Revisiting electroblotting of immobilized pH gradient gels: a new protocol for studying post-translational modification of proteins

Currently, one of the most important techniques in proteome analysis is two-dimensional electrophoresis that is widely used for separation of thousands of different protein spots. Nevertheless, characterization of special aspects in protein patterns, e.g., separation of protein isoforms generated by post-translational modifications, requires individual detection methods, e.g., immunoblotting. Blotting of proteins after fractionation in immobilized pH gradients has always caused some problems. In this paper we present an optimized protocol for immunoblotting after isoelectric focusing using immobilized pH gradient (IPG) strips cast on Net-Fix as an internal support that is permeable to electric current. The focusing procedure can be carried out in commonly used IPG systems, e.g., the IPGphor by Amersham Biosciences, where electrically assisted rehydration can be performed. This may be of interest for many laboratories, because the same system as used for the first dimension of two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) is involved. As an example, we describe separation and detection of up to seven isoforms of recombinant erythropoietin beta using semidry blotting of IPG strips and visualization by chemiluminescence detection.     

Theory and applications of a novel ion exchange chromatographic technology using controlled pH gradients for separating proteins on anionic and cationic stationary phases

pISep is a major new advance in low ionic strength ion exchange chromatography. It enables the formation of externally controlled pH gradients over the very broad pH range from 2 to 12. The gradients can be generated on either cationic or anionic exchangers over arbitrary pH ranges wherein the stationary phases remain totally charged. Associated pISep software makes possible the calculation of either linear, nonlinear or combined, multi-step, multi-slope pH gradients. These highly reproducible pH gradients, while separating proteins and glycoproteins in the order of their electrophoretic pIs, provide superior chromatographic resolution compared to salt. This paper also presents a statistical mechanical model for protein binding to ion exchange stationary phases enhancing the electrostatic interaction theory for the general dependence of retention factor k, on both salt and pH simultaneously. It is shown that the retention factors computed from short time isocratic salt elution data of a model protein can be used to accurately predict its salt elution concentration in varying slope salt elution gradients formed at varying isocratic pH as well as the pH at which it will be eluted from an anionic exchange column by a pISep pH gradient in the absence of salt.     

Optimization of azeotropic protein separations in gradient and isocratic ion-exchange simulated moving bed chromatography

The separation of dilute binary mixtures of proteins by salt aided ion-exchange simulated moving bed (SMB) chromatography is optimized with respect to throughput, desorbent consumption and salt consumption. The optimal flow-rate ratios are analytically determined via an adopted "triangle theory". Azeotropic phenomena are included in this procedure. The salt concentrations in the feed and recycled liquid are subsequently determined by numerical optimization. The azeotropic separation of bovine serum albumin and a yeast protein is used to illustrate the procedure. Gradient operation of the SMB is generally preferred over isocratic operation. A feed of azeotropic salt concentration can only be separated in a gradient SMB. Desorbent and salt consumption are always lower in gradient than in isocratic SMB chromatography.     

pH fractionation and identification of proteins: comparing column chromatofocusing versus liquid isoelectric focusing techniques

In proteomic investigations, a number of different separation techniques can be applied to fractionate whole cell proteomes into more manageable fractions for subsequent analysis. In this work, utilizing HPLC and mass spectrometry for protein identification, two different fractionation methods were compared and contrasted to determine the potential of each method for the simple and reproducible fractionation of a bacterial proteome. Column-based chromatofocusing and liquid-based isoelectric focusing both utilized pH gradients to produce similar results in terms of the numbers of proteins successfully identified (402 and 378 proteins) and the consistency of proteins identified from one experiment to the next (<10% change). However, there was limited overlap in the protein sets with <50% of the proteins identified as common between the sets of proteins identified by the different systems. In addition to the numbers of proteins identified and consistency of those identified, the reduced monetary costs of experimentation and increased assay flexibility produced by using isoelectric focusing was considered in order to adopt a system best suited for comparative proteomic projects.     

Ion-exchange displacement chromatography of proteins Dextran-based polyelectrolytes as high affinity displacerss

Dextran-based polyelectrolyte displacers were successfully employed for the displacement purification of proteins in ion-exchange displacement systems. The effect of molecular mass was investigated by examining the efficacy of DEAE-dextran and dextran sulfate displacers of various molecular masses in cation- and anion-exchange systems, respectively. Induced salt gradients produced during these displacement experiments were measured in order to study their effect on the protein separations. The unique characteristics of these displacements were well predicted by simulations obtained from a steric mass action (SMA) ion-exchange model. These displacements differ from the traditional vision of displacement chromatography in several important ways: the isotherm of the displacer does not necessarily lie above the feed component isotherms; the concentration of the displaced proteins can sometimes exceed that of the displacer; higher-molecular-mass displacers are not necesarily more efficacious than lower-molecular-mass compounds; and the salt gradients induced by the adsorption of the displacer produce different salt micro-environments for each displaced protein.     

Modeling the electrophoresis of peptides and proteins: improvements in the "bead method" to include ion relaxation and "finite size effects"

A bead model methodology developed in our lab (Xin et al. J. Phys. Chem. B 2006, 110, 1038) and applicable to modeling the free solution electrophoretic mobility of peptides and proteins is generalized in two significant ways. First, an approximate account is taken of the relaxation effect, which makes the methodology applicable to more highly charged peptides and proteins than was previously possible. Second, a more accurate account is taken of the finite size of the beads making up the model structure. This improvement makes the method applicable at higher salt concentrations and/or to models consisting of larger sized subunits. The relaxation effect is accounted for by correcting "unrelaxed" mobilities on the basis of model size and average electrostatic surface, or zeta potential. Correction factors are estimated using those of spheres with the same hydrodynamic radius and zeta potential as the model structure. The correction factors of spheres are readily determined. The more general methodology is first applied to two sets of peptides (74 different peptides total) varying in size from 2 to 42 amino acids. The sets also cover a wide range of net charges. It is shown that accounting for finite bead size results in a small change in model mobilities under the conditions of the experiments (35 mM monovalent salt). The correction for ion relaxation, however, can be significant for highly charged peptides and improves agreement between model and experimental mobilities. Our correction procedure is also tested by examining the electrophoretic mobility of a particular protein "charge ladder" (Carbeck et al. J. Am. Chem. Soc. 1999, 121, 10,671), where the protein charge is varied over a wide range yet the conformation remains essentially constant. In summary, the effects of ion relaxation can be significant if the absolute electrophoretic mobility of a peptide exceeds approximately 0.20 cm2/(kV s).     

Surfactant-mediated hydrophobic interaction chromatography of proteins: gradient elution

Addition of 3-[(3-cholamidopropyl)dimethylammonio]-l-propanesulphonate (CHAPS) to mobile phases in gradient elution hydrophobic interaction chromatography (HIC) on SynChropak Propyl causes changes in observed elution times for nine globular proteins. The nine proteins showed different percentage reductions in capacity factor, k', demonstrating the ability of CHAPS to change the selectivity of the separations. Three basic types of gradient experiments have been explored for surfactant-mediated gradient elution HIC. Type I gradients are conducted with constant salt and variable surfactant concentration. Type II gradients with variable salt and constant surfactant concentration, and Type III gradients with variable salt and surfactant concentrations. By the criterion of a linear relationship between gradient time and retention time the linear solvent strength condition applies to Type II and Type III gradients. Type III gradients, with the fastest re-equilibration time, are preferable for repetitive analyses. Type I gradients are relatively ineffective in making use of the solvent strength of CHAPS, and Types I and II gradients require long equilibration times due to large changes in surface concentration of CHAPS which occur during elution. The presence of CHAPS had a negligible effect on peak shapes of the proteins examined, except for bovine serum albumin which yielded a narrower, less distorted peak in the presence of CHAPS.     

Prediction of protein retention at gradient elution conditions in ion-exchange chromatography.

This work presents a prediction procedure for protein retention in ion-exchange chromatography, where two linear gradient experiments of different length give the protein retention time at other linear gradients. The procedure predicts the retention time of early and late eluting proteins with similar precision and predictions by extrapolation deviate approximately 3% or less from the experimental retention times. By using the ionic strength, this procedure predicts protein retention times obtained with divalent ions in the eluent more accurately than a well-established procedure that uses the protein co-ion concentration.     

Removing proteins from an aerated yeast fermentation by pulsing carbon dioxide

Salting-out is a common technique used for precipitating proteins and other materials from fermentation and tissue culture processes. It leaves a salt residue in the system. Foam fractionation can also be used to remove proteins by protein precipitation from a dilute solution. In doing so, there is usually a trade-off between enrichment and recovery. An increase in the airflow rate will increase the recovery, but only at the expense of the enrichment. A new method for increasing the recovery in foam fractionations and in yeast fermentations is to add a burst of CO₂ to the process and then restore the air. This CO₂ acts like a temporary salt, but it does not leave behind a residue. The recovery increases as a result of the joint use of these gases, perhaps by more than 10-fold, without sacrificing the enrichment. Chicken egg albumin in a foam fractionation column can serve as a simple, experimental model for the proposed recovery process in lieu of the fermentation process.     

Polyacrylamide gradient electrophoresis for protein purification on the milligram scale.

A preparative-scale electrophoretic technique for protein fractionation and elution on a discontinuous gradient of acrylamide is described, which permits the separation and elution of a pure protein from a mixture containing 4-20 electrophoretically different proteins. The sharpness of the gradient electrophoretic resolution is demonstrated by the separation of proteins consisting of bovine serum albumin polymers and lactate dehydrogenase and enzymes such as acid phosphatase. The compositions of various discontinuous gradients of acrylamide and their application to enzyme purification are discussed. It was found that 60% of the enzyme activity loaded on the gel is recovered after gel fractionation and elution.     

Off-line and on-line assay of membrane protein with o-phthaldialdehyde by flow-injection with post-column reaction

A rapid and convenient flow-injection absorption spectrosphotometric procedure was developed for the determination of protein and peptide concentrations in discrete samples that contain biological membranes (subcellular particles) which scatter light. With some modification, the same system serves as a post-column reactor to determine protein and peptide concentrations continuously in the effluent of a separation device. The procedure is based on the well known determination of primary amines by reaction with a thiol and o-phthaldialdehyde. Although designed for preparations of biological membranes, the procedure is applicable to any solution in which the primary amino groups are predominantly those belonging to the proteins and/or peptides present; this includes many protein solutions which are turbid at acidic or neutral pH but clear at alkaline pH. The off-line flow-injection procedure for discrete samples and the on-line post-column reactor for flowing column effluents have been found especially useful for determining the distribution of membrane protein in the chanel effluent after fractionation of subcellular particle preparations containing corn root mitochondria and microsomes.     

A calorimetric study of egg white proteins

Egg white is of great interest for many culinary and industrial applications. Egg white is used for coating, gluing, thickening and so on in pasta, desserts, etc. There is thus a great interest from the industrial point of view to better know this raw material, used in very large amounts in the dessert production for example, and to obtain egg white fractions with different functional properties.Various egg white fractions prepared by selected procedures were analyzed by differential scanning calorimetry (DSC). The products resulting from a given fractionation procedure can thus be described by the thermal denaturation parameters (temperatures and enthalpies) of the egg white proteins.This work demonstrates the interest of the DSC technique and proves that the fractionation procedures selected here give the expected protein fractions.     

Isolation of tomato pectin methylesterase and polygalacturonase on monolithic columns

An improved cation-exchange chromatographic procedure on Convective Interaction Media (CIM, BIA Separations, Ljubljana, Slovenia) short monolithic methacrylate disk columns was used for the isolation of salt-independent pectin methylesterase (PME; EC 3.1.1.11) isoform and endo-polygalacturonase PG1 (PG, EC 3.2.1.15) from ripe tomato fruit extract after studying the chromatographic conditions including type of disk, binding buffer, pH, eluent composition and different gradients. Between 10 and 20 microg of proteins gave reliable chromatograms. Both carboxymethyl (CM) and sulfonyl (SO3) disks were equally suitable for the fractionation of tomato extract using the new gradient, but only CM disk was appropriate for further purification of the PME and PG fractions, and provided fast and sharp separation of proteins. The isolation of pure PG1 could be achieved only by addition of 20% of acetonitrile to the mobile phase. About 200 microg of proteins were loaded at one chromatographic run at the fractionation and purification. Determination of the molecular weights of the separated proteins showed that dimer of salt-independent PME isoform was formed in concentrated solutions of the enzyme but dissociated upon dilution of the solution. From 6 kg of fresh tomato flesh, 28 mg of purified salt-independent PME, 12.5mg of purified and active PG1 and 4 mg of PG2 fraction contaminated with salt-dependent PME isoform were obtained by means of semi-preparative chromatography on CIM disks.     

Field-flow fractionation in microfluidic channels of low aspect ratio

The shape of the steady-state three-dimensional flow velocity profile established in carrier liquid flowing inside the rectangular cross-sectional channel for field-flow fractionation should be taken into account to optimize the separation. The central parts of this profile in the planes parallel to the main channel walls are flat with almost identical flow velocities which drop down to zero at the side walls. The separated species transported by the flow in the close-to-side walls regions move with lower average velocities compared to the species transported in the central part of the channel and are undesirably broadened. The hydrodynamic splitting of the carrier liquid at the entry of the channel where the sample is injected only into the central part of the channel eliminates the excessive zone broadening. The aspect ratio of the breadth to the thickness of the channel ratio can thus be reduced. The effect of various aspect ratios on the shape of the flow velocity profile is calculated and the results are used to optimize the aspect ratio of microfluidic channels. The experiments carried out by microthermal field-flow fractionation confirmed that the aspect ratio cannot be reduced to a value of 1, proposed by other authors.     

Proteomic analysis of Helicobacter pylori cellular proteins fractionated by ammonium sulfate precipitation

Among 1590 ORFs in the Helicobacter pylori genome, >250 have been identified as authentic genes by proteomic analysis. Low-abundance proteins need to be enriched to a minimal amount for MALDI-TOF analysis and salt precipitation has generally been used for protein enrichment. Here, a whole-cell extract of H. pylori strain 26695 was subjected to protein fractionation with stepwise concentrations of ammonium sulfate and the proteins were displayed by 2-DE. The protein spots were quantified using PDQUEST software and identified by peptide fingerprinting. The 2-DE profiles and intensities of individual protein spots differed among the protein fractions. Out of the 98 identified proteins, 61 were found in the stepwise ammonium sulfate fractions but not in the whole-cell extract. Out of these, 37 proteins, including KdsA, were found exclusively in a single fraction. In contrast, GroEL, UreA, UreB, TrxA, NapA, and FldA were ubiquitously present in all fractions. Iron-containing proteins such as NapA, SodB, CeuE, and Pfr were found predominantly in the 100% saturated ammonium sulfate precipitate. Additionally, 29 proteins were newly identified in this study. These data will facilitate the preparation of significant H. pylori proteins, as well as provide information about low-abundance proteins.     

A new method of high-speed cellular protein separation and insight into subcellular compartmentalization of proteins

Transglutaminase (TGM)-2 is a ubiquitous protein with important cellular functions such as regulation of cytoskeleton, cell adhesion, apoptosis, energy metabolism, and stress signaling. We identified several proteins that may interact with TGM-2 through a discovery-based proteomics method via pull down of flag-tagged TGM-2 peptide fragments. The distribution of these potential binding partners of TGM-2 was studied in subcellular fractions separated by density using novel high-speed centricollation technology. Centricollation is a compressed air-driven, low-temperature stepwise ultracentrifugation procedure where low extraction volumes can be processed in a relatively short time in non-denaturing separation conditions with high recovery yield. The fractions were characterized by immunoblots against known organelle markers. The changes in the concentrations of the binding partners were studied in cells expressing short hairpin RNA against TGM-2 (shTG). Desmin, mitochondrial intramembrane cleaving protease (PARL), protein tyrosine kinase (NTRK3), and serine protease (PRSS3) were found to be less concentrated in the 8.5%, 10%, 15%, and 20% sucrose fractions (SFs) from the lysate of shTG cells. The Golgi-associated protein (GOLGA2) was predominantly localized in 15% SF fraction, and in shTG, this shifted to predominantly in the 8.5% SF and showed larger aggregations in the cytosol of cells on immunofluorescent staining compared to control. Based on the relative concentrations of these proteins, we propose how trafficking of such proteins between cellular compartments can occur to regulate cell function. Centricollation is useful for elucidating biological function at the molecular level, especially when combined with traditional cell biology techniques.     

Protein extraction and 2-DE of water- and lipid-soluble proteins from bovine pericardium, a low-cellularity tissue

Bovine pericardium (BP) is an important biomaterial used in the production of glutaraldehyde-fixed heart valves and tissue-engineering applications. The ability to perform proteomic analysis on BP is useful for a range of studies, including investigation of immune rejection after implantation. However, proteomic analysis of fibrous tissues such as BP is challenging due to their relative low-cellularity and abundance of extracellular matrix. A variety of methods for tissue treatment, protein extraction, and fractionation were investigated with the aim of producing high-quality 2-DE gels for both water- and lipid-soluble BP proteins. Extraction of water-soluble proteins with 3-(benzyldimethylammonio)-propanesulfonate followed by n-dodecyl beta-D-maltoside extraction and ethanol precipitation for lipid-soluble proteins provided the best combination of yield, spot number, and resolution on 2-DE gels (Protocol E2). ESI-quadrupole/ion trap or MALDI-TOF/TOF MS protein identifications were performed to confirm bovine origin and appropriate subcellular prefractionation of resolved proteins. Twenty-five unique, predominantly cytoplasmic bovine proteins were identified from the water-soluble fraction. Thirty-two unique, predominantly membrane bovine proteins were identified from the lipid-soluble fraction. These results demonstrated that the final protocol produced high-quality proteomic data from this important tissue for both cytoplasmic and membrane proteins.     

Endothelial cell migration on surface-density gradients of fibronectin, VEGF, or both proteins

Cell migration is essential to many physiological processes, including angiogenesis, which is critical to the success of implanted biomaterials and tissue-engineered constructs. Gradients play an important role in cell migration. Previous work on cell migration has been mostly executed either in the concentration gradients of stimuli (e.g., VEGF) in bulk or hydrogels or on the surface-density gradients of ECM proteins (e.g., fibronectin) or small ligands (e.g., RGD). Little work has been done to investigate how cell migration responds to the surface-density gradients of growth factors. No work has been done to study how the surface gradients of both adhesive proteins and growth factors influence cell migration. In this work, we studied the effect of the surface-density gradients of fibronectin (FN), VEGF, or both proteins on endothelial cell migration. Gradients with different slopes were prepared to study how the gradient slope affects cell migration. The gradients were generated by first forming a counter-propagating C15COOH/C11OH self-assembled monolayer (SAM) gradient using a surface electrochemistry approach, followed by activating the -COOH moieties and covalently immobilizing proteins onto the surface. Fourier transform infrared spectra and X-ray photoelectron spectroscopy were used to characterize the SAM and protein gradients, respectively. A free cell migration assay using bovine aortic endothelial cells was performed on various gradient surfaces or on surfaces with uniform protein density. Results showed that cells on the surface-density gradients of FN, VEGF, or both proteins moved faster along the gradient direction than on the respective uniform control surface after 24-h cell culture. It is also shown that for each protein or protein combination, the directional cell displacement was not statistically different between two gradients with different slopes. Results show that the directional cell migration was increased by about 2-fold on the VEGF gradient as compared to the FN gradient and was further increased by another 2-fold on the combined gradients of both proteins as compared to the VEGF gradient alone. This is the first work to create surface-density gradients of VEGF and the first study to generate a combined surface gradient of growth factor and ECM protein to investigate their effect on cell migration on surfaces. This work broadens our understanding of the directional movement of endothelial cells. Our findings provide useful information for directing cell migration into tissue-engineered constructs and can be potentially used for those applications where cell migration is critical, such as angiogenesis.     

A Mixed Quantum-Classical Approach for Computing Effects of Intramolecular Motion on the Low-Barrier Hydrogen Bond

The fractionation factor is defined as the equilibrium constant for the reaction: R – H + DOH R – D + HOH. Of interest are values of fractionation factors for reactions where reactants and/or products form intramolecular low-barrier hydrogen bonds. Experimentally measured isotopic fractionation factors are usually interpreted via a one-dimensional potential energy surface along the intrinsic proton hydrogen bond coordinate. Such a one-dimensional picture cannot be completely correct. Intramolecular motions, such as vibrations and librations, can modulate the underlying potential energy surface along the hydrogen bond coordinate and thus affect the isotopic fractionation factor. We have recently generated a picture of the motion of the proton in a low-barrier hydrogen bond as taking place in an effective single-dimensional potential, which we term the potential of mean force (PMF). In this paper, we compute the PMF for a molecule with an intramolecular hydrogen bond in order to quantify the effect of intramolecular motions on the fractionation factor. The PMF and isotopic fractionation factor are computed with a combination of high-level density functional theory and molecular dynamics simulations.