Effects of catholytes on the mobilization of proteins after capillary isoelectric focusing

Mobilization in two-step capillary isoelectric focusing: Concepts assessed by computer simulation

The mobilization step in a two-step capillary isoelectric focusing protocol is discussed by means of dynamic computer simulation data for systems without and with spacer compounds that establish their zones at the beginning and end of the focusing column. After focusing in an electroosmosis-free environment (first step), mobilization (second step) can be induced electrophoretically, by the application of a hydrodynamic flow, or by a combination of both means. Dynamic simulations provide insight into the complexity of the various modes of electrophoretic mobilization and dispersion associated with hydrodynamic mobilization. The data are discussed together with the relevant literature.

Strategies for capillary electrophoresis: Method development and validation for pharmaceutical and biological applications-Updated and completely revised edition

This review is in support of the development of selective, precise, fast, and validated capillary electrophoresis (CE) methods. It follows up a similar article from 1998, Wätzig H, Degenhardt M, Kunkel A. "Strategies for capillary electrophoresis: method development and validation for pharmaceutical and biological applications," pointing out which fundamentals are still valid and at the same time showing the enormous achievements in the last 25 years. The structures of both reviews are widely similar, in order to facilitate their simultaneous use. Focusing on pharmaceutical and biological applications, the successful use of CE is now demonstrated by more than 600 carefully selected references. Many of those are recent reviews; therefore, a significant overview about the field is provided. There are extra sections about sample pretreatment related to CE and microchip CE, and a completely revised section about method development for protein analytes and biomolecules in general. The general strategies for method development are summed up with regard to selectivity, efficiency, precision, analysis time, limit of detection, sample pretreatment requirements, and validation.

The effect of pH adjusted electrolytes on capillary isoelectric focusing assessed by high-resolution dynamic computer simulation

The effect of the composition of electrolytes on capillary IEF is assessed for systems with carrier ampholytes covering two pH units and with catholytes of decreased pH, anolytes of increased pH, and both electrode solutions with adjusted pH values. For electrolytes composed of formic acid as anolyte and ammonium hydroxide as catholyte, simulation is demonstrated to provide the expected IEF system in which analytes with pI values within the formed pH gradient are focused and become immobile. Addition of formic acid to the catholyte results in the formation of an isotachophoretic zone structure that migrates toward the cathode. With ammonium hydroxide added to the anolyte migration occurs toward the anode. In the two cases, all carrier components and amphoteric analytes migrate isotachophoretically as cations or anions, respectively. The data reveal that millimolar amounts of a counter ion are sufficient to convert an IEF pattern into an ITP system. With increasing amounts of the added counter ion, the overall length of the migrating zone structure shrinks, the range of the pH gradient changes, and the migration rate increases. The studied examples indicate that systems of this type reported in the literature should be classified as ITP and not IEF. When both electrolytes are titrated, a non-uniform background electrolyte composed of formic acid and ammonium hydroxide is established in which analytes migrate according to local pH and conductivity without forming IEF or ITP zone structures. Simulation data are in qualitative agreement with previously published experimental data.

cIEF for rapid pKa determination of small molecules: a proof of concept

A capillary isoelectric focusing (cIEF) method was developed for the determination of the ionization constants (pKa) of small molecules. Two approaches used to decrease the electroosmotic flow (EOF) were compared: (i) a hydroxypropylcellulose (HPC) coated capillary in aqueous medium and (ii) the addition of glycerol to act as a viscosifying agent. The cIEF method with the glycerol medium was selected, and the ionization constants of 22 basic and 21 acidic compounds, including 15 pharmaceutical drugs, were determined, resulting in pKa values from 3.5 to 7.4 and 6.4 to 9.3, respectively. cIEF offers an interesting alternative to other techniques for pKa determination with low sample consumption, high throughput and low cost.

Structural characterization of a recombinant fusion protein by instrumental analysis and molecular modeling

Conbercept is a genetically engineered homodimeric protein for the treatment of wet age-related macular degeneration (wet AMD) that functions by blocking VEGF-family proteins. Its huge, highly variable architecture makes characterization and development of a functional assay difficult. In this study, the primary structure, number of disulfide linkages and glycosylation state of conbercept were characterized by high-performance liquid chromatography, mass spectrometry, and capillary electrophoresis. Molecular modeling was then applied to obtain the spatial structural model of the conbercept–VEGF-A complex, and to study its inter-atomic interactions and dynamic behavior. This work was incorporated into a platform useful for studying the structure of conbercept and its ligand binding functions.

Native capillary isoelectric focusing for the separation of protein complex isoforms and subcomplexes

Here we report the use of capillary isoelectric focusing under native conditions for the separation of protein complex isoforms and subcomplexes. Using biologically relevant HIS-tag and FLAG-tag purified protein complexes, we demonstrate the separations of protein complex isoforms of the mammalian target of rapamycin complex (mTORC1 and 2) and the subcomplexes and different phosphorylation states of the Dam1 complex. The high efficiency capillary isoelectric focusing separation allowed for resolution of protein complexes and subcomplexes similar in size and biochemical composition. By performing separations with native buffers and reduced temperature (15 degrees C) we were able to maintain the complex integrity of the more thermolabile mTORC2 during isoelectric focusing and detection (<45 min). Increasing the separation temperature allowed us to monitor dissociation of the Dam1 complex into its subcomplexes (25 degrees C) and eventually its individual protein components (30 degrees C). The separation of two different phosphorylation states of the Dam1 complex, generated from an in vitro kinase assay with Mps1 kinase, was straightforward due to the large pI shift upon multiple phosphorylation events. The separation of the protein complex isoforms of mTORC, on the other hand, required the addition of a small pI range (4-6.5) of ampholytes to improve resolution and stability of the complexes. We show that native capillary isoelectric focusing is a powerful method for the difficult separations of large, similar, unstable protein complexes. This method shows potential for differentiation of protein complex isoform and subcomplex compositions, post-translational modifications, architectures, stabilities, equilibria, and relative abundances under biologically relevant conditions.

Analysis of E. coli soluble proteins by non-denaturing micro 2-DE/3-DE and MALDI-MS-PMF

Escherichia coli (strain K-12)-soluble proteins were analyzed by nondenaturing micro 2-DE and MALDI-MS-PMF. The reported conditions of nondenaturing IEF in agarose column gels [Jin, Y., Manabe, T., Electrophoresis 2009, 30, 939-948] were modified to optimize the resolution of cellular soluble proteins. About 300 CBB-stained spots, the apparent molecular masses of which ranged from ca. 6000 to 10 kDa, were detected. All the spots on two reference 2-DE gels (one for wide mass range and one for low-molecular-mass range) were numbered and subjected to MALDI-MS-PMF for the assignment of constituting polypeptides. Most of the spots (310 spots out of 329) provided significant match (p<0.05) with polypeptides in Swiss-Prot database and totally 228 polypeptide species were assigned. Activity staining of enzymes such as alkaline phosphatase and catalases was performed on the 2-DE gels and the locations of the activity spots matched well with those of the MS-assigned polypeptides of the enzymes. Most of the polypeptides with subunit information in Swiss-Prot (119 polypeptides as homo-multimers and 25 as hetero-multimers out of the 228), such as pyruvate dehydrogenase complex which is composed of three enzymatic components, were detected at the apparent mass positions of their polymers, suggesting that the proteins were separated retaining their subunit structures. When a nondenaturing 2-DE gel was vertically cut into 2 mm strips and one of the strips was subjected to a third-dimension micro SDS-PAGE (micro 3-DE), about 190 CBB-stained spots were detected. The assignment of the polypeptides separated on the 3-DE gel would further provide information on protein/polypeptide interactions.

Improved capillary isoelectric focusing method for recombinant erythropoietin analysis

Human erythropoietin (EPO) is an endogenously produced glycoprotein, which plays a key role in the erythropoiesis process. Production of erythropoietin by recombinant DNA techniques has made possible its therapeutical use besides its misuse in sport competitions. The link between glycosylated form and protein activity makes necessary a method to analyze the glycoforms' distribution in the recombinant products. In this work, a capillary isoelectric focusing (cIEF) method is presented that allows the analysis of erythropoietin glycoforms. Besides, the cIEF method can be easily implemented in different laboratories. In order to get a feasible and precise cIEF method the following factors have been studied and optimized: (i) neutral coated capillaries, 27 cm long are employed, (ii) ampholytes in the pH range 2 to 10 are used, (iii) bovine beta-lactoglobulin A is chosen as internal standard, (iv) anolyte consisting of 91 mM H3PO4 in cIEF gel is made by weight and catholyte is prepared by titrating 20 mM NaOH with H3PO4 to pH 11.85-11.90, (v) sample is completely depleted of excipients and sodium chloride 10 mM final concentration is added, and (v) t(n)/t(I.S.) and (A(n) - A(I.S.))/A(I.S.), n being the recombinant EPO glycoform considered and I.S. the internal standard, are chosen as indexes to express migration time and area. As a result, a precise method to analyze erythropoietin by capillary isoelectric focusing is achieved with intra-assay RSD < or = 0.5% for index time and < or = 1.5% for index area and inter-sample, inter-anolyte, and inter-catholyte precision better than 3.4% for index time and RSD lower than 2.2% for index area.

One-step capillary isoelectric focusing of the proteins in cerebrospinal fluid and serum of patients with neurological disorders

One-step capillary isoelectric focusing (cIEF), which uses reduced but non-zero electroosmosis flow to mobilize the focused proteins, was applied to the analysis of proteins in cerebrospinal fluid (CSF) and serum of patients with various neurological disorders. Under the conditions employed, pathological changes in the CSF proteins were clearly detected on the electropherograms within 25 min, although the serum proteins did not vary significantly between samples. The present one-step cIEF system seems to be useful in routine laboratory examinations of a large number of CSF samples as an aid in neurological diagnosis.

On-target fraction collection for the off-line coupling of capillary isoelectric focusing with matrix-assisted laser desorption/ionization mass spectrometry

In the present work, we describe a collection system for the off-line coupling of capillary isoelectric focusing (CIEF) with matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. In this system, the capillary effluent is directly deposited in fractions onto the MALDI target via the use of a sheath liquid. The collected fractions are subsequently supplemented with matrix and further analysed by MALDI-TOF mass spectrometry for mass assignment. The experimental set-up includes a fiber optic based UV detector operating at 280 nm, which allows the study of the influence of the sheath liquid composition on the CIEF separation. The influence of the carrier ampholyte concentration on the protein MALDI spectra was also evaluated and the feasibility of the collection method was finally demonstrated with a mixture of four standard proteins.

Possibilities to improve automation, speed and precision of proteome analysis: a comparison of two-dimensional electrophoresis and alternatives

Proteome analysis requires fast methods with high separation efficiencies in order to screen the various cell and tissue types for their proteome expression and monitor the effect of environmental conditions and time on this expression. The established two-dimensional gel electrophoresis (2-DE) is by far too slow for a consequential screening. Moreover, it is not precise enough to observe changes in protein concentrations. There are various approaches that promise faster, automated proteome analysis. This article concentrates on capillary (CT isoelectric focusing coupled to mass spectrometry (CIEF-MSn) and preparative IEF followed by size-exclusion chromatography, hyphenated with MS (PIEF-SEC-MS). These two approaches provide a similar separation pattern as the established 2-DE technique and therefore allow for the continued use of data based on this traditional approach. Their performances have been discussed and compared to 2-DE, evaluating 169 recent articles. Data on analysis time, automation, the detection limit, quantitation, peak capacity, mass and pI accuracy, as well as on the required sample amount are compared in a table.

Combination of electrophoretic techniques for comprehensive analysis of complex protein systems

Analysis of proteins in complex mixtures such as cell lysates is presently performed by two-dimensional polyacrylamide gel electrophoresis under denaturing conditions (denaturing 2-D PAGE) followed by extraction of proteins from gel pieces and structural analysis of the proteins. This type of protein analysis is contributing to the correlation of information stored in DNA sequences with the structure of the product polypeptides. However, denaturing 2-D PAGE has its own limitations and it is necessary to develop various methods of protein analysis to reconstruct the total structure and function of proteins in complex systems. This review article summarizes the work in our laboratory to explore proteins in human plasma combining various electrophoretic techniques: nondenaturing and denaturing 2-D PAGE, capillary electrophoresis, and agarose gel isoelectric focusing.

Mass spectrometric detection for capillary isoelectric focusing separations of complex protein mixtures

Capillary isoelectric focusing (CIEF) can provide high-resolution separations of complex protein mixtures, but until recently it has primarily been used with conventional UV detection. This technique would be greatly enhanced by much more information-rich detection methods that can aid in protein characterization. We describe progress in the development of the combination of CIEF with Fourier transform ion cyclotron resonance (FTICR) mass spectrometry and its application to proteome characterization. Studies have revealed 400-1000 putative proteins in the mass range of 2-100 kDa from total injections of approximately 300 ng protein in single CIEF-FTICR analyses of cell lysates for both Escherichia coli (E. coli) and Deinococcus radiodurans (D. radiodurans). We also demonstrate the use of isotope labeling of the cell growth media to improve mass measurement accuracy and provide a means for quantitative proteome-wide measurements of protein expression. The ability to make such comprehensive and precise measurements of differences in protein expression in response to cellular perturbations should provide new insights into complex cellular processes.

One-step capillary isoelectric focusing for the separation of the recombinant human immunodeficiency virus envelope glycoprotein glycoforms

One-step capillary isoelectric focusing was investigated as a rapid method to resolve the glycoforms of the heterogeneous recombinant human immunodeficiency virus (HIV) envelope glycoprotein (rgp 160sMN/LAI). The separation was performed in a poly(vinyl alcohol) (PVA) coated capillary using a mixture of ampholyte of narrow and wide pH range. A combination of saccaharose and 3-(cyclohexylamino)-1-propanesulfonic acid was shown to be the most efficient additive to avoid protein precipitation which occurs at a pH close to its pI. Although the calibration curve [isoelectric point (pI) vs. migration times] showed a non-linear relationship, an adequate linearity could be yielded for short pI ranges permitting to exhibit the acidic character of the different glycoforms of the rgp 160s MN/LAI (pI from 4.00 to 4.95). Reproducibility evaluated by comparing the performance of a polyacrylamide and a PVA coated capillary showed that low RSD values were obtained for intra-day (0.5 to 1.9%) and inter-day (1.6 to 7.6%) measurements using the PVA capillary. Moreover, the long term stability of the PVA capillary was demonstrated by measuring the variation of migration times of the protein markers for a long period of use. Finally, this method was able to differentiate the glycoform pattern of two close glycoproteins such as the rgp 160 of two sub-populations of the virus HIV-1.

Separation of human cerebrospinal fluid proteins by capillary isoelectric focusing in the absence of denaturing agents

Conditions of capillary isoelectric focusing (CIEF) to separate human cerebrospinal fluid (CSF) proteins were examined referring to those which we have established for the separation of human plasma/serum proteins. Since the average protein concentration in CSF is about 1/200 of plasma and the salt concentration is at almost the same level as plasma, desalting of CSF samples with minimum dilution was a prerequisite for CIEF analysis of CSF proteins. We constructed an apparatus to dialyze CSF at the level of 20-30 microL, this volume being sufficient for 3-4 repeated analyses of the CSF sample. To trace the process of dialysis, a simple device to measure the conductivity of the dialyzate was also constructed. Most of the CIEF conditions for plasma protein analysis could be applied for CSF protein analysis. However, the addition of N,N,N',N'-tetramethylethylenediamine (TEMED) at a suitable concentration was necessary to improve the resolution of basic proteins (IgG region), since some CSF patterns showed peaks of basic proteins which are not obvious in the serum of the same patient. About 70 peaks and shoulders of CSF proteins could be detected by the established CIEF technique. The results of CIEF analysis of CSF samples suggested that the technique will be useful as a survey method to detect specific proteins in CSF, which might relate to disorders in the central nervous system.

Capillary electrophoresis of proteins for proteomic studies

Analyses of proteins in complex mixtures such as cell lyzates are presently performed mainly by sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis. For structural analysis, each protein in a spot is digested with proteases and the fragment peptides are subjected to Edman sequencing and/or mass spectrometry. These works aim at the total analysis of proteins in a complex mixture and reconstruction of their cooperative functions. Genomic studies are now being combined with these proteomic studies. This review article focuses on the application of capillary electrophoresis aiming at the total analysis of complex protein systems or structural analysis of each separated protein. From this viewpoint, articles on capillary zone electrophoresis, capillary isoelectric focusing, and sieving SDS capillary electrophoresis are reviewed. Since these techniques of capillary electrophoresis have been thoroughly reviewed previously, papers published in 1997 and 1998 are mainly covered.

Electrophoretic methods for process monitoring and the quality assessment of recombinant glycoproteins

In many ways electrophoretic techniques appear ideal for quality monitoring of proteins and are thus well suited for the analysis of recombinant glycoproteins. The requirements of high throughput, comparative analysis and resolution of many variants are met by several electrophoretic techniques. A wide variety of such techniques are available to biotechnologists in the rapidly developing area of recombinant glycoproteins. It is the aim of this review to specifically cover recent work which has been applied to the analysis of DNA-derived glycoproteins, both from a process control standpoint and final product validation. All major areas of electrophoresis including sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), isoelectric focusing and techniques utilizing capillary electrophoresis are covered, with emphasis on analysis of glycoforms and oligosaccharide profiles of recombinant glycoproteins. As illustration, actual examples rather than standard glycoproteins are given to indicate the potential and limitations which may be encountered. It is anticipated that this review will prove a useful and practical guide to the latest developments by indicating the relevant merits of different methods.

Size separation of sodium dodecyl sulfate complexes of human plasma proteins by capillary electrophoresis employing linear polyacrylamide as a sieving polymer

Electrophoretic conditions to separate sodium dodecyl sulfate (SDS) complexes of human plasma proteins according to their size differences, by capillary electrophoresis employing linear polyacrylamide as a sieving matrix (LPA-CE), have been examined. Using the optimized separation conditions, SDS complexes of human plasma proteins not treated with reducing agents were separated into about 40 peaks and shoulders within 60 min. The molecular mass values of major peaks in a separation pattern were estimated from a plot of molecular mass and migration time for standard proteins and some of the major plasma proteins have been identified on the pattern. The electrophoretic conditions were successfully applied for the analysis of proteins in immunoglobulin G (IgG) myeloma sera.

Correlation of plasma protein separation patterns obtained by two-dimensional polyacrylamide gel electrophoresis and by capillary electrophoresis

We used three different electrophoretic techniques for the analysis of human plasma proteins: (i) two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), with sodium dodecyl sulfate (SDS) used only in slab gel electrophoresis; (ii) capillary isoelectric focusing (CIEF) with no denaturants; (iii) linear polyacrylamide (LPA)-filled capillary electrophoresis with SDS (SDS-CE). With technique (i), data on isoelectric point and molecular size of plasma proteins can be obtained. Techniques (ii) and (iii) are suited to obtain quantitative information on proteins. The separation principle used in technique (ii) is closely related to that used in the first dimension of technique (i), and that used in technique (iii) related to that in the second dimension of technique (i). Therefore, we could successfully correlate protein separation patterns obtained by 2-D PAGE and those obtained by capillary electrophoresis. The advantages of correlating data obtained by various electrophoretic techniques in the course of constructing a comprehensive database on human plasma proteins are discussed.

Separation of human plasma/serum proteins by capillary isoelectric focusing in the absence of denaturing agents

Human plasma/serum proteins were separated by capillary isoelectric focusing in the absence of denaturing agents. Proteins focused in a fused silica capillary were mobilized by replacing the catholyte sodium hydroxide to acetic acid. The performance of the separation of human plasma proteins has been examined by changing the duration of the step of isoelectric focusing, carrier ampholyte concentration, and plasma protein concentration. The separation patterns of plasma proteins were compared with those obtained by micro two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) run in the absence of denaturants in order to locate the major plasma proteins on the capillary electropherograms. Using the established electrophoretic conditions and the results of peak identification, proteins in the sera of IgG myeloma patients were analyzed by capillary isoelectric focusing. The advantages of capillary isoelectric focusing in plasma protein analysis compared with 2-D PAGE are discussed.