Variations on a theme: Changes to electrophoretic separations that can make a difference

Protein Quantitation and Analysis of Purity

The accurate quantitation of proteins and an analysis of their purity is essential in numerous areas of scientific research and is a critical factor in many clinical applications. The large number and variety of techniques employed for this purpose is therefore not surprising. The selection of a suitable assay is dependent on such factors as the level of sensitivity required, the presence of interfering agents, and the composition of the protein itself. In this chapter, protocols for the most commonly used protein determination methodologies are outlined, including an overview of the highly sensitive real-time quantitative immuno-polymerase chain reaction assay. In addition, an approach to validate the UV protein absorption assay is outlined, which can be applied to any procedure for method validation.

The Whereabouts of 2D Gels in Quantitative Proteomics

Two-dimensional gel electrophoresis has been instrumental in the development of proteomics. Although it is no longer the exclusive scheme used for proteomics, its unique features make it a still highly valuable tool, especially when multiple quantitative comparisons of samples must be made, and even for large samples series. However, quantitative proteomics using two-dimensional gels is critically dependent on the performances of the protein detection methods used after the electrophoretic separations. This chapter therefore examines critically the various detection methods, (radioactivity, dyes, fluorescence, and silver) as well as the data analysis issues that must be taken into account when quantitative comparative analysis of two-dimensional gels is performed.

What Room for Two-Dimensional Gel-Based Proteomics in a Shotgun Proteomics World?

Two-dimensional gel electrophoresis was instrumental in the birth of proteomics in the late 1980s. However, it is now often considered as an outdated technique for proteomics—a thing of the past. Although this opinion may be true for some biological questions, e.g., when analysis depth is of critical importance, for many others, two-dimensional gel electrophoresis-based proteomics still has a lot to offer. This is because of its robustness, its ability to separate proteoforms, and its easy interface with many powerful biochemistry techniques (including western blotting). This paper reviews where and why two-dimensional gel electrophoresis-based proteomics can still be profitably used. It emerges that, rather than being a thing of the past, two-dimensional gel electrophoresis-based proteomics is still highly valuable for many studies. Thus, its use cannot be dismissed on simple fashion arguments and, as usual, in science, the tree is to be judged by the fruit.

Simplified Tracking of a Soy Allergen in Processed Food Using a Monoclonal Antibody-Based Sandwich ELISA Targeting the Soybean 2S Albumin Gly m 8

Soybean allergens in food samples are currently detected in most cases using enzyme-linked immunosorbent assays (ELISAs) based on antibodies raised against bulk soybean proteins or specifically targeting soybean trypsin inhibitor, conglycinin, or glycinin. The various commercial ELISAs lack standardized reference material, and the results are often inaccurate because the antibodies cross-react with proteins from other legumes. Furthermore, the isolation of allergenic proteins involves laborious denaturing extraction conditions. To tackle these challenges, we have developed a novel sandwich ELISA based on monoclonal antibodies raised against the soybean 2S albumin Gly m 8 and a recombinant Gly m 8 reference protein with native-analogous characteristics. The antibodies do not cross-react with other legume proteins, and the extraordinary stability and solubility of Gly m 8 allows it to be extracted even from complex matrices after processing. The Gly m 8 ELISA therefore achieves greater specificity and reproducibility than current ELISA tests.

Two-Dimensional 16-BAC/SDS Polyacrylamide Gel Electrophoresis of Mitochondrial Membrane Proteins

The substitution of the reverse polarity benzyldimethyl-n-hexadecylammonium chloride (16-BAC) polyacrylamide gel electrophoresis (PAGE) for isoelectric focusing (IEF) in the first dimension of electrophoresis improves the solubility of extremely hydrophobic proteins and their recovery compared to conventional 2D IEF/SDS PAGE. The acidic environment of 16-BAC PAGE has also been shown to better preserve the labile methylation of basic proteins such as the histones. Several improvements of the 2D 16-BAC/SDS PAGE method are collectively described here with particular emphasis on the separation of mitochondrial membrane proteins of low molecular mass. Lowering the 16-BAC concentration 50-fold in the gel and buffers decreases the formation of mixed 16-BAC/SDS micelles, which otherwise interferes with the separation of very low molecular mass proteins in second dimension SDS PAGE, and consequently improved the resolution of mitochondrial membrane proteins in the 10-30 kDa range.

Multi-gel casting apparatus for vertical polyacrylamide gels with in-built solution flow system and liquid level detectors

PAGE is the most widely used technique for the separation and biochemical analysis of biomolecules. The ever growing field of proteomics and genomics necessitates the analysis of many proteins and nucleic acid samples to understand further about the structure and function of cells. Simultaneous analysis of multiple protein samples often requires casting of many PAGE gels. Several variants of multi-gel casting/electrophoresis apparatuses are frequently used in research laboratories. Requirement of supplementary gels to match the growing demand for analyzing additional protein samples sometimes become a cause of concern. Available apparatuses are not amenable to and therefore, not recommended for any modification to accommodate additional gel casting units other than what is prescribed by the manufacturer. A novel apparatus is described here for casting multiple PAGE gels comprising four detachable components that provide enhanced practicability and performance of the apparatus. This newly modified apparatus promises to be a reliable source for making multiple gels in less time without hassle. Synchronized functioning of unique components broaden the possibilities of developing inexpensive, safe, and time-saving multi-gel casting apparatus. This apparatus can be easily fabricated and modified to accommodate desired number of gel casting units. The estimated cost (∼$300) for fabrication of the main apparatus is very competitive and effortless assembly procedure can be completed within ∼30 min.

A Comprehensive Guide for Performing Sample Preparation and Top-Down Protein Analysis

Methodologies for the global analysis of proteins in a sample, or proteome analysis, have been available since 1975 when Patrick O′Farrell published the first paper describing two-dimensional gel electrophoresis (2D-PAGE). This technique allowed the resolution of single protein isoforms, or proteoforms, into single ‘spots’ in a polyacrylamide gel, allowing the quantitation of changes in a proteoform′s abundance to ascertain changes in an organism′s phenotype when conditions change. In pursuit of the comprehensive profiling of the proteome, significant advances in technology have made the identification and quantitation of intact proteoforms from complex mixtures of proteins more routine, allowing analysis of the proteome from the ‘Top-Down’. However, the number of proteoforms detected by Top-Down methodologies such as 2D-PAGE or mass spectrometry has not significantly increased since O’Farrell’s paper when compared to Bottom-Up, peptide-centric techniques. This article explores and explains the numerous methodologies and technologies available to analyse the proteome from the Top-Down with a strong emphasis on the necessity to analyse intact proteoforms as a better indicator of changes in biology and phenotype. We arrive at the conclusion that the complete and comprehensive profiling of an organism′s proteome is still, at present, beyond our reach but the continuing evolution of protein fractionation techniques and mass spectrometry brings comprehensive Top-Down proteome profiling closer.

Protein Quantitation and Analysis of Purity

The accurate quantitation of proteins and an analysis of their purity are essential in numerous areas of scientific research, and is a critical factor in many clinical applications. The large number and variety of techniques employed for this purpose is therefore not surprising. The selection of a suitable assay is dependent on such factors as the level of sensitivity required, the presence of interfering agents, and the composition of the protein itself. Here, protocols for the most commonly used protein determination methodologies are outlined, as well as for the more recently adapted technique of quantitative immuno-Polymerase Chain Reaction.

Anionic branched surfactants as alternative denaturing agents for protein separations

Denaturation of a group of model proteins of diverse size and composition with three branched alkyl surfactants-sodium 2-ethylhexyl sulfate (2-EHS), sodium 3,7-dimethyloctyl sulfate (3,7-DMOS), and sodium 2-butyloctyl sulfate (2-BOS)-has been investigated using circular dichroism (CD), small-angle X-ray scattering, and polyacrylamide gel electrophoresis (PAGE). Circular dichroism reveals that 2-BOS disrupts to a higher extent the secondary structure for most of the proteins. Also, it is found that upon adsorption the shape of the protein-surfactant complexes varies from "pearl necklace" to ellipsoidal depending on the surfactant that is used. Macroscopic separations also reveal that branching sodium alkyl sulfates with n-butyl (2-BOS) and n-methyl (3,7-DMOS) groups significantly affects their performance in PAGE. 3,7-DMOS and 2-BOS result in anomalous migrations that deviate from the expected electrophoretic mobility. A combined interpretation of spectroscopy, scattering, and polyacrylamide gel electrophoresis suggests that 2-BOS promotes stronger modification of proteins during denaturation. The findings in this work aim to improve protein electrophoretic separations and the design of novel surfactants.

Analysis of differently expressed proteins involved in metastatic niche of lung

BACKGROUND

The "seed and soil" hypothesis for metastasis was a pivotal milestone in the study of malignant disease. Recently, growing studies have focused on the tumor secretory factors that may mediate preparation of the "metastatic soil." A suitable environment for the metastatic lesions was created by many inflammatory cytokines in the lung, whichwas verified by in vivo experimental models. In 2005, a pre-metastatic niche and metastatic niche modelwere suggested by David Lyden and Bethan Psaila, to delineate the interactions between malignant cells and their microenvironment at the metastatic site, whichsoon became the most importanthypothesis. However, the evidence is limited to animal models. More clinical evidence is needed to support this hypothesis.

METHODS

Human lung specimens were taken from different regions within metastatic lung tissue and normal lung tissue. Differently expressed proteins were analyzed by using the two dimensional fluorescent difference gel electrophoresis (2-D DIGE) technology: about 0.5-1 cm (Tissue 1) of lung tissue was taken adjacent to the metastatic tumor; about 1 cm (Tissue 2) of lung tissue was taken far away from the metastatic tumor; and normal lung tissue of the inflammatory pseudotumor (Tissue 3) was taken at least 3 cm away from the pseudotumor. We usedmatrix-assisted laser desorption/ ionization time of flight mass spectrometry (MALDI-TOF/TOFMS) analysis to identify differently expressed proteins in T1, T2, andT3 samples.

RESULTS

T1 samples were different from T2 samples in the expression of 27 proteins. T2 samples had different expressions in 24 proteins, compared to T3 samples.Nine proteins were expressed differently between T1 and T3 samples. These proteins are mainly involved inenergy metabolism, protect the tumor cell from immunologic engraftment of metastatic tumor cells, and migration. Some of thesehave been reported to be related to the tumor metastatic niche hypothesis: Type VI collagen, heat shock protein 90, and Fibrinogen.

CONCLUSION

The type VI collagen, heat shock protein 90, and Fibrinogen were selected aspotential niche proteins. These findings support the metastatic niche hypothesis and encourage further studies.

Environmental effects on allergen levels in commercially grown non-genetically modified soybeans: assessing variation across north america

Soybean (Glycinemax) is a hugely valuable soft commodity that generates tens of billions of dollars annually. This value is due in part to the balanced composition of the seed which is roughly 1:2:2 oil, starch, and protein by weight. In turn, the seeds have many uses with various derivatives appearing broadly in processed food products. As is true with many edible seeds, soybeans contain proteins that are anti-nutritional factors and allergens. Soybean, along with milk, eggs, fish, crustacean shellfish, tree nuts, peanuts, and wheat, elicit a majority of food allergy reactions in the United States. Soybean seed composition can be affected by breeding, and environmental conditions (e.g., temperature, moisture, insect/pathogen load, and/or soil nutrient levels). The objective of this study was to evaluate the influence of genotype and environment on allergen and anti-nutritional proteins in soybean. To address genetic and environmental effects, four varieties of non-GM soybeans were grown in six geographically distinct regions of North America (Georgia, Iowa, Kansas, Nebraska, Ontario, and Pennsylvania). Absolute quantification of proteins by mass spectrometry can be achieved with a technique called multiple reaction monitoring (MRM), during which signals from an endogenous protein are compared to those from a synthetic heavy-labeled internal standard. Using MRM, eight allergens were absolutely quantified for each variety in each environment. Statistical analyses show that for most allergens, the effects of environment far outweigh the differences between varieties brought about by breeding.

Monocyte/macrophage proteomics: recent findings and biomedical applications

Macrophages, originating from the migration and differentiation of circulating monocytes into virtually all tissues, are extremely flexible and plastic cells that play vital homeostatic roles, but also contribute to the pathophysiology of many human diseases. For these reasons, they are intensively studied by different approaches, recently including proteomics. Macrophage cells can be taken from a range of different sources, including blood monocytes and macrophages from tissues. Macrophages can also be generated by in vitro culture from blood monocytes, and cell lines derived from this lineage can be used. Similarly, many different proteomic techniques can be used, ranging from classic approaches based on 2D gel electrophoresis to more recent high-throughput gel-free techniques essentially based on mass spectrometry. Here, we review the application of such techniques to the study of monocytes/macrophages, and summarize some results potentially relevant to two paradigmatic conditions - atherosclerosis and disorders of iron metabolism.

The whereabouts of 2D gels in quantitative proteomics

Two-dimensional gel electrophoresis has been instrumental in the development of proteomics. Although it is no longer the exclusive scheme used for proteomics, its unique features make it a still highly valuable tool, especially when multiple quantitative comparisons of samples must be made, and even for large samples series. However, quantitative proteomics using 2D gels is critically dependent on the performances of the protein detection methods used after the electrophoretic separations. This chapter therefore examines critically the various detection methods (radioactivity, dyes, fluorescence, and silver) as well as the data analysis issues that must be taken into account when quantitative comparative analysis of 2D gels is performed.

Two-dimensional gel electrophoresis in proteomics: a tutorial

Two-dimensional electrophoresis of proteins has preceded, and accompanied, the birth of proteomics. Although it is no longer the only experimental scheme used in modern proteomics, it still has distinct features and advantages. The purpose of this tutorial paper is to guide the reader through the history of the field, then through the main steps of the process, from sample preparation to in-gel detection of proteins, commenting the constraints and caveats of the technique. Then the limitations and positive features of two-dimensional electrophoresis are discussed (e.g. its unique ability to separate complete proteins and its easy interfacing with immunoblotting techniques), so that the optimal type of applications of this technique in current and future proteomics can be perceived. This is illustrated by a detailed example taken from the literature and commented in detail. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 2).

Recent advances in electrophoretic techniques for the characterization of protein biomolecules: a poker of aces

The four classical modes of electrophoresis of protein molecules (sodium dodecyl sulphate electrophoresis, SDS-PAGE, isoelectric focusing, IEF, and immobilized pH gradients, IPGs, two-dimensional maps, 2D, and capillary electrophoresis, CE) are here reviewed, with special emphasis on recent innovations. Thus, in the case of SDS-PAGE, a novel method, consisting in focusing SDS-protein micelles against a gradient of cationic charges grafted onto a polyacrylamide gel is presented. In the case of IEF, the recent decoding of the structure, polydispersity, molecular mass distribution and buffering properties of the soluble carrier ampholyte buffers are here discussed. In regard to two dimensional mapping, recent instrumentation for performing 2D maps in horizontal, large gel slabs (up to 30 cm × 40 cm) and in a radial format for the SDS dimension is here evaluated. Finally, in the case of CE, three major applications are presented: a thorough study of capillary IEF and of all experimental variables, a method of importance in screening of rDNA products; the possibility of running proteins and peptide separations in very acidic, amphoteric, isoelectric buffers in absence of any capillary coating; finally, the possibility of producing a facile, user friendly, covalent coating of the wall silanols via bonding of quaternarized piperazines endowed with an iodinated tail. In acidic, volatile buffers, such protein/peptide runs can be directly interfaced with mass spectrometry instrumentation.

Overview: the maturing of proteomics in cardiovascular research

Proteomic technologies are used to study the complexity of proteins, their roles, and biological functions. It is based on the premise that the diversity of proteins, comprising their isoforms, and posttranslational modifications (PTMs) underlies biology. Based on an annotated human cardiac protein database, 62% have at least one PTM (phosphorylation currently dominating), whereas ≈25% have more than one type of modification. The field of proteomics strives to observe and quantify this protein diversity. It represents a broad group of technologies and methods arising from analytic protein biochemistry, analytic separation, mass spectrometry, and bioinformatics. Since the 1990s, the application of proteomic analysis has been increasingly used in cardiovascular research. Technology development and adaptation have been at the heart of this progress. Technology undergoes a maturation, becoming routine and ultimately obsolete, being replaced by newer methods. Because of extensive methodological improvements, many proteomic studies today observe 1000 to 5000 proteins. Only 5 years ago, this was not feasible. Even so, there are still road blocks. Nowadays, there is a focus on obtaining better characterization of protein isoforms and specific PTMs. Consequently, new techniques for identification and quantification of modified amino acid residues are required, as is the assessment of single-nucleotide polymorphisms in addition to determination of the structural and functional consequences. In this series, 4 articles provide concrete examples of how proteomics can be incorporated into cardiovascular research and address specific biological questions. They also illustrate how novel discoveries can be made and how proteomic technology has continued to evolve.