which indicate differences in the isoelectric point of proteins within the eosinophil granule, were also confirmed by HPTS staining of protein blots as model substrates. Spectral analysis of HPTS at pH 10 and 12 showed practically identical absorption and emission spectra with peaks at 450 nm and 510 nm, respectively. Our results indicate that mainly ionic binding occurs between cationic proteins and HPTS in alkaline solution, and that the most cationic proteins (with isoelectric points at pH higher than 12) are located in the peripheral annular region of horse eosinophil granules.     

Isoelectric points of multi-domain proteins

Although the distribution of protein isoelectric points is multi-modal, large proteins show isoelectric points less variable than small proteins and their isoelectric points tend to converge to a unique value, close to the pH of the milieu in which the proteins are functional, as far as the protein dimension increases. This study demonstrates that large proteins, which contain more than a single domain, do have isoelectric points less variable than small proteins, which contains a single domain. However, the distribution of the isoelectric points of the single domains, contained in large proteins, resembles that of small proteins, which contain a single domain. Thus, large proteins can be soluble even if their pI is very close to the pH of the milieu, in which they perform their function, since they can contain several domains, the electrostatic properties of each of which mirror those of small proteins.     

Evolution of the isoelectric point of mammalian proteins as a consequence of indels and adaptive evolution

Although important shifts in the isoelectric point of prokaryotic proteins, mainly due to adaptation to environmental pH, have been widely reported, such studies have not covered mammalian proteins, where pH changes may relate to changes in subcellular or tissue compartmentalization. We explored the isoelectric point of the proteome of 13 mammalian species. We detected proteins that have shifted their pI the most among 13 mammalian species, and investigated if these differences reflect adaptations of the orthologous proteins to different conditions. We find that proteins exhibiting a high isoelectric point change are enriched in certain GO terms, including immune defense, and mitochondrial proteins. We show that the shift in pI between orthologous proteins is not strongly associated with the overall rate of protein evolution, nor with protein length. Our results reveal that insertions/deletions are the main reason behind the shift of pI. However, for some proteins we find evidence of selection shifting the pI of the protein through amino acid replacement. Finally, we argue that shifts in pI might relate to the gain of additional activities, such as new interacting partners, in one ortholog as opposed to the other, and may potentially relate to functional differences between mammals.     

Induced binding of proteins by ammonium sulfate in affinity and ion-exchange column chromatography

In general, proteins bind to affinity or ion-exchange columns at low salt concentrations, and the bound proteins are eluted by raising the salt concentration, changing the solvent pH, or adding competing ligands. Blue-Sepharose is often used to remove bovine serum albumin (BSA) from samples, but when we applied BSA to Blue-Sepharose in 20 mM phosphate, pH 7.0, 50%-60% of the protein flowed through the column; however, complete binding of BSA was achieved by the addition of 2 M ammonium sulfate (AS) to the column equilibration buffer and the sample. The bound protein was eluted by decreasing the AS concentration or by adding 1 M NaCl or arginine. AS at high concentrations resulted in binding of BSA even to an ion-exchange column, Q-Sepharose, at pH 7.0. Thus, although moderate salt concentrations elute proteins from Blue-Sepharose or ion-exchange columns, proteins can be bound to these columns under extreme salting-out conditions. Similar enhanced binding of proteins by AS was observed with an ATP-affinity column.