Non-covalent and covalent protein labeling in two-dimensional gel electrophoresis

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 However, it is now often considered as an outdated technique for proteomics—a thing of the past.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.

Characterization of Contractile Proteins from Skeletal Muscle Using Gel-Based Top-Down Proteomics

The mass spectrometric analysis of skeletal muscle proteins has used both peptide-centric and protein-focused approaches. The term 'top-down proteomics' is often used in relation to studying purified proteoforms and their post-translational modifications. Two-dimensional gel electrophoresis, in combination with peptide generation for the identification and characterization of intact proteoforms being present in two-dimensional spots, plays a critical role in specific applications of top-down proteomics. A decisive bioanalytical advantage of gel-based and top-down approaches is the initial bioanalytical focus on intact proteins, which usually enables the swift identification and detailed characterisation of specific proteoforms. In this review, we describe the usage of two-dimensional gel electrophoretic top-down proteomics and related approaches for the systematic analysis of key components of the contractile apparatus, with a special focus on myosin heavy and light chains and their associated regulatory proteins. The detailed biochemical analysis of proteins belonging to the thick and thin skeletal muscle filaments has decisively improved our biochemical understanding of structure-function relationships within the contractile apparatus. Gel-based and top-down proteomics has clearly established a variety of slow and fast isoforms of myosin, troponin and tropomyosin as excellent markers of fibre type specification and dynamic muscle transition processes.

Comparative Skeletal Muscle Proteomics Using Two-Dimensional Gel Electrophoresis

The pioneering work by Patrick H. O’Farrell established two-dimensional gel electrophoresis as one of the most important high-resolution protein separation techniques of modern biochemistry (Journal of Biological Chemistry1975, 250, 4007–4021). The application of two-dimensional gel electrophoresis has played a key role in the systematic identification and detailed characterization of the protein constituents of skeletal muscles. Protein changes during myogenesis, muscle maturation, fibre type specification, physiological muscle adaptations and natural muscle aging were studied in depth by the original O’Farrell method or slightly modified gel electrophoretic techniques. Over the last 40 years, the combined usage of isoelectric focusing in the first dimension and sodium dodecyl sulfate polyacrylamide slab gel electrophoresis in the second dimension has been successfully employed in several hundred published studies on gel-based skeletal muscle biochemistry. This review focuses on normal and physiologically challenged skeletal muscle tissues and outlines key findings from mass spectrometry-based muscle proteomics, which was instrumental in the identification of several thousand individual protein isoforms following gel electrophoretic separation. These muscle-associated protein species belong to the diverse group of regulatory and contractile proteins of the acto-myosin apparatus that forms the sarcomere, cytoskeletal proteins, metabolic enzymes and transporters, signaling proteins, ion-handling proteins, molecular chaperones and extracellular matrix proteins.

Consensus brain-derived protein, extraction protocol for the study of human and murine brain proteome using both 2D-DIGE and mini 2DE immunoblotting

Two-dimensional gel electrophoresis (2DE) is a powerful tool to uncover proteome modifications potentially related to different physiological or pathological conditions. Basically, this technique is based on the separation of proteins according to their isoelectric point in a first step, and secondly according to their molecular weights by SDS polyacrylamide gel electrophoresis (SDS-PAGE). In this report an optimized sample preparation protocol for little amount of human post-mortem and mouse brain tissue is described. This method enables to perform both two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) and mini 2DE immunoblotting. The combination of these approaches allows one to not only find new proteins and/or protein modifications in their expression thanks to its compatibility with mass spectrometry detection, but also a new insight into markers validation. Thus, mini-2DE coupled to western blotting permits to identify and validate post-translational modifications, proteins catabolism and provides a qualitative comparison among different conditions and/or treatments. Herein, we provide a method to study components of protein aggregates found in AD and Lewy body dementia such as the amyloid-beta peptide and the alpha-synuclein. Our method can thus be adapted for the analysis of the proteome and insoluble proteins extract from human brain tissue and mice models too. In parallel, it may provide useful information for the study of molecular and cellular pathways involved in neurodegenerative diseases as well as potential novel biomarkers and therapeutic targets.

Comparative and Quantitative Global Proteomics Approaches: An Overview

Proteomics became a key tool for the study of biological systems. The comparison between two different physiological states allows unravelling the cellular and molecular mechanisms involved in a biological process. Proteomics can confirm the presence of proteins suggested by their mRNA content and provides a direct measure of the quantity present in a cell. Global and targeted proteomics strategies can be applied. Targeted proteomics strategies limit the number of features that will be monitored and then optimise the methods to obtain the highest sensitivity and throughput for a huge amount of samples. The advantage of global proteomics strategies is that no hypothesis is required, other than a measurable difference in one or more protein species between the samples. Global proteomics methods attempt to separate quantify and identify all the proteins from a given sample. This review highlights only the different techniques of separation and quantification of proteins and peptides, in view of a comparative and quantitative global proteomics analysis. The in-gel and off-gel quantification of proteins will be discussed as well as the corresponding mass spectrometry technology. The overview is focused on the widespread techniques while keeping in mind that each approach is modular and often recovers the other.

Proteomics to study the diversity and dynamics of proteasome complexes: from fundamentals to the clinic

This article covers the latest contributions of proteomics to the structural and functional characterization of proteasomes and their associated proteins, but also to the detection of proteasomes as clinical biomarkers in diseases. Proteasomes are highly heterogenous supramolecular complexes and constitute important cellular proteases controlling the pool of proteins involved in key cellular functions. The comprehension of the structure/function relationship of proteasomes is therefore of major interest in biology. Numerous biochemical methods have been employed to purify proteasomes, and have led to the identification of complexes of various compositions - depending on the experimental conditions and the type of strategy used. In association with protein separation and enrichment techniques, modern mass spectrometry instruments and mass spectrometry-based quantitative methods, they have led to unprecedented breakthroughs in the in-depth analysis of the diversity and dynamics of proteasome composition and localization under various stimuli or pathological contexts. Proteasome inhibitors are now used in clinics for the treatment of cancer, and recent studies propose that the proteasome should be considered as a predictive biomarker for various pathologies.

Pathobiochemical changes in diabetic skeletal muscle as revealed by mass-spectrometry-based proteomics

Insulin resistance in skeletal muscle tissues and diabetes-related muscle weakness are serious pathophysiological problems of increasing medical importance. In order to determine global changes in the protein complement of contractile tissues due to diabetes mellitus, mass-spectrometry-based proteomics has been applied to the investigation of diabetic muscle. This review summarizes the findings from recent proteomic surveys of muscle preparations from patients and established animal models of type 2 diabetes. The potential impact of novel biomarkers of diabetes, such as metabolic enzymes and molecular chaperones, is critically examined. Disease-specific signature molecules may be useful for increasing our understanding of the molecular and cellular mechanisms of insulin resistance and possibly identify new therapeutic options that counteract diabetic abnormalities in peripheral organ systems. Importantly, the biomedical establishment of biomarkers promises to accelerate the development of improved diagnostic procedures for characterizing individual stages of diabetic disease progression, including the early detection of prediabetic complications.

Image Analysis Workflow for 2-D Electrophoresis Gels Based on ImageJ

A number of commercial software packages are currently available to perform digital two-dimensional electrophoresis (2D-GE) gel analysis. However, both the high cost of the commercial packages and the unavailability of a standard data analysis workflow, have prompted several groups to develop freeware systems to perform certain steps of gel analysis. Unfortunately, to the best of our knowledge none of them offer a package that performs all the steps envisaged in a 2D-GE gel analysis. Here we describe an ImageJ-based procedure, able to manage all the steps of a 2D-GE gel analysis. ImageJ is a free available image processing and analysis application developed by National Institutes of Health (NIH) and widely used in different life sciences fields as medical imaging, microscopy, western blotting and PAGE. Nevertheless no one has yet developed a procedure enabled to compare spots on 2D-GE gels. We collected all used ImageJ tools in a plug-in that allows us to perform the whole 2D-GE analysis. To test it, we performed a set of 2D-GE experiments on plasma samples from 9 patients victims of acute myocardial infarction and 8 controls, and we compared the results obtained by our procedure to those obtained using a widely diffuse commercial package, finding similar performances.

Fluorescent labeling of proteins with amine-specific 1,3,2-(2H)-dioxaborine polymethine dye

A novel water-soluble amine-reactive dioxaborine trimethine dye was synthesized in a good yield and characterized. The potential of the dye as a specific reagent for protein labeling was demonstrated with bovine serum albumin and lysozyme. Its interaction with proteins was studied by fluorescence spectroscopy and gel electrophoresis. The covalent binding of this almost nonfluorescent dye to proteins results in a 75- to 78-fold increase of its emission intensity accompanied by a red shift of the fluorescence emission maximum by 27 to 45 nm, with fluorescence wavelengths of labeled biomolecules being more than 600 nm. The dye does not require activation for the labeling reaction and can be used in a variety of bioassay applications.

Skeletal muscle proteomics: current approaches, technical challenges and emerging techniques

Background

Skeletal muscle fibres represent one of the most abundant cell types in mammals. Their highly specialised contractile and metabolic functions depend on a large number of membrane-associated proteins with very high molecular masses, proteins with extensive posttranslational modifications and components that exist in highly complex supramolecular structures. This makes it extremely difficult to perform conventional biochemical studies of potential changes in protein clusters during physiological adaptations or pathological processes.

Results

Skeletal muscle proteomics attempts to establish the global identification and biochemical characterisation of all members of the muscle-associated protein complement. A considerable number of proteomic studies have employed large-scale separation techniques, such as high-resolution two-dimensional gel electrophoresis or liquid chromatography, and combined them with mass spectrometry as the method of choice for high-throughput protein identification. Muscle proteomics has been applied to the comprehensive biochemical profiling of developing, maturing and aging muscle, as well as the analysis of contractile tissues undergoing physiological adaptations seen in disuse atrophy, physical exercise and chronic muscle transformation. Biomedical investigations into proteome-wide alterations in skeletal muscle tissues were also used to establish novel biomarker signatures of neuromuscular disorders. Importantly, mass spectrometric studies have confirmed the enormous complexity of posttranslational modifications in skeletal muscle proteins.

Conclusions

This review critically examines the scientific impact of modern muscle proteomics and discusses its successful application for a better understanding of muscle biology, but also outlines its technical limitations and emerging techniques to establish new biomarker candidates.

Quantitative DY-maleimide-based proteomic 2-DE-labeling strategies using human skin proteins

Sensitive differential proteomic analysis is challenging and often limited by distinct labeling or tagging strategies. In this study, we have examined the sensitivity, linearity, and photophysical properties of novel protein labeling DY-maleimide dyes (DY-505-MAL, DY-555-MAL and DY-635-MAL). All MS compatible DY-maleimide dyes exhibited excellent emission spectra, high sensitivity, and high linearity, when applied to standard 1-DE protein analysis. Correspondingly, 2-DE analysis of DY-635-MAL or DY-505-MAL maximal-labeled human keratinocyte proteins displayed remarkably high sensitivity. Compared with a standard fluorescent protein stain, DY-635-MAL or DY-505-MAL 2-DE analysis demonstrated equally high spot quality with an overall increase in the number of spots detectable (up to threefold higher;>1000 spots/gel). However, as determined with a FLA-5100 imaging system, comparative MultiGauge, and Delta2D analysis, not all DY-maleimide dyes possessed DIGE compatible fluorescent emission properties. However, DY-505-MAL and DY-635-MAL were found to be suitable for more complex, time and gel intensive, focused multiplexing analyses. Notably - as demonstrated with allergen-stimulated human skin proteins - defined, singular DY-maleimide dye protein labeling (SDPL) allows high quality, time saving, simple, and reliable differential proteomic examination.

Chemical biology approaches to probe the proteome

Understanding disease-associated cellular defects at a molecular level is critical for the development of pharmacological intervention strategies. Recent breakthroughs in microarray and sequencing technologies have provided powerful tools to rapidly reveal the cellular defects caused by alterations in the genome or transcriptome. However, the picture of how the cellular proteome is affected in a disease state and how changes in DNA and RNA affect protein function is often incomplete. This is perhaps not surprising because the functions of proteins are not just determined by primary sequence and abundance, but are under the control of many regulatory mechanisms. Here, we highlight several recent advances in proteomics technologies that are being developed to generate comprehensive human proteome maps and discuss them in the context of strategies that have been developed in simple model organisms. Chemical biology will play a critical role in drafting a map of the proteome with functional information. Chemical genetic approaches that use high-throughput small molecule screening have resulted in the public availability of small molecule datasets through web interfaces such as PubChem. With such approaches, the opportunities to investigate disease and to explore the proteome with chemistry are rapidly increasing. In addition, new tools are being developed to probe protein function. Here we highlight recent developments in chemical biology and the exciting opportunities that are arising with them.