Concentrating Proteins by Salt, Polyethylene Glycol, Solvent, SDS Precipitation, Three-Phase Partitioning, Dialysis, Centrifugation, Ultrafiltration, Lyophilization, Affinity Chromatography, Immunoprecipitation or Increased Temperature for Protein Isolation, Drug Interaction, and Proteomic and Peptidomic Evaluation

In protein isolation, drug interaction studies, and proteomic or peptidomic procedures, protein solutions are often concentrated to remove solvents and undesirable molecules, to separate protein fractions, or to increase protein concentrations. Proteins can be concentrated by precipitation from solution with ammonium sulfate, polyethylene glycol, organic solvents, trichloroacetic acid, potassium chloride/sodium dodecyl sulfate thermal denaturation, and three-phase partitioning. Solvents can be removed by passage through a semipermeable barrier where protein solutions are forced against the barrier in a centrifuge tube or with increased pressure, concentrating proteins in the remaining solution. The semipermeable barrier can be surrounded by a hygroscopic reagent to draw the solvent across the membrane. Proteins can be concentrated by freeze-drying (lyophilization). Unique ligand interactions with proteins can be used to select for proteins by affinity purification or immunoprecipitation. All these methods to concentrate proteins are discussed.

Enhanced Mass Spectrometry Detection of MHC Peptides

Mass spectrometry (MS)-based immunopeptidomics (MHC peptides) is a promising approach for neoantigen discovery through searching MS data against patient-specific protein databases built from exome or transcriptome sequences. MS analysis enables mapping of posttranslational modifications that cannot be predicted from genome sequencing alone but can be more efficient in triggering immune responses. Although MS-based immunopeptidomics has demonstrated its potential in discovering neoantigens as vaccine candidates, the problems such as efficient isolation and sensitive detection (identification) of MHC peptides still hinder the application of its clinical application. Herein, we describe a method based on chemical derivatization and LC-MS/MS for the enhanced detection of MHC peptides.

Shotgun Proteomic Profiling of Bloodborne Nanoscale Extracellular Vesicles

Analyses of bloodborne nanoscale extracellular vesicles (nsEVs) have shown tremendous promise in enabling the development of noninvasive blood-based clinical diagnostic tests, predicting and monitoring the efficacy of treatment programs, and identifying new drug targets in the context of health conditions such as cancer and Alzheimer's disease. In this chapter we present a protocol for generating global nsEV proteomic profiles that can further the utility of nsEV analysis for the above biomedical applications by enlightening us of differences in protein abundance across normal and disease state nsEVs. This protocol features the use of magnetic particle-based immunoprecipitation to enrich highly purified populations of nsEVs directly from plasma or serum samples. The constituent proteins of these vesicles are subsequently characterized using a comparative shotgun proteomics approach that entails bottom-up, tandem mass spectrometric analysis of peptides generated by proteolytic digestion of nsEV-derived proteins. The methods described here are compatible with parallel processing of dozens of plasma or serum samples and can be valuable tools in enabling nsEV biomarker discoveries that have high translational relevance in the development of both novel therapeutics and blood sample diagnostic assays.

Dot Blot Analysis for Measuring Global N6-Methyladenosine Modification of RNA

Posttranscriptional modification of mRNAs plays an important role in establishing the functional diversity of the proteome. The m⁶A modification is found in many species of RNA, including tRNA, mRNA, rRNA, and long noncoding RNAs. The physiological role of m⁶A modification of RNA is not fully explored and is a topic of current research. It is predicted that the major effect of m⁶A modification of mRNAs is on its stability and/or translation. The global changes in m⁶A levels in total RNA or particular species of RNAs can be measured by dot blot analysis using m⁶A specific antibodies or using mass spectrometry following chromatographic separation. The dot blot method for detection of global m⁶A changes is a relatively straightforward method to quantitate m⁶A modification but suffers from low sensitivity when the fraction of m⁶A-modified RNA is small in analyzed samples. Here, we describe a modified dot blot method that is sensitive and quantitative for detecting m⁶A-modified RNA by adding an immunoprecipitation step to enrich for m⁶A-modified RNA.

Evaluating the susceptibility of AGO2-loaded microRNAs to degradation by nucleases in vitro

MicroRNAs (miRNAs) comprise a class of small non-coding RNAs that regulate the stability and/or translatability of most protein-coding transcripts. Steady-state levels of mature miRNAs can be controlled through mechanisms that influence their biogenesis and/or decay rates. Pathways that mediate mature miRNA decay are less well understood than those that mediate miRNA biogenesis. We recently described Tudor-staphylococcal/micrococcal-like nuclease (TSN)-mediated miRNA decay (TumiD) as a cellular pathway that promotes the sequence-specific endonucleolytic decay of miRNAs that harbor a CA and/or UA dinucleotide. Here, we describe an in vitro assay for evaluating the susceptibility of AGO2-loaded miRNAs to degradation by different classes of nucleases. This in vitro approach can be used to complement in vivo studies that aim to identify novel miRNA decay factors.

Characterization of Transplantable Insulinoma Cells

This chapter describes the propagation and characterization of transplantable insulinoma cells as model of insulin-producing pancreatic islet cells in the rat. Here, the cells are propagated by transplantation into rats followed by harvesting after growth for approximately 1 month. The cells are then purified by Percoll density gradient centrifugation and characterized by pulse-chase radiolabelling and immunoprecipitation of the insulin-related peptides. The results show that the transplantable insulinoma cells produce insulin in a manner similar to that found in normal pancreatic islets.

A two-step immunoassay for the simultaneous assessment of Aβ38, Aβ40 and Aβ42 in human blood plasma supports the Aβ42/Aβ40 ratio as a promising biomarker candidate of Alzheimer's disease

Background

The quantification of amyloid-beta (Aβ) peptides in blood plasma as potential biomarkers of Alzheimer’s disease (AD) is hampered by very low Aβ concentrations and the presence of matrix components that may interfere with the measurements.

Methods

We developed a two-step immunoassay for the simultaneous measurement of the relative levels of Aβ38, Aβ40 and Aβ42 in human EDTA plasma. The assay was employed for the study of 23 patients with dementia of the Alzheimer’s type (AD-D) and 17 patients with dementia due to other reasons (OD). We examined relationships with the clinical diagnosis, cerebral Aβ load as quantified by amyloid-positron emission tomography, apolipoprotein E genotype, Aβ levels and Tau protein in cerebrospinal fluid.

Results

Preconcentration of plasma Aβ peptides by immunoprecipitation substantially facilitated their immunological measurements. The Aβ42/Aβ40 and Aβ42/Aβ38 ratios were statistically significantly lower in the AD-D patients than in the OD group. The areas under the receiver operating characteristic curves reached 0.87 for the Aβ42/Aβ40 ratio and 0.80 for the Aβ42/Aβ38 ratio.

Conclusions

The measurement of plasma Aβ peptides with an immunological assay can be improved by preconcentration via immunoprecipitation with an antibody against the Aβ amino-terminus and elution of the captured peptides by heating in a mild detergent-containing buffer. Our findings support the Aβ42/Aβ40 ratio in blood plasma as a promising AD biomarker candidate which correlates significantly with the validated core biomarkers of AD. Further studies will be needed for technical advancement of the assay and validation of the biomarker findings.

Electronic supplementary material

The online version of this article (10.1186/s13195-018-0448-x) contains supplementary material, which is available to authorized users.

Immunofixation Electrophoresis for Identification of Proteins and Specific Antibodies

Immunofixation electrophoresis (IFE) is a technique for the identification of proteins within complex mixtures after separation by either conventional zone electrophoresis or isoelectric focusing. Most commonly antigens (which are often immunoglobulins) are separated by electrophoresis followed by precipitation with specific antibodies in situ. However, immunoglobulins with specific reactivity can be also precipitated with the proper antigens after electrophoresis in reverse or reversed IFE. Because of its great versatility, potentially high sensitivity, ease to perform and customize, and relatively low cost with no requirement for expensive instrumentation, manual IFE remains a valuable tool for both clinical diagnostic testing and research. Any low-viscosity body fluid specimen or, possibly, culture fluid could be tested with IFE if proper antibodies (or antigens in reverse[d] IFE) are available. After pretreatment with chaotropic and/or reducing agents, even high-viscosity specimens might be amenable to testing with IFE.

SDS-PAGE for 35S Immunoprecipitation and Immunoprecipitation Western Blotting

This report discusses recent methods of sample preparation and gel electrophoresis for ³⁵S immunoprecipitation (IP) and IP western blotting. In both methods, IP is used to obtain purified proteins, and sodium dodecyl sulfate polyacrylamide gel electrophoresis is used to separate the proteins on a gel. In ³⁵S IP, the proteins are radiolabeled and visualized on film by fluorography; in IP blotting, proteins are transferred onto nitrocellulose paper, and antibodies are used to detect specific proteins. A similar IP and SDS-PAGE method can be used for both procedures, but IP blotting has the potential advantages of improvement in sensitivity for low-abundance proteins and enhanced specificity for identification of proteins from a mixture. Some of the technical adaptations discussed here to facilitate IP blotting and avoid loss of beads or purified proteins may also be useful for ³⁵S IP.

Analysis of ubiquitination and ligand-dependent trafficking of group I mGluRs

Group I metabotropic glutamate receptors (mGluRs) are G-protein coupled receptors (GPCRs). They have been implicated in multiple forms of synaptic plasticity, as well as in various neuropsychiatric disorders. The signaling of these receptors is governed by the mechanisms of desensitization, internalization and resensitization of these receptors. Various post-translational modifications determine the signaling as well as trafficking of these receptors. Ubiquitination is a post-translational modification that has emerged as an essential regulatory process which governs group I mGluR trafficking. In this chapter, we have discussed the strategies to investigate the ubiquitination and the ligand-mediated trafficking of group I mGluRs in HEK293T cells and in primary hippocampal neurons, respectively. We have illustrated the protocols of (i) maintenance and transient transfection in HEK293T cells and primary hippocampal neurons, (ii) immunoprecipitation and western blot analysis to identify the ubiquitination of group I mGluRs, (iii) endocytosis and recycling assay and (iv) image acquisition and analysis.

Selective Isolation of Retroviruses from Extracellular Vesicles by Intact Virion Immunoprecipitation

There exists a wide variety of techniques to isolate and purify viral particles from cell culture supernatants. However, these techniques vary greatly in ease of use, purity, yield and impact on viral structural integrity. Most importantly, it is becoming evident that secreted extracellular vesicles (EVs) co-purify with retroviruses using nearly all purification methods due to nearly indistinguishable biophysical characteristics such as size, buoyant density and nucleic acid content. Recently, our group has illustrated a means of isolating intact and highly enriched retroviral virions from EV-containing cell supernatants using an immunoprecipitation approach targeting the viral envelope glycoprotein of the Moloney Murine Leukemia Virus ( Renner et al., 2018 ). This technique, that we call intact virion immunoprecipitation (IVIP), enabled us to characterize the accessibility of epitopes on the surface of these retroviruses and assess the orientation of the virus-encoded integral membrane protein Glycogag (gPr80) in the viral envelope. Proper implementation of this protocol enables fast, simple and reproducible preparations of intact and highly purified retroviral particles devoid of detectable EV contaminants.

Characterization of the TNFR1-SC Using "Modified Tandem Affinity Purification" in Conjunction with Liquid Chromatography-Mass Spectrometry (LC-MS)

Mass spectrometry enables the unbiased characterization of protein complexes. The success of this approach and the amount of information that can be retrieved are highly dependent on the achieved purity of the protein complex to be analyzed. Here we describe a modified tandem affinity purification (moTAP) approach which can be used to isolate the tumor necrosis factor receptor 1 signaling complex for subsequent analysis by liquid chromatography-tandem mass spectrometry. Indeed, this approach can easily be adapted to the isolation of other membrane-bound and intracellular signaling complexes. This methodology allows for a highly sensitive analysis and characterization of complex components, including posttranslational modifications and for the identification of novel complex components.

iCLIP of the PIWI Protein Aubergine in Drosophila Embryos

Piwi-interacting RNAs (piRNAs) are a class of small noncoding RNAs bound to specific Argonaute proteins, the PIWI proteins. piRNAs target mRNAs by complementarity to silence them; they play an important role in the repression of transposable elements in the germ line of many species. piRNAs and PIWI proteins are also involved in diverse biological processes through their role in the regulation of cellular mRNAs. In the Drosophila embryo, they contribute to the maternal mRNA decay occurring during the maternal-to-zygotic transition. CLIP (UV cross-linking and immunoprecipitation) techniques have been used to identify target mRNAs of Argonaute proteins. Here we describe the iCLIP (individual-nucleotide resolution CLIP) protocol that we have adapted for the PIWI protein Aubergine in Drosophila embryos.

DNA methylation and genetic degeneration of the Y chromosome in the dioecious plant Silene latifolia

Background

S. latifolia is a model organism for the study of sex chromosome evolution in plants. Its sex chromosomes include large regions in which recombination became gradually suppressed. The regions tend to expand over time resulting in the formation of evolutionary strata. Non-recombination and later accumulation of repetitive sequences is a putative cause of the size increase in the Y chromosome. Gene decay and accumulation of repetitive DNA are identified as key evolutionary events. Transposons in the X and Y chromosomes are distributed differently and there is a regulation of transposon insertion by DNA methylation of the target sequences, this points to an important role of DNA methylation during sex chromosome evolution in Silene latifolia. The aim of this study was to elucidate whether the reduced expression of the Y allele in S. latifolia is caused by genetic degeneration or if the cause is methylation triggered by transposons and repetitive sequences.

Results

Gene expression analysis in S. latifolia males has shown expression bias in both X and Y alleles. To determine whether these differences are caused by genetic degeneration or methylation spread by transposons and repetitive sequences, we selected several sex-linked genes with varying degrees of degeneration and from different evolutionary strata. Immunoprecipitation of methylated DNA (MeDIP) from promoter, exon and intron regions was used and validated through bisulfite sequencing. We found DNA methylation in males, and only in the promoter of genes of stratum I (older). The Y alleles in genes of stratum I were methylation enriched compared to X alleles. There was also abundant and high percentage methylation in the CHH context in most sequences, indicating de novo methylation through the RdDM pathway.

Conclusions

We speculate that TE accumulation and not gene decay is the cause of DNA methylation in the S. latifolia Y sex chromosome with influence on the process of heterochromatinization.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4936-y) contains supplementary material, which is available to authorized users.

Isolation and Characterization of Endogenous RNPs from Brain Tissues

Identification of physiological target RNAs and protein interactors bound to RNA-binding proteins is a key prerequisite to understand the underlying mechanisms of posttranscriptional expression control and RNA granule assembly. Here, we describe a multistep biochemical approach to isolate endogenous ribonucleoprotein particles from brain tissues by exploiting differential centrifugation and gradient fractionation followed by immunoprecipitation with monospecific, affinity-purified antibodies directed against selected RNA-binding proteins. This protocol results in highly enriched endogenous ribonucleoprotein particles that then can be analyzed by mass spectrometry (for proteins composition) and microarray or RNA sequencing technologies (for target mRNAs).

Identification of In Planta Protein-Protein Interactions Using IP-MS

Gene regulation by transcription factors involves complex protein interaction networks, which include chromatin remodeling and modifying proteins as an integral part. Decoding these protein interactions is crucial for our understanding of chromatin-mediated gene regulation. Here, we describe a method for the immunoprecipitation of in planta nuclear protein complexes followed by mass spectrometry (IP-MS) to identify interactions between transcription factors and chromatin remodelers/modifiers in plants. In addition to a step-by-step bench protocol for immunoprecipitation and subsequent mass spectrometry, we provide guidelines and pointers on necessary controls and data analysis approaches.

Identification of Acetylated Proteins in Borrelia burgdorferi

Posttranslational modification (PTM) of proteins has emerged as a major regulatory mechanism in all three domains of life. One emerging PTM is Nε-lysine acetylation-the acetylation of the epsilon amino group of lysine residues. Nε-lysine acetylation is known to regulate multiple cellular processes. In eukaryotes, it regulates chromatin structure, transcription, metabolism, signal transduction, and the cytoskeleton. Recently, multiple groups have detected Nε-lysine acetylation in diverse bacterial phyla, but no work on protein acetylation in Borrelia burgdorferi has been reported. Here, we describe a step-by-step protocol to identify Nε-lysine acetylated proteins in B. burgdorferi.

Oocyte-G1 promotes male germ cell apoptosis through activation of Caspase-3

Apoptosis plays a vital role in the developmental process of the mammalian reproduction system, such as during folliculogenesis or spermatogenesis. Kinesin superfamily (Kif) proteins are responsible for intercellular transportation, and their malfunction can induce cell apoptosis. Oocyte-G1 is a new Kif member. Our previous study suggested that abnormal expression of Oocyte-G1 induced abnormal development of ovarian follicle and testes, but the underlying mechanism was not fully discovered. Therefore, in this study, the cellular role and mechanism of Oocyte-G1 were investigated. Transferase-mediated deoxyuridine triphosphate-biotin nick end labeling (TUNEL) result showed that overexpression of Oocyte-G1 increased apoptosis in cultured cells. Oocyte-G1 transgenic mice also showed an increased apoptotic rate in male germ cells compared with controls. Immunoprecipitation and co-localization experiments revealed an interaction between Oocyte-G1 and Caspase-3. Expression levels of Caspase-3 were upregulated in cells overexpressing Oocyte-G1 and downregulated in Oocyte-G1 knockdown cells. These results suggest that Oocyte-G1 may promote male germ cell apoptosis through activating Caspase-3.

Purification of kinetochores from the budding yeast Saccharomyces cerevisiae

Chromosome segregation relies on forces generated by spindle microtubules that are translated into chromosome movement through interactions with kinetochores, highly conserved macromolecular machines that assemble on a specialized centromeric chromatin structure. Kinetochores not only have to stably attach to growing and shrinking microtubules, but they also need to recruit spindle assembly checkpoint proteins to halt cell cycle progression when there are attachment defects. Even the simplest kinetochore in budding yeast contains more than 50 unique components that are present in multiple copies, totaling more than 250 proteins in a single kinetochore. The complex nature of kinetochores makes it challenging to elucidate the contributions of individual components to its various functions. In addition, it is difficult to manipulate forces in vivo to understand how they regulate kinetochore-microtubule attachments and the checkpoint. To address these issues, we developed a technique to purify kinetochores from budding yeast that can be used to analyze kinetochore functions and composition as well as to reconstitute kinetochore-microtubule attachments in vitro.

Quantification of RNA Content in Reconstituted Ebola Virus Nucleocapsids by Immunoprecipitation

Immunoprecipitations are commonly used to isolate proteins or protein complexes and assess protein-protein interactions; however, they can also be used to assess protein-RNA complexes. Here we describe an adapted RNA immunoprecipitation technique that permits the quantification of RNA content in Ebola virus nucleocapsids that have been reconstituted in vitro by transient transfection.

Functional coupling between adenosine A1 receptors and G-proteins in rat and postmortem human brain membranes determined with conventional guanosine-5'-O-(3-[35S]thio)triphosphate ([35S]GTPγS) binding or [35S]GTPγS/immunoprecipitation assay

Adenosine signaling plays a complex role in multiple physiological processes in the brain, and its dysfunction has been implicated in pathophysiology of neuropsychiatric diseases such as schizophrenia and affective disorders. In the present study, the coupling between adenosine A₁ receptor and G-protein was assessed by means of two [³⁵S]GTPγS binding assays, i.e., conventional filtration method and [³⁵S]GTPγS binding/immunoprecipitation in rat and human brain membranes. The latter method provides information about adenosine A₁ receptor-mediated Gα_i-3 activation in rat as well as human brain membranes. On the other hand, adenosine-stimulated [³⁵S]GTPγS binding determined with conventional assay derives from functional activation of Gα_i/o proteins (not restricted only to Gα_i-3) coupled to adenosine A₁ receptors. The determination of adenosine concentrations in the samples used in the present study indicates the possibility that the assay mixture under our experimental conditions contains residual endogenous adenosine at nanomolar concentrations, which was also suggested by the results on the effects of adenosine receptor antagonists on basal [³⁵S]GTPγS binding level. The effects of adenosine deaminase (ADA) on basal binding also support the presence of adenosine. Nevertheless, the varied patterns of ADA discouraged us from adding ADA into assay medium routinely. The concentration-dependent increases elicited by adenosine were determined in 40 subjects without any neuropsychiatric disorders. The increases in %E_max values determined by conventional assay according to aging and postmortem delay should be taken into account in future studies focusing on the effects of psychiatric disorders on adenosine A₁ receptor/G-protein interaction in postmortem human brain tissue.

Immunoprecipitation of Death Inducing Signaling Complex by Caspase-8

Analysis of CD95/Fas complexes by immunoprecipitation has long relied on the monoclonal antibody APO1 or tagged recombinant Fas ligand. Immunoprecipitation is an elegant and efficient procedure to investigate endogenous protein interactions or complexes. Provided that the targeted complex is soluble in mild detergent these complexes can be recovered using protein A/G-coupled Sepharose beads and further analyzed after denaturation and electrophoretic separation by western blotting or mass spectrometry. Herein, we describe in detail the method used in our laboratory to immunoprecipitate and analyze by immunoblot complexes containing caspase-8, using a commercial antibody directed against caspase-8.

Multiplex Sequential Immunoprecipitation of Insulin Secretory Granule Proteins from Radiolabeled Pancreatic Islets

Pulse radiolabeling of cells with radioactive amino acids is a common method for tracking the biosynthesis of proteins. Specific proteins can then be immunoprecipitated and analyzed by electrophoresis and imaging techniques. This chapter presents a protocol for the biosynthetic labeling of pancreatic islets with ³⁵S-methionine, followed by multiplex sequential immunoprecipitation of insulin and three other secretory granule accessory proteins. This provided a means of distinguishing those pancreatic islet proteins with different biosynthetic rates in response to the media glucose concentrations.

Preparation of Cell Lysates of Fission Yeast for Immunoprecipitation

Immunoprecipitation is one of the most important and widely used techniques for the detection and purification of a protein of interest. Thanks to highly specific interaction between antigen and antibody, a target protein is purified and concentrated effectively. To obtain reasonable amounts of a target protein, it is crucially important to prepare total cell lysates in which the target protein is present in a soluble form. Here, we describe methods to prepare total cell lysates of fission yeast, which are then used directly for immunoprecipitation. We also describe some tips to select reagents for preparing buffers having a substantial impact on protein solubility, because there is essentially no reagent that can accommodate the full range of proteins having different characteristics.

A fully validated liquid chromatography-mass spectrometry method for the quantification of the soluble receptor of advanced glycation end-products (sRAGE) in serum using immunopurification in a 96-well plate format

The study of proteins is central to unraveling (patho)physiological processes and has contributed greatly to our understanding of biological systems. Corresponding studies often employ procedures to enrich proteins from their biological matrix using antibodies or other affinity binders coupled to beads with a large surface area and a correspondingly high binding capacity. Striving for maximal binding capacity may, however, not always be required or desirable, for example for proteins of low abundance. Here we describe a simplified immunoprecipitation in 96-well ELISA format (IPE) approach for fast and easy enrichment of proteins. The applicability of this approach for enriching low-abundant proteins was demonstrated by an IPE-based quantitative workflow using liquid chromatography-mass spectrometry (LC-MS) for the soluble Receptor of Advanced Glycation End-products (sRAGE), a promising biomarker in chronic obstructive pulmonary disease (COPD). The method was validated according to U.S. Food and Drug Administration (FDA) and European Medicines Agency (EMA) guidelines and enabled accurate quantitation of sRAGE between 0.1 and 10 ng/mL in 50 µL serum. The assay showed substantial correlation with the two most commonly-used sRAGE immunoassays (ELISAs) (R²-values between 0.7 and 0.8). However, the LC-MS method reported 2-4 times higher sRAGE levels compared to the ELISAs, which is largely due to a suboptimal amount of capturing antibody and/or calibration strategy used by the immunoassays. In conclusion, our simplified IPE approach proved to be an efficient strategy for enriching the low-abundant protein sRAGE from serum and may provide an easy to use platform for enriching other (low-abundant) proteins from complex, biological matrices.