RESUMO
BACKGROUND: For many years, basic and clinical researchers have taken advantage of the analytical sensitivity and specificity afforded by mass spectrometry in the measurement of proteins. Clinical laboratories are now beginning to deploy these work flows as well. For assays that use proteolysis to generate peptides for protein quantification and characterization, synthetic stable isotope-labeled internal standard peptides are of central importance. No general recommendations are currently available surrounding the use of peptides in protein mass spectrometric assays. CONTENT: The Clinical Proteomic Tumor Analysis Consortium of the National Cancer Institute has collaborated with clinical laboratorians, peptide manufacturers, metrologists, representatives of the pharmaceutical industry, and other professionals to develop a consensus set of recommendations for peptide procurement, characterization, storage, and handling, as well as approaches to the interpretation of the data generated by mass spectrometric protein assays. Additionally, the importance of carefully characterized reference materials-in particular, peptide standards for the improved concordance of amino acid analysis methods across the industry-is highlighted. The alignment of practices around the use of peptides and the transparency of sample preparation protocols should allow for the harmonization of peptide and protein quantification in research and clinical care.
Assuntos
Técnicas de Laboratório Clínico , Espectrometria de Massas , Peptídeos/análise , Proteômica , Manejo de Espécimes , Guias como Assunto , Humanos , Peptídeos/isolamento & purificação , PesquisadoresRESUMO
The selective removal of dysfunctional mitochondria, a process termed mitophagy, is critical for cellular health and impairments have been linked to aging, Parkinson disease, and other neurodegenerative conditions. A central mitophagy pathway is orchestrated by the ubiquitin (Ub) kinase PINK1 together with the E3 Ub ligase PRKN/Parkin. The decoration of damaged mitochondrial domains with phosphorylated Ub (p-S65-Ub) mediates their elimination though the autophagy system. As such p-S65-Ub has emerged as a highly specific and quantitative marker of mitochondrial damage with significant disease relevance. Existing p-S65-Ub antibodies have been successfully employed as research tools in a range of applications including western blot, immunocytochemistry, immunohistochemistry, and enzyme-linked immunosorbent assay. However, physiological levels of p-S65-Ub in the absence of exogenous stress are very low, therefore difficult to detect and require reliable and ultrasensitive methods. Here we generated and characterized a collection of novel recombinant, rabbit monoclonal p-S65-Ub antibodies with high specificity and affinity in certain applications that allow the field to better understand the molecular mechanisms and disease relevance of PINK1-PRKN signaling. These antibodies may also serve as novel diagnostic or prognostic tools to monitor mitochondrial damage in various clinical and pathological specimens.Abbreviations: AD: Alzheimer disease; CCCP: carbonyl cyanide 3-chlorophenylhydrazone; ELISA: enzyme-linked immunosorbent assay; HEK293E cell: human embryonic kidney E cell; ICC: immunocytochemistry; IHC: immunohistochemistry: KO: knockout; LoB: limit of blank; LoD: limit of detection; LoQ: limit of quantification; MEF: mouse embryonic fibroblast; MSD: Meso Scale Discovery; n.s.: non-significant; nonTg: non-transgenic; PBMC: peripheral blood mononuclear cell; PD: Parkinson disease; p-S65-PRKN: phosphorylated PRKN at serine 65; p-S65-Ub: phosphorylated Ub at serine 65; Ub: ubiquitin; WT: wild-type.
Assuntos
Proteínas Quinases , Transdução de Sinais , Ubiquitina-Proteína Ligases , Ubiquitina , Humanos , Proteínas Quinases/metabolismo , Animais , Ubiquitina/metabolismo , Fosforilação , Ubiquitina-Proteína Ligases/metabolismo , Mitocôndrias/metabolismo , Camundongos , Coelhos , Mitofagia , Células HEK293 , Anticorpos , Anticorpos MonoclonaisRESUMO
The selective removal of dysfunctional mitochondria, a process termed mitophagy, is critical for cellular health and impairments have been linked to aging, Parkinson disease, and other neurodegenerative conditions. A central mitophagy pathway is orchestrated by the ubiquitin (Ub) kinase PINK1 together with the E3 Ub ligase PRKN/Parkin. The decoration of damaged mitochondrial domains with phosphorylated Ub (p-S65-Ub) mediates their elimination though the autophagy system. As such p-S65-Ub has emerged as a highly specific and quantitative marker of mitochondrial damage with significant disease relevance. Existing p-S65-Ub antibodies have been successfully employed as research tools in a range of applications including western blot, immunocytochemistry, immunohistochemistry, and ELISA. However, physiological levels of p-S65-Ub in the absence of exogenous stress are very low, therefore difficult to detect and require reliable and ultrasensitive methods. Here we generated and characterized a collection of novel recombinant, rabbit monoclonal p-S65-Ub antibodies with high specificity and affinity in certain applications that allow the field to better understand the molecular mechanisms and disease relevance of PINK1-PRKN signaling. These antibodies may also serve as novel diagnostic or prognostic tools to monitor mitochondrial damage in various clinical and pathological specimens.
RESUMO
The F(1)F(0)-ATP synthase provides approximately 90% of cardiac ATP, yet little is known regarding its regulation under normal or pathological conditions. Previously, we demonstrated that protein kinase Cdelta (PKCdelta) inhibits F(1)F(0) activity via an interaction with the "d" subunit of F(1)F(0)-ATP synthase (dF(1)F(0)) in neonatal cardiac myocytes (NCMs) (Nguyen, T., Ogbi, M., and Johnson, J. A. (2008) J. Biol. Chem. 283, 29831-29840). We have now identified a dF(1)F(0)-derived peptide (NH(2)-(2)AGRKLALKTIDWVSF(16)-COOH) that inhibits PKCdelta binding to dF(1)F(0) in overlay assays. We have also identified a second dF(1)F(0)-derived peptide (NH(2)-(111)RVREYEKQLEKIKNMI(126)-COOH) that facilitates PKCdelta binding to dF(1)F(0). Incubation of NCMs with versions of these peptides containing HIV-Tat protein transduction and mammalian mitochondrial targeting sequences resulted in their delivery into mitochondria. Preincubation of NCMs, with 10 nm extracellular concentrations of the mitochondrially targeted PKCdelta-dF(1)F(0) interaction inhibitor, decreased 100 nm 4beta-phorbol 12-myristate 13-acetate (4beta-PMA)-induced co-immunoprecipitation of PKCdelta with dF(1)F(0) by 50 +/- 15% and abolished the 30 nm 4beta-PMA-induced inhibition of F(1)F(0)-ATPase activity. A scrambled sequence (inactive) peptide, which contained HIV-Tat and mitochondrial targeting sequences, was without effect. In contrast, the cell-permeable, mitochondrially targeted PKCdelta-dF(1)F(0) facilitator peptide by itself induced the PKCdelta-dF(1)F(0) co-immunoprecipitation and inhibited F(1)F(0)-ATPase activity. In in vitro PKC add-back experiments, the PKCdelta-F(1)F(0) inhibitor blocked PKCdelta-mediated inhibition of F(1)F(0)-ATPase activity, whereas the facilitator induced inhibition. We have developed the first cell-permeable, mitochondrially targeted modulators of the PKCdelta-dF(1)F(0) interaction in NCMs. These novel peptides will improve our understanding of cardiac F(1)F(0) regulation and may have potential as therapeutics to attenuate cardiac injury.
Assuntos
Permeabilidade da Membrana Celular/efeitos dos fármacos , Desenho de Fármacos , Mitocôndrias/metabolismo , ATPases Mitocondriais Próton-Translocadoras/metabolismo , Miócitos Cardíacos/enzimologia , Peptídeos/farmacologia , Proteína Quinase C-delta/metabolismo , Sequência de Aminoácidos , Animais , Animais Recém-Nascidos , Ensaios Enzimáticos , Imunoprecipitação , Mitocôndrias/efeitos dos fármacos , ATPases Mitocondriais Próton-Translocadoras/antagonistas & inibidores , ATPases Mitocondriais Próton-Translocadoras/química , Dados de Sequência Molecular , Miócitos Cardíacos/efeitos dos fármacos , Peptídeos/síntese química , Peptídeos/química , Ligação Proteica/efeitos dos fármacos , Proteína Quinase C-delta/química , Sinais Direcionadores de Proteínas , Subunidades Proteicas/antagonistas & inibidores , Subunidades Proteicas/química , Subunidades Proteicas/metabolismo , Ratos , Ratos Sprague-Dawley , Acetato de Tetradecanoilforbol/farmacologia , Produtos do Gene tat do Vírus da Imunodeficiência Humana/farmacologiaRESUMO
There are many uses for antibodies labeled with metal ions. Most of these methods involve first attaching a metal chelator to the antibody molecule. This is achieved using standard cross-linking chemistry and then adding the desired metal at appropriate concentration and pH. The method described here outlines a basic procedure for creating a lanthanide conjugate. Lanthanide conjugates are used for proximity assays, as MRI contrast agents, or for mass cytometry experiments. Different metals and chelators can be substituted, but the basic procedures are similar.
Assuntos
Anticorpos/química , Quelantes/química , Európio/química , Coloração e Rotulagem/métodos , Clorofórmio/química , Reagentes de Ligações Cruzadas/química , Concentração de Íons de Hidrogênio , Metais/químicaRESUMO
Colloidal gold-antibody conjugates are easy to prepare and are an excellent choice for microscopic applications. Colloidal gold is an aqueous suspension of nanometer-sized particles of gold. Typically, chloroauric acid, HAuCl4, is reduced with dilute solutions of sodium citrate, as described here. This will cause the gold to form small aggregates that will associate with proteins. Gold particles of specific sizes can be isolated and differentiated microscopically, allowing these particles to be used for multiple-label experiments. Colloidal gold-labeled antibodies are widely used in electron microscopy (EM), and can be used for light microscopy but require additional steps (silver enhancement).
Assuntos
Anticorpos/química , Coloide de Ouro/química , Coloração e Rotulagem/métodos , Animais , Anticorpos/ultraestrutura , Bovinos , Concentração de Íons de Hidrogênio , Microscopia Eletrônica , Soroalbumina Bovina/químicaRESUMO
Labeling antibodies with biotin (biotinylation) is a useful and simple technique. Biotin's small size (244 Da) usually has little effect on the biological activity of the protein target. The most common way to biotinylate an antibody is to cross-link a biotin succinimidyl ester to a primary amine. There are many commercially available types of biotin analogs that can be used for labeling. They vary in reactive group chemistry as well as spacer length. For example, a common analog used for biotinylation is the succinimidyl ester of biotin with an aminohexanoic acid spacer (Long Chain or LC-Biotin), utilized here. A PEG spacer of varying length can also be used.
Assuntos
Anticorpos/metabolismo , Biotina/metabolismo , Coloração e Rotulagem/métodos , Succinimidas/metabolismoRESUMO
There are several techniques for biotinylating antibodies, from the most basic (using NHS-ester biotin to label primary amines) to more complex experiments (modifying sulfhydryls and carbohydrates). Biotinylation of free sulfhydryls, described here, can be effectively mediated using haloacetyl biotin derivatives. To modify an antibody using this reagent, sulfhydryls must be available. Digestion of antibodies by the enzyme pepsin produces F(ab')2 fragments, which can be separated by mild reduction into two sulfhydryl-containing, univalent Fab' fragments. Alternatively, thiol groups can be added by modifying amines with an appropriate cross-linker.
Assuntos
Anticorpos/metabolismo , Biotina/metabolismo , Iodoacetamida/química , Polietilenoglicóis/química , Coloração e Rotulagem/métodos , BiotinilaçãoRESUMO
Hydrazide derivatives are useful for biotinylating antibodies at oxidized carbohydrate groups. This protocol uses oxidation conditions that will convert most if not all possible hydroxyl sites to aldehydes. Each antibody may require different oxidation conditions to optimize labeling. Some monoclonal antibodies may be deficient in glycosylation, making this method suboptimal. Other labeling reagents (fluorophores) are also available as hydrazides. Hetero-bifunctional cross-linkers (e.g., ß-maleimidopropionic acid hydrazide [BMPH]) are also available to cross-link other targets to carbonyls.
Assuntos
Anticorpos/metabolismo , Biotina/análogos & derivados , Coloração e Rotulagem/métodos , Biotina/química , BiotinilaçãoRESUMO
Iodination, a chemical or enzymatic incorporation of 125I to specific amino acid side chains, is a commonly used method for labeling antibodies with radioisotopes. Commercially available products make iodination of antibodies a simple and quick process. One example, used here and available at Pierce, is the "Iodination bead," or N-chloro-benzenesulfonamide immobilized on nonporous, polystyrene beads.
Assuntos
Anticorpos/química , Radioisótopos do Iodo/química , Marcação por Isótopo/métodos , Microesferas , Poliestirenos/química , Sulfonamidas/química , Halogenação , Oxirredução , BenzenossulfonamidasRESUMO
Many antibody labeling procedures call for a desalting or purification step requiring size-exclusion chromatography (SEC). The method outlined here contains information needed to desalt an antibody conjugate. Similar procedures would be used for ion-exchange chromatography using a gradient of increasing ionic strength. Resins can be purchased in bulk (as in this protocol), or commercially available columns are available.
Assuntos
Anticorpos/química , Anticorpos/isolamento & purificação , Cromatografia em Gel/métodos , Coloração e Rotulagem/métodos , Anticorpos Monoclonais/química , Anticorpos Monoclonais/isolamento & purificação , Cromatografia por Troca Iônica/métodos , Dextranos/química , Resinas Sintéticas/químicaRESUMO
This introduction outlines general strategies for labeling proteins, with an emphasis on methods that are used primarily for labeling antibodies. It covers the specific site of modification, cross-linker options, types of labels, and postlabeling cleanup methodology, along with the advantages and disadvantages of each method. In general, polyclonal antibodies are more versatile and resistant to activity loss than are monoclonal antibodies. Greater care must be taken when labeling monoclonal antibodies to ensure a quality conjugate. The methods outlined here can be adapted for a variety of labels including multiple labels on the same immunoglobulin. The most important consideration when undertaking an antibody labeling experiment is to maintain the activity of the antibody. This is an empirical process and will often require additional experiments to optimize the label of a particular antibody. When successful, these reagents are very useful and adaptable biomolecules. This introduction provides the reader with methods and options for producing a variety of labeled immunological tools.
Assuntos
Anticorpos/química , Reagentes de Ligações Cruzadas/química , Imunoconjugados/química , Coloração e Rotulagem/métodos , Doença de Alzheimer/diagnóstico , Doença de Alzheimer/imunologia , Peptídeos beta-Amiloides/química , Peptídeos beta-Amiloides/imunologia , Biotina/química , Carboidratos/química , Cisteína/química , Coloide de Ouro/química , Humanos , Imunoconjugados/imunologia , Marcação por Isótopo/métodos , Proteínas Luminescentes/química , Compostos de Sulfidrila/químicaRESUMO
N-Hydroxysuccinimide (NHS)-ester derivatives are among the most commonly used reagents for labeling proteins. The method described here can be adapted to use practically any NHS fluorophore. Generally, a fluorophore is covalently bound to a macromolecule such as an antibody and acts as a reporter molecule used to measure the presence of the macromolecule. These fluorescently labeled bioactive reagents are suitable for use in immunofluorescence, flow cytometry, and numerous other biological applications. There are several widely used dyes available in convenient formats. This protocol can be used with any amine-reactive (e.g., PFP, isothiocyanate) fluorophore derivative.
Assuntos
Anticorpos/química , Fluoresceína/química , Corantes Fluorescentes/química , Succinimidas/química , Citometria de FluxoRESUMO
Fluorophore-maleimide derivatives are effective for labeling sulfhydryl-containing molecules. Maleimide groups react with free thiols at pH 6.5-7.5 forming a covalent bond. Reducing agents should be avoided during the conjugation step. This protocol uses the cross-linker N-succinimidyl S-acetylthioacetate (SATA) to introduce thiol groups on the antibody while maintaining the divalent nature of the antibody. Alternatively, the antibody can be digested and reduced to monovalent Fab fragments, which can then be labeled directly with maleimido derivatives.
Assuntos
Anticorpos/química , Corantes Fluorescentes/química , Maleimidas/química , Fragmentos Fab das Imunoglobulinas/químicaRESUMO
Because IgG from most species (other than rodents) tends to have an isoelectric point around neutral, two approaches can be used when separating IgG using diethylaminoethyl (DEAE) resins. When serum containing antibodies is applied to DEAE at a slightly acidic pH, the IgG flows through the column while most other serum proteins bind to the DEAE. This method is best performed using a batch method. The DEAE beads can be kept in a disposable syringe containing a polypropylene frit, a glass reactor containing a coarse-sintered glass frit, or other suitable vessel. If the antibody solution is adjusted to a basic pH of 8-8.5, then IgG binds to the DEAE resin. After washing the column, the antibody is eluted by adding a buffer of increasing ionic strength to the column. Prepacked columns of many sizes are available for the isolation of antibodies by DEAE chromatography. Alternatively, DEAE medium can be swelled or prepped according to the manufacturer's instructions and a column can be poured when needed.
Assuntos
Cromatografia por Troca Iônica/métodos , Etanolaminas/metabolismo , Imunoglobulina G/isolamento & purificação , Etanolaminas/química , Concentração de Íons de Hidrogênio , Ligação Proteica , Soro/químicaRESUMO
Protein A and Protein G are immunoglobulin-binding proteins expressed in Staphylococcus aureus and Streptococcus sp., respectively, that have been adapted for use in purifying large amounts of IgG. They are available covalently attached to affinity resins such as 4% cross-linked agarose, making them suitable for low-pressure antibody isolation. Protein A is not recommended for the isolation of mouse mAbs because it lacks affinity for mouse IgG1, or for the isolation of antibodies from sheep, goat, chicken, hamster, or rat. IgGs from most species bind to Protein G at near physiological pH and ionic strength with a higher affinity than IgG binding to Protein A. Therefore, the pH required to dissociate bound IgG is lower, resulting in the loss of activity for some antibodies. If this is observed, Protein A may be an alternative if the IgG from the species being isolated can be purified using Protein A. Neither Protein A nor Protein G can be used for the isolation of chicken antibodies.
Assuntos
Proteínas de Bactérias/metabolismo , Cromatografia de Afinidade/métodos , Imunoglobulina G/isolamento & purificação , Imunoglobulina G/metabolismo , Proteína Estafilocócica A/metabolismo , Concentração de Íons de Hidrogênio , Concentração Osmolar , Ligação ProteicaRESUMO
Thiol-reactive linkers, such as iodoacetyl or maleimide, bound to cross-linked agarose are used to attach cysteine-containing peptides covalently to this resin for use in affinity-purification protocols. It is critical to confirm that the peptide contains a reduced cysteine so that the thiol is available for conjugation to the thiol-reactive linker. The column should be sized appropriately for the amount of peptide to be used and the volume of serum to be processed. Excess binding sites on the column must be blocked with free cysteine before use.
Assuntos
Anticorpos/isolamento & purificação , Cromatografia de Afinidade/métodos , Peptídeos/química , Compostos de Sulfidrila/químicaRESUMO
This protocol describes antibody purification using a peptide affinity column. Peptides can be designed that use naturally occurring cysteines within the protein target's primary sequence, or a cysteine can be added to either end of the peptide to provide free thiols for attachment. The peptides can then be covalently attached to resins bearing thiol-reactive linkers. The most commonly used thiol-reactive moieties are iodoacetyl and maleimide, both of which react selectively with peptides containing cysteine thiols. Although gravity can be used to cycle the antibody solution (e.g., serum) over the column (it is recommended that the antibody be cycled multiple times to obtain maximal yield), the use of a pump to apply the serum to the column in a continuous flow manner improves the yield of antibody. Similarly, washing the column after application of the antibody without and with 0.5 m NaCl should be performed with at least 20 column volumes.
Assuntos
Anticorpos/isolamento & purificação , Cromatografia de Afinidade/métodos , Peptídeos/química , Compostos de Sulfidrila/químicaRESUMO
Antibodies have become a common and necessary tool in biochemistry, cell biology, and immunology laboratories. There are many different types of antibodies and antibody fragments being used for a myriad of applications. As a result, many different purification protocols have been developed to obtain antibodies of the desired specificity and sensitivity. Here, we introduce the options for small- to large-scale antibody purification and isolation of polyclonal and monoclonal antibodies (and fragments generated from these) that target-specific proteins, as well as methods to properly purify antibodies that recognize posttranslational modifications. Optimal conditions for the long-term storage of antibodies are also discussed.
Assuntos
Anticorpos/isolamento & purificação , Animais , Precipitação Química , Cromatografia de Afinidade , Imunoglobulina G/isolamento & purificação , Troca IônicaRESUMO
Antibodies conjugated with horseradish peroxidase (HRP) are one of the most widely used bioreagents in the biological sciences. This protocol is a basic method for adding HRP to a thiolated antibody and can be adapted for use with different cross-linkers. Conjugation methods usually focus on linking through the lysines on HRP because there are only six of them and their modification does not adversely affect enzyme activity.