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Multiplexed complexome profiling using tandem mass tags. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148448. [PMID: 34015258 DOI: 10.1016/j.bbabio.2021.148448] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 05/05/2021] [Accepted: 05/13/2021] [Indexed: 12/28/2022]
Abstract
Complexome profiling is a rapidly spreading, powerful technique to gain insight into the nature of protein complexes. It identifies and quantifies protein complexes separated into multiple fractions of increasing molecular mass using mass spectrometry-based, label-free bottom-up proteomics. Complexome profiling enables a sophisticated and thorough characterization of the composition, molecular mass, assembly, and interactions of protein complexes. However, in practice, its application is limited by the large number of samples it generates and the related time of mass spectrometry analyses. Here, we report an improved process workflow that implements tandem mass tags for multiplexing complexome profiling. This workflow substantially reduces the number of samples and measuring time without compromising protein identification or quantification reliability. In profiles from mitochondrial fractions of cells recovering from chloramphenicol treatment, tandem mass tags-multiplexed complexome profiling exhibited migration patterns of mature ATP synthase (complex V) and assembly intermediates that were consistent in composition and abundance with profiles obtained by the label-free approach. Reporter ion quantifications of proteins and complexes unaffected by the chloramphenicol treatment presented less variation in comparison to the label-free method. Incorporation of tandem mass tags enabled an efficient and robust complexome profiling analysis and may foster broader application for protein complex profiling in biomedical research and diagnostics.
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2
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Harb F, Tinland B. Toward Electrophoretic Separation of Membrane Proteins in Supported n-Bilayers. ACS OMEGA 2020; 5:27741-27748. [PMID: 33163756 PMCID: PMC7643068 DOI: 10.1021/acsomega.0c01196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 09/28/2020] [Indexed: 06/11/2023]
Abstract
Membrane proteins are key constituents of the proteome of cells but are poorly characterized, mainly because they are difficult to solubilize. Proteome analysis involves separating proteins as a preliminary step toward their characterization. Currently, the most common method is "solubilizing" them with sophisticated detergent and lipid mixtures for later separation via, for instance, sodium dodecyl sulfate polyacrylamide gel electrophoresis. However, this later step induces loss of 3D structure (denaturation). Migration in a medium that mimics the cell membrane should therefore be more appropriate. Here, we present a successful electrophoretic separation of a mixture first of two and then of three different membrane objects in supported n-bilayers. These "objects" are composed of membrane proteins sulfide quinone reductase and α-hemolysin. Sulfide quinone reductase forms an object from three monomers together and self-inserts into the upper leaflet. α-Hemolysin inserts as a spanning heptamer into a bilayer or can build stable dimers of α-hemolysin heptamers under certain conditions. By appropriately adjusting the pH, it proved possible to move them in different ways. This work holds promise for separating membrane proteins without losing their 3D structure, thus their bioactivity, within a lipidic environment that is closer to physiological conditions and for building drug/diagnostic platforms.
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Affiliation(s)
- Frédéric
F. Harb
- Department
of Biology; Faculty of Sciences − Section II, Lebanese University, Beirut 90656, Lebanon
| | - Bernard Tinland
- Aix-Marseille
Université, CNRS, CINaM UMR 7325, Marseille 13288, France
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Meisrimler CN, Schwendke A, Lüthje S. Two-dimensional phos-tag zymograms for tracing phosphoproteins by activity in-gel staining. FRONTIERS IN PLANT SCIENCE 2015; 6:230. [PMID: 25926840 PMCID: PMC4396385 DOI: 10.3389/fpls.2015.00230] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 03/23/2015] [Indexed: 06/04/2023]
Abstract
Protein phosphorylation is one of the most common post-translational modifications regulating many cellular processes. The phos-tag technology was combined with two-dimensional zymograms, which consisted of non-reducing IEF PAGE or NEPHGE in the first dimension and high resolution clear native electrophoresis (hrCNE) in the second dimension. The combination of these electrophoresis methods was mild enough to accomplish in-gel activity staining for Fe(III)-reductases by NADH/Fe(III)-citrate/ferrozine, 3,3'-Diaminobenzidine/H2O2 or TMB/H2O2 in the second dimension. The phos-tag zymograms can be used to investigate phosphorylation-dependent changes in enzyme activity. Phos-tag zymograms can be combined with further downstream analysis like mass spectrometry. Non-reducing IEF will resolve proteins with a pI of 3-10, whereas non-reducing NEPHGE finds application for alkaline proteins with a pI higher than eight. Advantages and disadvantages of these new methods will be discussed in detail.
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Affiliation(s)
- Claudia-Nicole Meisrimler
- Plant Physiology, Biocenter Klein Flottbek and Botanical Garden, University of HamburgHamburg, Germany
- Laboratoire de Biologie du Développement des Plantes, Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Biologie, Environnementale et de BiotechnologieSaint-Paul-lez-Durance, France
| | - Alexandra Schwendke
- Plant Physiology, Biocenter Klein Flottbek and Botanical Garden, University of HamburgHamburg, Germany
| | - Sabine Lüthje
- Plant Physiology, Biocenter Klein Flottbek and Botanical Garden, University of HamburgHamburg, Germany
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4
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Posttranslational Modifications. Atherosclerosis 2015. [DOI: 10.1002/9781118828533.ch34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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5
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A new enabling proteomics methodology to investigate membrane associated proteins from parasitic nematodes: case study using ivermectin resistant and ivermectin susceptible isolates of Caenorhabditis elegans and Haemonchus contortus. Vet Parasitol 2014; 207:266-75. [PMID: 25537855 DOI: 10.1016/j.vetpar.2014.12.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 11/23/2014] [Accepted: 12/06/2014] [Indexed: 01/06/2023]
Abstract
The mechanisms involved in anthelmintic resistance (AR) are complex but a greater understanding of AR management is essential for effective and sustainable control of parasitic helminth worms in livestock. Current tests to measure AR are time consuming and can be technically problematic, gold standard diagnostics are therefore urgently required to assist in combatting the threat from drug resistant parasites. For anthelmintics such as ivermectin (IVM), target proteins may be present in the cellular membrane. As proteins usually act in complexes and not in isolation, AR may develop and be measurable in the target associated proteins present in the parasite membrane. The model nematode Caenorhabditis elegans was used to develop a sub-proteomic assay to measure protein expression differences, between IVM resistant and IVM susceptible isolates in the presence and absence of drug challenge. Evaluation of detergents including CHAPS, ASB-14, C7BzO, Triton ×100 and TBP (tributyl phosphine) determined optimal conditions for the resolution of membrane proteins in Two Dimensional Gel Electrophoresis (2DE). These sub-proteomic methodologies were then translated and evaluated using IVM-susceptible and IVM-resistant Haemonchus contortus; a pathogenic blood feeding parasitic nematode which is of global importance in livestock health, welfare and productivity. We have demonstrated the successful resolution of membrane associated proteins from both C. elegans and H. contortus isolates, using a combination of CHAPS and the zwitterionic amphiphilic surfactant ASB-14 to further support the detection of markers for AR.
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Rath A, Deber CM. Correction factors for membrane protein molecular weight readouts on sodium dodecyl sulfate–polyacrylamide gel electrophoresis. Anal Biochem 2013. [DOI: 10.1016/j.ab.2012.11.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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7
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Sapp E, Valencia A, Li X, Aronin N, Kegel KB, Vonsattel JP, Young AB, Wexler N, DiFiglia M. Native mutant huntingtin in human brain: evidence for prevalence of full-length monomer. J Biol Chem 2012; 287:13487-99. [PMID: 22375012 DOI: 10.1074/jbc.m111.286609] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Huntington disease (HD) is caused by polyglutamine expansion in the N terminus of huntingtin (htt). Analysis of human postmortem brain lysates by SDS-PAGE and Western blot reveals htt as full-length and fragmented. Here we used Blue Native PAGE (BNP) and Western blots to study native htt in human postmortem brain. Antisera against htt detected a single band broadly migrating at 575-850 kDa in control brain and at 650-885 kDa in heterozygous and Venezuelan homozygous HD brains. Anti-polyglutamine antisera detected full-length mutant htt in HD brain. There was little htt cleavage even if lysates were pretreated with trypsin, indicating a property of native htt to resist protease cleavage. A soluble mutant htt fragment of about 180 kDa was detected with anti-htt antibody Ab1 (htt-(1-17)) and increased when lysates were treated with denaturants (SDS, 8 M urea, DTT, or trypsin) before BNP. Wild-type htt was more resistant to denaturants. Based on migration of in vitro translated htt fragments, the 180-kDa segment terminated ≈htt 670-880 amino acids. If second dimension SDS-PAGE followed BNP, the 180-kDa mutant htt was absent, and 43-50 kDa htt fragments appeared. Brain lysates from two HD mouse models expressed native full-length htt; a mutant fragment formed if lysates were pretreated with 8 M urea + DTT. Native full-length mutant htt in embryonic HD(140Q/140Q) mouse primary neurons was intact during cell death and when cell lysates were exposed to denaturants before BNP. Thus, native mutant htt occurs in brain and primary neurons as a soluble full-length monomer.
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Affiliation(s)
- Ellen Sapp
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts 02129, USA
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Kota U, Goshe MB. Advances in qualitative and quantitative plant membrane proteomics. PHYTOCHEMISTRY 2011; 72:1040-60. [PMID: 21367437 DOI: 10.1016/j.phytochem.2011.01.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Revised: 01/13/2011] [Accepted: 01/19/2011] [Indexed: 05/08/2023]
Abstract
The membrane proteome consists of integral and membrane-associated proteins that are involved in various physiological and biochemical functions critical for cellular function. It is also dynamic in nature, where many proteins are only expressed during certain developmental stages or in response to environmental stress. These proteins can undergo post-translational modifications in response to these different conditions, allowing them to transiently associate with the membrane or other membrane proteins. Along with their increased size, hydrophobicity, and the additional organelle and cellular features of plant cells relative to mammalian systems, the characterization of the plant membrane proteome presents unique challenges for effective qualitative and quantitative analysis using mass spectrometry (MS) analysis. Here, we present the latest advancements developed for the isolation and fractionation of plant organelles and their membrane components amenable to MS analysis. Separations of membrane proteins from these enriched preparations that have proven effective are discussed for both gel- and liquid chromatography-based MS analysis. In this context, quantitative membrane proteomic analyses using both isotope-coded and label-free approaches are presented and reveal the potential to establish a wider-biological interpretation of the function of plant membrane proteins that will ultimately lead to a more comprehensive understanding of plant physiology and their response mechanisms.
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Affiliation(s)
- Uma Kota
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695-7622, USA
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Agnetti G, Husberg C, Van Eyk JE. Divide and conquer: the application of organelle proteomics to heart failure. Circ Res 2011; 108:512-26. [PMID: 21335433 PMCID: PMC3936251 DOI: 10.1161/circresaha.110.226910] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Accepted: 11/19/2010] [Indexed: 01/16/2023]
Abstract
Chronic heart failure is a worldwide cause of mortality and morbidity and is the final outcome of a number of different etiologies. This reflects both the complexity of the disease and our incomplete understanding of its underlying molecular mechanisms. One experimental approach to address this is to study subcellular organelles and how their functions are activated and synchronized under physiological and pathological conditions. In this review, we discuss the application of proteomic technologies to organelles and how this has deepened our perception of the cellular proteome and its alterations with heart failure. The use of proteomics to monitor protein quantity and posttranslational modifications has revealed a highly intricate and sophisticated level of protein regulation. Posttranslational modifications have the potential to regulate organelle function and interplay most likely by targeting both structural and signaling proteins throughout the cell, ultimately coordinating their responses. The potentials and limitations of existing proteomic technologies are also discussed emphasizing that the development of novel methods will enhance our ability to further investigate organelles and decode intracellular communication.
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Affiliation(s)
- Giulio Agnetti
- The Johns Hopkins Bayview Proteomics Center, Johns Hopkins University, Baltimore, US
- INRC, Dept. of Biochemistry, University of Bologna, Italy
| | - Cathrine Husberg
- The Johns Hopkins Bayview Proteomics Center, Johns Hopkins University, Baltimore, US
- Institute for Experimental Medical Research, Oslo University Hospital - Ullevaal, Norway
| | - Jennifer E. Van Eyk
- The Johns Hopkins Bayview Proteomics Center, Johns Hopkins University, Baltimore, US
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Thangthaeng N, Sumien N, Forster MJ, Shah RA, Yan LJ. Nongradient blue native gel analysis of serum proteins and in-gel detection of serum esterase activities. J Chromatogr B Analyt Technol Biomed Life Sci 2011; 879:386-94. [PMID: 21237726 PMCID: PMC3034814 DOI: 10.1016/j.jchromb.2010.12.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 12/22/2010] [Accepted: 12/23/2010] [Indexed: 12/21/2022]
Abstract
The objective of the present study was to analyze serum protein complexes and detect serum esterase activities using nongradient blue native polyacrylamide gel electrophoresis (BN-PAGE). For analysis of potential protein complexes, serum from rat was used. Results demonstrate that a total of 8 gel bands could be clearly distinguished after Coomassie blue staining, and serum albumin could be isolated nearly as a pure protein. Moreover, proteins in these bands were identified by electrospray mass spectrometry and low-energy collision induced dissociation (CID)-MS/MS peptide sequencing and the existence of serum dihydrolipoamide dehydrogenase (DLDH) was confirmed. For studies of in-gel detection of esterase activities, serum from rat, mouse, and human was used. In-gel staining of esterase activity was achieved by the use of either α-naphthylacetate or β-naphthylacetate in the presence of Fast blue BB salt. There were three bands exhibiting esterase activities in the serum of both rat and mouse. In contrast, there was only one band showing esterase activity staining in the human serum. When serum samples were treated with varying concentrations of urea, esterase activity staining was abolished for all the bands except the one containing esterase 1 (Es1) protein that is known to be a single polypeptide enzyme, indicating that majority of these esterases were protein complexes or multimeric proteins. We also identified the human serum esterase as butyrylcholinesterase following isolation and partial purification using ammonium sulfate fractioning and ion exchange column chromatographies. Where applicable, demonstrations of the gel-based method for measuring serum esterase activities under physiological or pathophysiological conditions were illustrated. Results of the present study demonstrate that nongradient BN-PAGE can serve as a feasible analytical tool for proteomic and enzymatic analysis of serum proteins.
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Affiliation(s)
- Nopporn Thangthaeng
- Department of Pharmacology and Neuroscience and Institute for Aging and Alzheimer’s Disease Research, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Nathalie Sumien
- Department of Pharmacology and Neuroscience and Institute for Aging and Alzheimer’s Disease Research, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Michael J. Forster
- Department of Pharmacology and Neuroscience and Institute for Aging and Alzheimer’s Disease Research, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Ruchir A. Shah
- Department of Pharmacology and Neuroscience and Institute for Aging and Alzheimer’s Disease Research, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Liang-Jun Yan
- Department of Pharmacology and Neuroscience and Institute for Aging and Alzheimer’s Disease Research, University of North Texas Health Science Center, Fort Worth, TX, USA
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Fanarraga ML, Carranza G, Castaño R, Nolasco S, Avila J, Zabala JC. Nondenaturing electrophoresis as a tool to investigate tubulin complexes. Methods Cell Biol 2010; 95:59-75. [PMID: 20466130 DOI: 10.1016/s0091-679x(10)95005-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
A protein molecule may exist as a monomer, homo-oligomer, or hetero-oligomer in a multiprotein complex. One-dimensional (1-D) native electrophoresis has long been used to characterize tubulins and their complexes. In this chapter, we describe the simplest way to identify the state of aggregation of commercial or homemade tubulins for further studies based on 1-D electrophoresis under nondenaturing conditions. We present a series of detailed protocols that can be used to analyze the maturation of alpha- and beta-tubulins and to identify the complexes formed during the folding and dimerization pathway as well as their stability.
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Affiliation(s)
- Mónica López Fanarraga
- Departamento de Biología Molecular, Facultad de Medicina, IFIMAV-Universidad de Cantabria, 39011 Santander, Spain
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