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Abstract
In-gel digestion of protein spots derived from two-dimensional gels and their subsequent identification by mass spectrometry is involved in a multitude of mass spectrometry-driven proteomic experiments, including fluorescence two-dimensional difference gel electrophoresis (2D-DIGE). This type of proteomic methodology has been involved in the establishment of comparative proteome maps and in the identification of differentially expressed proteins and their isoforms in health and disease. Most in-gel digestion protocols follow a number of common steps including excision of the protein spots of interest, destaining, reduction and alkylation (for silver-stained gels), and dehydration and overnight digestion with the proteolytic enzyme of choice. While trypsin has been a mainstay of peptide digestion for many years, it does have its shortcomings, particularly related to incomplete peptide digestion, and this has led to a rise in popularity for other proteolytic enzymes either used alone or in combination. This chapter discusses the alternative enzymes available and describes the process of in-gel digestion using the enzyme trypsin.
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Affiliation(s)
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
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2
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Chan H, Chen L, Chiu H, Chen Y. Membrane proteomic profiling enhances drug target detection. J CHIN CHEM SOC-TAIP 2022. [DOI: 10.1002/jccs.202200265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Hsin‐Ju Chan
- Institute of Chemistry, Academia Sinica Taipei Taiwan
- Department of Chemistry National Taiwan University Taipei Taiwan
| | - Li‐Yu Chen
- Institute of Chemistry, Academia Sinica Taipei Taiwan
- Department of Chemistry National Taiwan University Taipei Taiwan
| | - Huan‐Chi Chiu
- Institute of Chemistry, Academia Sinica Taipei Taiwan
- Department of Chemistry National Taiwan University Taipei Taiwan
| | - Yu‐Ju Chen
- Institute of Chemistry, Academia Sinica Taipei Taiwan
- Department of Chemistry National Taiwan University Taipei Taiwan
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3
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Masuda T, Inamori Y, Furukawa A, Yamahiro M, Momosaki K, Chang CH, Kobayashi D, Ohguchi H, Kawano Y, Ito S, Araki N, Ong SE, Ohtsuki S. Water Droplet-in-Oil Digestion Method for Single-Cell Proteomics. Anal Chem 2022; 94:10329-10336. [PMID: 35817413 PMCID: PMC9330287 DOI: 10.1021/acs.analchem.1c05487] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Recent advances in
single-cell proteomics highlight the promise
of sensitive analyses in limited cell populations. However, technical
challenges remain for sample recovery, throughput, and versatility.
Here, we first report a water droplet-in-oil digestion (WinO) method
based on carboxyl-coated beads and phase transfer surfactants for
proteomic analysis using limited sample amounts. This method was developed
to minimize the contact area between the sample solution and the container
to reduce the loss of proteins and peptides by adsorption. This method
increased protein and peptide recovery 10-fold. The proteome profiles
obtained from 100 cells using the WinO method highly correlated with
those from 10,000 cells using the in-solution digestion method. We
successfully applied the WinO method to single-cell proteomics and
quantified 462 proteins. Using the WinO method, samples can be easily
prepared in a multi-well plate, making it a widely applicable and
suitable method for single-cell proteomics.
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Affiliation(s)
- Takeshi Masuda
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan.,Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973, Japan
| | - Yuma Inamori
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973, Japan
| | - Arisu Furukawa
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973, Japan
| | - Maki Yamahiro
- Department of Pharmaceutical Microbiology, School of Pharmacy, Kumamoto University, Kumamoto 862-0973, Japan
| | - Kazuki Momosaki
- Department of Pharmaceutical Microbiology, School of Pharmacy, Kumamoto University, Kumamoto 862-0973, Japan
| | - Chih-Hsiang Chang
- Department of Tumor Genetics and Biology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Daiki Kobayashi
- Department of Tumor Genetics and Biology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto 860-8556, Japan.,Department of Omics Biology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan
| | - Hiroto Ohguchi
- Division of Disease Epigenetics, Institute of Resource Development and Analysis, Kumamoto University, Kumamoto 860-0811, Japan
| | - Yawara Kawano
- Department of Hematology, Rheumatology, and Infectious Diseases, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Shingo Ito
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan.,Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973, Japan
| | - Norie Araki
- Department of Tumor Genetics and Biology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Shao-En Ong
- Department of Pharmacology, University of Washington, Seattle, Washington 98195, United States
| | - Sumio Ohtsuki
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan.,Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973, Japan
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4
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Van Simaeys D, De La Fuente A, Zilio S, Zoso A, Kuznetsova V, Alcazar O, Buchwald P, Grilli A, Caroli J, Bicciato S, Serafini P. RNA aptamers specific for transmembrane p24 trafficking protein 6 and Clusterin for the targeted delivery of imaging reagents and RNA therapeutics to human β cells. Nat Commun 2022; 13:1815. [PMID: 35383192 PMCID: PMC8983715 DOI: 10.1038/s41467-022-29377-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/08/2022] [Indexed: 12/20/2022] Open
Abstract
The ability to detect and target β cells in vivo can substantially refine how diabetes is studied and treated. However, the lack of specific probes still hampers a precise characterization of human β cell mass and the delivery of therapeutics in clinical settings. Here, we report the identification of two RNA aptamers that specifically and selectively recognize mouse and human β cells. The putative targets of the two aptamers are transmembrane p24 trafficking protein 6 (TMED6) and clusterin (CLUS). When given systemically in immune deficient mice, these aptamers recognize the human islet graft producing a fluorescent signal proportional to the number of human islets transplanted. These aptamers cross-react with endogenous mouse β cells and allow monitoring the rejection of mouse islet allografts. Finally, once conjugated to saRNA specific for X-linked inhibitor of apoptosis (XIAP), they can efficiently transfect non-dissociated human islets, prevent early graft loss, and improve the efficacy of human islet transplantation in immunodeficient in mice.
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Affiliation(s)
- Dimitri Van Simaeys
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Adriana De La Fuente
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Serena Zilio
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Alessia Zoso
- Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Victoria Kuznetsova
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Oscar Alcazar
- Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Peter Buchwald
- Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Andrea Grilli
- Center for Genome Research, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Jimmy Caroli
- Center for Genome Research, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Silvio Bicciato
- Center for Genome Research, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Paolo Serafini
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, USA. .,Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, FL, USA. .,Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, USA.
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5
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Kirkemo LL, Elledge SK, Yang J, Byrnes JR, Glasgow JE, Blelloch R, Wells JA. Cell-surface tethered promiscuous biotinylators enable comparative small-scale surface proteomic analysis of human extracellular vesicles and cells. eLife 2022; 11:73982. [PMID: 35257663 PMCID: PMC8983049 DOI: 10.7554/elife.73982] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/07/2022] [Indexed: 11/24/2022] Open
Abstract
Characterization of cell surface proteome differences between cancer and healthy cells is a valuable approach for the identification of novel diagnostic and therapeutic targets. However, selective sampling of surface proteins for proteomics requires large samples (>10e6 cells) and long labeling times. These limitations preclude analysis of material-limited biological samples or the capture of rapid surface proteomic changes. Here, we present two labeling approaches to tether exogenous peroxidases (APEX2 and HRP) directly to cells, enabling rapid, small-scale cell surface biotinylation without the need to engineer cells. We used a novel lipidated DNA-tethered APEX2 (DNA-APEX2), which upon addition to cells promoted cell agnostic membrane-proximal labeling. Alternatively, we employed horseradish peroxidase (HRP) fused to the glycan-binding domain of wheat germ agglutinin (WGA-HRP). This approach yielded a rapid and commercially inexpensive means to directly label cells containing common N-Acetylglucosamine (GlcNAc) and sialic acid glycans on their surface. The facile WGA-HRP method permitted high surface coverage of cellular samples and enabled the first comparative surface proteome characterization of cells and cell-derived small extracellular vesicles (EVs), leading to the robust quantification of 953 cell and EV surface annotated proteins. We identified a newly recognized subset of EV-enriched markers, as well as proteins that are uniquely upregulated on Myc oncogene-transformed prostate cancer EVs. These two cell-tethered enzyme surface biotinylation approaches are highly advantageous for rapidly and directly labeling surface proteins across a range of material-limited sample types.
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Affiliation(s)
- Lisa L Kirkemo
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| | - Susanna K Elledge
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| | - Jiuling Yang
- Department of Urology, University of California, San Francisco, San Francisco, United States
| | - James R Byrnes
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| | - Jeff E Glasgow
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| | - Robert Blelloch
- Department of Urology, University of California, San Francisco, San Francisco, United States
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
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6
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de Clauser L, Kappert C, Sondermann JR, Gomez-Varela D, Flatters SJL, Schmidt M. Proteome and Network Analysis Provides Novel Insights Into Developing and Established Chemotherapy-Induced Peripheral Neuropathy. Front Pharmacol 2022; 13:818690. [PMID: 35250568 PMCID: PMC8895144 DOI: 10.3389/fphar.2022.818690] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/12/2022] [Indexed: 01/09/2023] Open
Abstract
Chemotherapy-induced peripheral neuropathy (CIPN) is a debilitating side-effect of cancer therapies. So far, the development of CIPN cannot be prevented, neither can established CIPN be reverted, often leading to the cessation of necessary chemotherapy. Thus, there is an urgent need to explore the mechanistic basis of CIPN to facilitate its treatment. Here we used an integrated approach of quantitative proteome profiling and network analysis in a clinically relevant rat model of paclitaxel-induced peripheral neuropathy. We analysed lumbar rat DRG at two critical time points: (1) day 7, right after cessation of paclitaxel treatment, but prior to neuropathy development (pre-CIPN); (2) 4 weeks after paclitaxel initiation, when neuropathy has developed (peak-CIPN). In this way we identified a differential protein signature, which shows how changes in the proteome correlate with the development and maintenance of CIPN, respectively. Extensive biological pathway and network analysis reveals that, at pre-CIPN, regulated proteins are prominently implicated in mitochondrial (dys)function, immune signalling, neuronal damage/regeneration, and neuronal transcription. Orthogonal validation in an independent rat cohort confirmed the increase of β-catenin (CTNNB1) at pre-CIPN. More importantly, detailed analysis of protein networks associated with β-catenin highlights translationally relevant and potentially druggable targets. Overall, this study demonstrates the enormous value of combining animal behaviour with proteome and network analysis to provide unprecedented insights into the molecular basis of CIPN. In line with emerging approaches of network medicine our results highlight new avenues for developing improved therapeutic options aimed at preventing and treating CIPN.
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Affiliation(s)
- Larissa de Clauser
- Wolfson Centre for Age-Related Diseases, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
- *Correspondence: Larissa de Clauser, ; Manuela Schmidt,
| | - Christin Kappert
- Max Planck Institute of Experimental Medicine, Goettingen, Germany
| | - Julia R. Sondermann
- Division of Pharmacology and Toxicology, Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - David Gomez-Varela
- Division of Pharmacology and Toxicology, Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Sarah J. L. Flatters
- Wolfson Centre for Age-Related Diseases, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Manuela Schmidt
- Division of Pharmacology and Toxicology, Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
- *Correspondence: Larissa de Clauser, ; Manuela Schmidt,
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7
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Noriega LG, Melo Z, Rajaram RD, Mercado A, Tovar AR, Velazquez‐Villegas LA, Castañeda‐Bueno M, Reyes‐López Y, Ryu D, Rojas‐Vega L, Magaña‐Avila G, López‐Barradas AM, Sánchez‐Hernández M, Debonneville A, Doucet A, Cheval L, Torres N, Auwerx J, Staub O, Gamba G. SIRT7 modulates the stability and activity of the renal K-Cl cotransporter KCC4 through deacetylation. EMBO Rep 2021; 22:e50766. [PMID: 33749979 PMCID: PMC8097349 DOI: 10.15252/embr.202050766] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 02/03/2021] [Accepted: 02/19/2021] [Indexed: 11/09/2022] Open
Abstract
SIRT7 is a NAD+ -dependent deacetylase that controls important aspects of metabolism, cancer, and bone formation. However, the molecular targets and functions of SIRT7 in the kidney are currently unknown. In silico analysis of kidney transcripts of the BXD murine genetic reference population revealed a positive correlation between Sirt7 and Slc12a7 mRNA expression, suggesting a link between the corresponding proteins that these transcripts encode, SIRT7, and the K-Cl cotransporter KCC4, respectively. Here, we find that protein levels and activity of heterologously expressed KCC4 are significantly modulated depending on its acetylation status in Xenopus laevis oocytes. Moreover, SIRT7 interacts with KCC4 in a NAD+ -dependent manner and increases its stability and activity in HEK293 cells. Interestingly, metabolic acidosis increases SIRT7 expression in kidney, as occurs with KCC4. In contrast, total SIRT7-deficient mice present lower KCC4 expression and an exacerbated metabolic acidosis than wild-type mice during an ammonium chloride challenge. Altogether, our data suggest that SIRT7 interacts with, stabilizes and modulates KCC4 activity through deacetylation, and reveals a novel role for SIRT7 in renal physiology.
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Affiliation(s)
- Lilia G Noriega
- Department of Nutrition PhysiologyInstituto Nacional de Ciencias Médicas y Nutrición Salvador ZubiránMexico CityMexico
| | - Zesergio Melo
- Department of Nephrology and Mineral MetabolismInstituto Nacional de Ciencias Médicas y Nutrición Salvador ZubiránMexico CityMexico
- CONACYT‐Centro de Investigación Biomédica de OccidenteInstituto Mexicano del Seguro SocialGuadalajaraJaliscoMexico
| | - Renuga D Rajaram
- Department of Pharmacology and ToxicologyUniversity of LausanneLausanneSwitzerland
- National Centre of Competence in Research, “Kidney.ch”ZurichSwitzerland
| | - Adriana Mercado
- Department of NephrologyInstituto Nacional de Cardiología Ignacio ChávezMexico CityMexico
| | - Armando R Tovar
- Department of Nutrition PhysiologyInstituto Nacional de Ciencias Médicas y Nutrición Salvador ZubiránMexico CityMexico
| | - Laura A Velazquez‐Villegas
- Department of Nutrition PhysiologyInstituto Nacional de Ciencias Médicas y Nutrición Salvador ZubiránMexico CityMexico
| | - María Castañeda‐Bueno
- Department of Nephrology and Mineral MetabolismInstituto Nacional de Ciencias Médicas y Nutrición Salvador ZubiránMexico CityMexico
| | - Yazmín Reyes‐López
- Department of Nutrition PhysiologyInstituto Nacional de Ciencias Médicas y Nutrición Salvador ZubiránMexico CityMexico
| | - Dongryeol Ryu
- Laboratory of Integrative and Systems Physiology (LISP)École Polytechnique Fédérale de LausanneLausanneSwitzerland
- Present address:
Department of Molecular Cell BiologySungkyunkwan University School of MedicineSuwonKorea
| | - Lorena Rojas‐Vega
- Department of Nephrology and Mineral MetabolismInstituto Nacional de Ciencias Médicas y Nutrición Salvador ZubiránMexico CityMexico
| | - German Magaña‐Avila
- Department of Nephrology and Mineral MetabolismInstituto Nacional de Ciencias Médicas y Nutrición Salvador ZubiránMexico CityMexico
| | - Adriana M López‐Barradas
- Department of Nutrition PhysiologyInstituto Nacional de Ciencias Médicas y Nutrición Salvador ZubiránMexico CityMexico
| | | | - Anne Debonneville
- Department of Pharmacology and ToxicologyUniversity of LausanneLausanneSwitzerland
- National Centre of Competence in Research, “Kidney.ch”ZurichSwitzerland
| | - Alain Doucet
- Centre de Recherche des CordeliersINSERM, Sorbonne Universités, USPC, Université Paris Descartes, Université Paris Diderot, Physiologie Rénale et TubulopathiesCNRS ERL 8228ParisFrance
| | - Lydie Cheval
- Centre de Recherche des CordeliersINSERM, Sorbonne Universités, USPC, Université Paris Descartes, Université Paris Diderot, Physiologie Rénale et TubulopathiesCNRS ERL 8228ParisFrance
| | - Nimbe Torres
- Department of Nutrition PhysiologyInstituto Nacional de Ciencias Médicas y Nutrición Salvador ZubiránMexico CityMexico
| | - Johan Auwerx
- Laboratory of Integrative and Systems Physiology (LISP)École Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Olivier Staub
- Department of Pharmacology and ToxicologyUniversity of LausanneLausanneSwitzerland
- National Centre of Competence in Research, “Kidney.ch”ZurichSwitzerland
| | - Gerardo Gamba
- Department of Nephrology and Mineral MetabolismInstituto Nacional de Ciencias Médicas y Nutrición Salvador ZubiránMexico CityMexico
- Molecular Physiology UnitInstituto de Investigaciones BiomédicasUniversidad Nacional Autónoma de MéxicoMexico CityMexico
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8
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Chen Y, Weckwerth W. Mass Spectrometry Untangles Plant Membrane Protein Signaling Networks. TRENDS IN PLANT SCIENCE 2020; 25:930-944. [PMID: 32359835 DOI: 10.1016/j.tplants.2020.03.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/26/2020] [Accepted: 03/30/2020] [Indexed: 06/11/2023]
Abstract
Plasma membranes (PMs) act as primary cellular checkpoints for sensing signals and controlling solute transport. Membrane proteins communicate with intracellular processes through protein interaction networks. Deciphering these signaling networks provides crucial information for elucidating in vivo cellular regulation. Large-scale proteomics enables system-wide characterization of the membrane proteome, identification of ligand-receptor pairs, and elucidation of signals originating at membranes. In this review we assess recent progress in the development of mass spectrometry (MS)-based proteomic pipelines for determining membrane signaling pathways. We focus in particular on current techniques for the analysis of membrane protein phosphorylation and interaction, and how these proteins may be connected to downstream changes in gene expression, metabolism, and physiology.
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Affiliation(s)
- Yanmei Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
| | - Wolfram Weckwerth
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MOSYS), University of Vienna, Vienna, 1090, Austria; Vienna Metabolomics Center (VIME), University of Vienna, Vienna, 1090, Austria.
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9
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Zheng Y, Liu Z, Xing J, Zheng Z, Pi Z, Song F, Liu S. In situ analysis of single cell and biological samples with rGO-Cu functional probe ESI-MS spectrometry. Talanta 2020; 211:120751. [DOI: 10.1016/j.talanta.2020.120751] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/12/2020] [Accepted: 01/14/2020] [Indexed: 01/17/2023]
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10
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Subedi P, Schneider M, Philipp J, Azimzadeh O, Metzger F, Moertl S, Atkinson MJ, Tapio S. Comparison of methods to isolate proteins from extracellular vesicles for mass spectrometry-based proteomic analyses. Anal Biochem 2019; 584:113390. [PMID: 31401005 DOI: 10.1016/j.ab.2019.113390] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 08/05/2019] [Accepted: 08/06/2019] [Indexed: 12/15/2022]
Abstract
Extracellular vesicles (EVs) are cell-derived membrane-bound organelles that have generated interest as they reflect the physiological condition of their source. Mass spectrometric (MS) analyses of protein cargo of EVs may lead to the discovery of biomarkers for diseases. However, for a comprehensive MS-based proteomics analysis, an optimal lysis of the EVs is required. Six methods for the protein extraction from EVs secreted by the head and neck cell line BHY were compared. Commercial radioimmunoprecipitation assay (RIPA) buffer outperformed the other buffers investigated in this study (Tris-SDS, Tris-Triton, GuHCl, urea-thiourea, and commercial Cell-lysis buffer). Following lysis with RIPA buffer, 310 proteins and 1469 peptides were identified using LTQ OrbitrapXL mass spectrometer. Among these, 86% of proteins and 72% of peptides were identified in all three replicates. In the case of other buffers, Tris-Triton identified on average 277 proteins, Cell-lysis buffer 257 proteins, and Tris-SDS, GuHCl and urea-thiourea each 267 proteins. In total, 399 proteins including 74 of the top EV markers (Exocarta) were identified, the most of the latter (73) using RIPA. The proteins exclusively identified using RIPA represented all Gene Ontology cell compartments. This study suggests that RIPA is an optimal lysis buffer for EVs in combination with MS.
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Affiliation(s)
- Prabal Subedi
- Helmholtz Zentrum München, German Research Centre for Environmental Health GmbH, Institute of Radiation Biology, Neuherberg, Germany.
| | - Michael Schneider
- Helmholtz Zentrum München, German Research Centre for Environmental Health GmbH, Institute of Radiation Biology, Neuherberg, Germany
| | - Jos Philipp
- Helmholtz Zentrum München, German Research Centre for Environmental Health GmbH, Institute of Radiation Biology, Neuherberg, Germany
| | - Omid Azimzadeh
- Helmholtz Zentrum München, German Research Centre for Environmental Health GmbH, Institute of Radiation Biology, Neuherberg, Germany
| | - Fabian Metzger
- Helmholtz Zentrum München, German Research Centre for Environmental Health GmbH, Research Unit Protein Science, Munich, Germany
| | - Simone Moertl
- Helmholtz Zentrum München, German Research Centre for Environmental Health GmbH, Institute of Radiation Biology, Neuherberg, Germany
| | - Michael J Atkinson
- Helmholtz Zentrum München, German Research Centre for Environmental Health GmbH, Institute of Radiation Biology, Neuherberg, Germany
| | - Soile Tapio
- Helmholtz Zentrum München, German Research Centre for Environmental Health GmbH, Institute of Radiation Biology, Neuherberg, Germany
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11
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Kaushal P, Kwon Y, Ju S, Lee C. An SDS-PAGE based proteomic approach for N-terminome profiling. Analyst 2019; 144:7001-7009. [DOI: 10.1039/c9an01616c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Schematic diagram of the SDS-PAGE based N-termini enrichment (GelNrich) workflow.
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Affiliation(s)
- Prashant Kaushal
- Center for Theragnosis
- Korea Institute of Science and Technology
- Seoul 02792
- Korea
- Division of Bio-Medical Science & Technology
| | - Yumi Kwon
- Center for Theragnosis
- Korea Institute of Science and Technology
- Seoul 02792
- Korea
- Department of Life Science and Research Institute for Natural Sciences
| | - Shinyeong Ju
- Center for Theragnosis
- Korea Institute of Science and Technology
- Seoul 02792
- Korea
- Department of Life Science and Research Institute for Natural Sciences
| | - Cheolju Lee
- Center for Theragnosis
- Korea Institute of Science and Technology
- Seoul 02792
- Korea
- Division of Bio-Medical Science & Technology
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12
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Kaur H. Recent developments in cell-SELEX technology for aptamer selection. Biochim Biophys Acta Gen Subj 2018; 1862:2323-2329. [PMID: 30059712 DOI: 10.1016/j.bbagen.2018.07.029] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/19/2018] [Accepted: 07/25/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND SELEX technique is employed to select aptamers against wide range of targets. The in vitro method of aptamer selection using live cells as the target is referred as cell-SELEX. SCOPE OF THE REVIEW The review provides a comprehensive description on the development of aptamers through various cell-SELEX methods and list of aptamers identified through this method. In addition, it pinpoints the advantages and limitations of the cell-SELEX process and its variants. MAJOR CONCLUSIONS The use of aptamers as therapeutic and diagnostic agents is rapidly evolving, selection techniques such as Cell-SELEX could be beneficial in identifying aptamers when the target is in its native conformation and without prior information of the cognate target, thereby bringing the aptamer development one step closer to the clinic. GENERAL SIGNIFICANCE The information in this review can serve as a database for the design and development of futuristic oligonucleotide based diagnostics and therapeutics work.
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13
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Abstract
In-gel digestion of protein spots derived from two-dimensional gels and their subsequent identification by mass spectrometry is involved in a multitude of mass spectrometry-driven proteomic experiments, including fluorescence difference gel electrophoresis (DIGE). This type of proteomic methodology has been involved in the establishment of comparative proteome maps and in the identification of differentially expressed proteins and protein isoforms in health and disease. Most in-gel digestion protocols follow a number of common steps including excision of the protein spots of interest, de-staining, reduction and alkylation (for silver-stained gels), dehydration and overnight digestion with the proteolytic enzyme of choice. While trypsin has been a mainstay of peptide digestion for many years, it does have its shortcomings, particularly related to incomplete peptide digestion, and this has led to a rise in popularity for other proteolytic enzymes either used alone or in combination. This chapter discusses the alternative enzymes available and describes the process of in-gel digestion using the enzyme trypsin.
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Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland.
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14
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Pandya M, Liu H, Dangaria SJ, Zhu W, Li LL, Pan S, Abufarwa M, Davis RG, Guggenheim S, Keiderling T, Luan X, Diekwisch TGH. Integrative Temporo-Spatial, Mineralogic, Spectroscopic, and Proteomic Analysis of Postnatal Enamel Development in Teeth with Limited Growth. Front Physiol 2017; 8:793. [PMID: 29114228 PMCID: PMC5660681 DOI: 10.3389/fphys.2017.00793] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 09/27/2017] [Indexed: 12/11/2022] Open
Abstract
Tooth amelogenesis is a complex process beginning with enamel organ cell differentiation and enamel matrix secretion, transitioning through changes in ameloblast polarity, cytoskeletal, and matrix organization, that affects crucial biomineralization events such as mineral nucleation, enamel crystal growth, and enamel prism organization. Here we have harvested the enamel organ including the pliable enamel matrix of postnatal first mandibular mouse molars during the first 8 days of tooth enamel development to conduct a step-wise cross-sectional analysis of the changes in the mineral and protein phase. Mineral phase diffraction pattern analysis using single-crystal, powder sample X-ray diffraction analysis indicated conversion of calcium phosphate precursors to partially fluoride substituted hydroxyapatite from postnatal day 4 (4 dpn) onwards. Attenuated total reflectance spectra (ATR) revealed a substantial elevation in phosphate and carbonate incorporation as well as structural reconfiguration between postnatal days 6 and 8. Nanoscale liquid chromatography coupled with tandem mass spectrometry (nanoLC-MS/MS) demonstrated highest protein counts for ECM/cell surface proteins, stress/heat shock proteins, and alkaline phosphatase on postnatal day 2, high counts for ameloblast cytoskeletal proteins such as tubulin β5, tropomyosin, β-actin, and vimentin on postnatal day 4, and elevated levels of cofilin-1, calmodulin, and peptidyl-prolyl cis-trans isomerase on day 6. Western blot analysis of hydrophobic enamel proteins illustrated continuously increasing amelogenin levels from 1 dpn until 8 dpn, while enamelin peaked on days 1 and 2 dpn, and ameloblastin on days 1-5 dpn. In summary, these data document the substantial changes in the enamel matrix protein and mineral phase that take place during postnatal mouse molar amelogenesis from a systems biological perspective, including (i) relatively high levels of matrix protein expression during the early secretory stage on postnatal day 2, (ii) conversion of calcium phosphates to apatite, peak protein folding and stress protein counts, and increased cytoskeletal protein levels such as actin and tubulin on day 4, as well as (iii) secondary structure changes, isomerase activity, highest amelogenin levels, and peak phosphate/carbonate incorporation between postnatal days 6 and 8. Together, this study provides a baseline for a comprehensive understanding of the mineralogic and proteomic events that contribute to the complexity of mammalian tooth enamel development.
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Affiliation(s)
- Mirali Pandya
- Texas A&M Center for Craniofacial Research and Diagnosis, Dallas, TX, United States
| | - Hui Liu
- Brodie Laboratory for Craniofacial Genetics, University of Illinois at Chicago, Chicago, IL, United States
| | - Smit J Dangaria
- Brodie Laboratory for Craniofacial Genetics, University of Illinois at Chicago, Chicago, IL, United States
| | - Weiying Zhu
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, United States
| | - Leo L Li
- Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Shuang Pan
- Brodie Laboratory for Craniofacial Genetics, University of Illinois at Chicago, Chicago, IL, United States
| | - Moufida Abufarwa
- Texas A&M Center for Craniofacial Research and Diagnosis, Dallas, TX, United States
| | - Roderick G Davis
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States
| | - Stephen Guggenheim
- Department of Earth and Environmental Sciences, University of Illinois at Chicago, Chicago, IL, United States
| | | | - Xianghong Luan
- Brodie Laboratory for Craniofacial Genetics, University of Illinois at Chicago, Chicago, IL, United States
| | - Thomas G H Diekwisch
- Texas A&M Center for Craniofacial Research and Diagnosis, Dallas, TX, United States
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15
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Edlinger C, Einfalt T, Spulber M, Car A, Meier W, Palivan CG. Biomimetic Strategy To Reversibly Trigger Functionality of Catalytic Nanocompartments by the Insertion of pH-Responsive Biovalves. NANO LETTERS 2017; 17:5790-5798. [PMID: 28851220 DOI: 10.1021/acs.nanolett.7b02886] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We describe an innovative strategy to generate catalytic compartments with triggered functionality at the nanoscale level by combining pH-reversible biovalves and enzyme-loaded synthetic compartments. The biovalve has been engineered by the attachment of stimuli-responsive peptides to a genetically modified channel porin, enabling a reversible change of the molecular flow through the pores of the porin in response to a pH change in the local environment. The biovalve functionality triggers the reaction inside the cavity of the enzyme-loaded compartments by switching the in situ activity of the enzymes on/off based on a reversible change of the permeability of the membrane, which blocks or allows the passage of substrates and products. The complex functionality of our catalytic compartments is based on the preservation of the integrity of the compartments to protect encapsulated enzymes. An increase of the in situ activity compared to that of the free enzyme and a reversible on/off switch of the activity upon the presence of a specific stimulus is achieved. This strategy provides straightforward solutions for the development of catalytic nanocompartments efficiently producing desired molecules in a controlled, stimuli-responsive manner with high potential in areas, such as medicine, analytical chemistry, and catalysis.
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Affiliation(s)
- Christoph Edlinger
- Department of Chemistry, University of Basel , Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Tomaz Einfalt
- Department of Chemistry, University of Basel , Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Mariana Spulber
- Department of Chemistry, University of Basel , Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Anja Car
- Department of Chemistry, University of Basel , Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Wolfgang Meier
- Department of Chemistry, University of Basel , Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Cornelia G Palivan
- Department of Chemistry, University of Basel , Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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16
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Abstract
Aptamers are nucleic acids referred to as chemical antibodies as they bind to their specific targets with high affinity and selectivity. They are selected via an iterative process known as ‘selective evolution of ligands by exponential enrichment’ (SELEX). Aptamers have been developed against numerous cancer targets and among them, many tumor cell-membrane protein biomarkers. The identification of aptamers targeting cell-surface proteins has mainly been performed by two different strategies: protein- and cell-based SELEX, when the targets used for selection were proteins and cells, respectively. This review aims to update the literature on aptamers targeting tumor cell surface protein biomarkers, highlighting potentials, pitfalls of protein- and cell-based selection processes and applications of such selected molecules. Aptamers as promising agents for diagnosis and therapeutic approaches in oncology are documented, as well as aptamers in clinical development.
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17
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Technologies for Proteome-Wide Discovery of Extracellular Host-Pathogen Interactions. J Immunol Res 2017; 2017:2197615. [PMID: 28321417 PMCID: PMC5340944 DOI: 10.1155/2017/2197615] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 01/19/2017] [Indexed: 12/26/2022] Open
Abstract
Pathogens have evolved unique mechanisms to breach the cell surface barrier and manipulate the host immune response to establish a productive infection. Proteins exposed to the extracellular environment, both cell surface-expressed receptors and secreted proteins, are essential targets for initial invasion and play key roles in pathogen recognition and subsequent immunoregulatory processes. The identification of the host and pathogen extracellular molecules and their interaction networks is fundamental to understanding tissue tropism and pathogenesis and to inform the development of therapeutic strategies. Nevertheless, the characterization of the proteins that function in the host-pathogen interface has been challenging, largely due to the technical challenges associated with detection of extracellular protein interactions. This review discusses available technologies for the high throughput study of extracellular protein interactions between pathogens and their hosts, with a focus on mammalian viruses and bacteria. Emerging work illustrates a rich landscape for extracellular host-pathogen interaction and points towards the evolution of multifunctional pathogen-encoded proteins. Further development and application of technologies for genome-wide identification of extracellular protein interactions will be important in deciphering functional host-pathogen interaction networks, laying the foundation for development of novel therapeutics.
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18
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Collins CA, Leslie ME, Peck SC, Heese A. Simplified Enrichment of Plasma Membrane Proteins from Arabidopsis thaliana Seedlings Using Differential Centrifugation and Brij-58 Treatment. Methods Mol Biol 2017; 1564:155-168. [PMID: 28124253 DOI: 10.1007/978-1-4939-6813-8_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The plasma membrane (PM) forms a barrier between a plant cell and its environment. Proteins at this subcellular location play diverse and complex roles, including perception of extracellular signals to coordinate cellular changes. Analyses of PM proteins, however, are often limited by the relatively low abundance of these proteins in the total cellular protein pool. Techniques traditionally used for enrichment of PM proteins are time consuming, tedious, and require extensive optimization. Here, we provide a simple and reproducible enrichment procedure for PM proteins from Arabidopsis thaliana seedlings starting from total microsomal membranes isolated by differential centrifugation. To enrich for PM proteins, total microsomes are treated with the nonionic detergent Brij-58 to decrease the abundance of contaminating organellar proteins. This protocol combined with the genetic resources available in Arabidopsis provides a powerful tool that will enhance our understanding of proteins at the PM.
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Affiliation(s)
- Carina A Collins
- Division of Biochemistry, Interdisciplinary Plant Group (IPG), University of Missouri, Columbia, MO, 65211, USA
| | - Michelle E Leslie
- Division of Biochemistry, Interdisciplinary Plant Group (IPG), University of Missouri, Columbia, MO, 65211, USA
| | - Scott C Peck
- Division of Biochemistry, Interdisciplinary Plant Group (IPG), University of Missouri, Columbia, MO, 65211, USA.
| | - Antje Heese
- Division of Biochemistry, Interdisciplinary Plant Group (IPG), University of Missouri, Columbia, MO, 65211, USA
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19
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Zhang X. Detergents: Friends not foes for high-performance membrane proteomics toward precision medicine. Proteomics 2016; 17. [PMID: 27633951 DOI: 10.1002/pmic.201600209] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/31/2016] [Accepted: 09/13/2016] [Indexed: 01/05/2023]
Abstract
Precision medicine, particularly therapeutics, emphasizes the atomic-precise, dynamic, and systems visualization of human membrane proteins and their endogenous modifiers. For years, bottom-up proteomics has grappled with removing and avoiding detergents, yet faltered at the therapeutic-pivotal membrane proteins, which have been tackled by classical approaches and are known for decades refractory to single-phase aqueous or organic denaturants. Hydrophobicity and aggregation commonly challenge tissue and cell lysates, biofluids, and enriched samples. Frequently, expected membrane proteins and peptides are not identified by shotgun bottom-up proteomics, let alone robust quantitation. This review argues the cause of this proteomic crisis is not detergents per se, but the choice of detergents. Recently, inclusion of compatible detergents for membrane protein extraction and digestion has revealed stark improvements in both quantitative and structural proteomics. This review analyzes detergent properties behind recent proteomic advances, and proposes that rational use of detergents may reconcile outstanding membrane proteomics dilemmas, enabling ultradeep coverage and minimal artifacts for robust protein and endogenous PTM measurements. The simplicity of detergent tools confers bottom-up membrane proteomics the sophistication toward precision medicine.
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Affiliation(s)
- Xi Zhang
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
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20
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Turk R, Hsiao JJ, Smits MM, Ng BH, Pospisil TC, Jones KS, Campbell KP, Wright ME. Molecular Signatures of Membrane Protein Complexes Underlying Muscular Dystrophy. Mol Cell Proteomics 2016; 15:2169-85. [PMID: 27099343 PMCID: PMC5083101 DOI: 10.1074/mcp.m116.059188] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Indexed: 01/16/2023] Open
Abstract
Mutations in genes encoding components of the sarcolemmal dystrophin-glycoprotein complex (DGC) are responsible for a large number of muscular dystrophies. As such, molecular dissection of the DGC is expected to both reveal pathological mechanisms, and provides a biological framework for validating new DGC components. Establishment of the molecular composition of plasma-membrane protein complexes has been hampered by a lack of suitable biochemical approaches. Here we present an analytical workflow based upon the principles of protein correlation profiling that has enabled us to model the molecular composition of the DGC in mouse skeletal muscle. We also report our analysis of protein complexes in mice harboring mutations in DGC components. Bioinformatic analyses suggested that cell-adhesion pathways were under the transcriptional control of NFκB in DGC mutant mice, which is a finding that is supported by previous studies that showed NFκB-regulated pathways underlie the pathophysiology of DGC-related muscular dystrophies. Moreover, the bioinformatic analyses suggested that inflammatory and compensatory mechanisms were activated in skeletal muscle of DGC mutant mice. Additionally, this proteomic study provides a molecular framework to refine our understanding of the DGC, identification of protein biomarkers of neuromuscular disease, and pharmacological interrogation of the DGC in adult skeletal muscle https://www.mda.org/disease/congenital-muscular-dystrophy/research.
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Affiliation(s)
- Rolf Turk
- From the ‡Howard Hughes Medical Institute, §Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, ¶Department of Molecular Physiology and Biophysics, ‖Department of Neurology, **Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | | | | | - Brandon H Ng
- ¶Department of Molecular Physiology and Biophysics
| | - Tyler C Pospisil
- From the ‡Howard Hughes Medical Institute, §Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, ¶Department of Molecular Physiology and Biophysics, ‖Department of Neurology, **Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Kayla S Jones
- From the ‡Howard Hughes Medical Institute, §Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, ¶Department of Molecular Physiology and Biophysics, ‖Department of Neurology, **Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Kevin P Campbell
- From the ‡Howard Hughes Medical Institute, §Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, ¶Department of Molecular Physiology and Biophysics, ‖Department of Neurology, **Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, Iowa
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21
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Papanastasiou M, Orfanoudaki G, Kountourakis N, Koukaki M, Sardis MF, Aivaliotis M, Tsolis KC, Karamanou S, Economou A. Rapid label-free quantitative analysis of the E. coli
BL21(DE3) inner membrane proteome. Proteomics 2015; 16:85-97. [DOI: 10.1002/pmic.201500304] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 09/05/2015] [Accepted: 10/12/2015] [Indexed: 12/12/2022]
Affiliation(s)
- Malvina Papanastasiou
- Institute of Molecular Biology and Biotechnology; Foundation for Research & Technology; Iraklio Greece
- Department Pathology & Laboratory Medicine, Perelman School of Medicine; University of Pennsylvania; Philadelphia USA
| | - Georgia Orfanoudaki
- Institute of Molecular Biology and Biotechnology; Foundation for Research & Technology; Iraklio Greece
- Department of Biology; University of Crete; Iraklio Greece
| | - Nikos Kountourakis
- Institute of Molecular Biology and Biotechnology; Foundation for Research & Technology; Iraklio Greece
| | - Marina Koukaki
- Institute of Molecular Biology and Biotechnology; Foundation for Research & Technology; Iraklio Greece
| | - Marios Frantzeskos Sardis
- Institute of Molecular Biology and Biotechnology; Foundation for Research & Technology; Iraklio Greece
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology; Katholieke Universiteit Leuven; Leuven Belgium
| | - Michalis Aivaliotis
- Institute of Molecular Biology and Biotechnology; Foundation for Research & Technology; Iraklio Greece
| | - Konstantinos C. Tsolis
- Institute of Molecular Biology and Biotechnology; Foundation for Research & Technology; Iraklio Greece
- Department of Biology; University of Crete; Iraklio Greece
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology; Katholieke Universiteit Leuven; Leuven Belgium
| | - Spyridoula Karamanou
- Institute of Molecular Biology and Biotechnology; Foundation for Research & Technology; Iraklio Greece
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology; Katholieke Universiteit Leuven; Leuven Belgium
| | - Anastassios Economou
- Institute of Molecular Biology and Biotechnology; Foundation for Research & Technology; Iraklio Greece
- Department of Biology; University of Crete; Iraklio Greece
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology; Katholieke Universiteit Leuven; Leuven Belgium
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22
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Battchikova N, Angeleri M, Aro EM. Proteomic approaches in research of cyanobacterial photosynthesis. PHOTOSYNTHESIS RESEARCH 2015; 126:47-70. [PMID: 25359503 DOI: 10.1007/s11120-014-0050-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 10/18/2014] [Indexed: 05/03/2023]
Abstract
Oxygenic photosynthesis in cyanobacteria, algae, and plants is carried out by a fabulous pigment-protein machinery that is amazingly complicated in structure and function. Many different approaches have been undertaken to characterize the most important aspects of photosynthesis, and proteomics has become the essential component in this research. Here we describe various methods which have been used in proteomic research of cyanobacteria, and demonstrate how proteomics is implemented into on-going studies of photosynthesis in cyanobacterial cells.
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Affiliation(s)
- Natalia Battchikova
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014, Turku, Finland.
| | - Martina Angeleri
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014, Turku, Finland
| | - Eva-Mari Aro
- Laboratory of Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014, Turku, Finland
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23
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Fang X, Qiao L, Yan G, Yang P, Liu B. Multifunctional nanoreactor for comprehensive characterization of membrane proteins based on surface functionalized mesoporous foams. Anal Chem 2015; 87:9360-7. [PMID: 26305297 DOI: 10.1021/acs.analchem.5b02135] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
An integrated protocol is proposed here for efficient analysis of membrane proteins based on surface functionalized mesoporous graphene foams (MGF). The inherent hydrophobic nature of MGF and surface modification with hydrophilic chitosan (CS) make it highly suitable for the enrichment of hydrophobic membrane proteins from organic solvent, while remaining well-dispersed in aqueous solution for subsequent proteolysis. Therefore, such a multifunctional reactor ensures a facile solvent adjustment route. Furthermore, as a chitosan modified nanoporous reactor, it also provides a biocompatible nanoenvironment that can maintain the stability and activity of enzymes to realize efficient in situ digestion of the enriched membrane proteins. The concept was first proved with a standard hydrophobic membrane protein, bacteriorhodopsin, where a high number of identified peptides and amino acid sequence coverage were achieved even at extremely low protein concentration. The mesoporous reaction system was further applied to the analysis of complex real-case proteome samples, where 931 membrane proteins were identified in triplicate analyses by 2D LC-MS/MS. In contrast, with in-solution proteolysis, only 73 membrane proteins were identified from the same sample by the same 2D LC-MS/MS. The identified membrane proteins by the MGF-CS protocol include many biomarkers of the cell line. These results suggest that the multifunctional MGF-CS protocol is of great value to facilitate the comprehensive characterization of membrane proteins in the proteome research.
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Affiliation(s)
- Xiaoni Fang
- Department of Chemistry, Institutes of Biomedical Sciences and State Key Lab of Molecular Engineering of Polymers, Fudan University , Shanghai 200433, China
| | - Liang Qiao
- Department of Chemistry, Institutes of Biomedical Sciences and State Key Lab of Molecular Engineering of Polymers, Fudan University , Shanghai 200433, China
| | - Guoquan Yan
- Department of Chemistry, Institutes of Biomedical Sciences and State Key Lab of Molecular Engineering of Polymers, Fudan University , Shanghai 200433, China
| | - Pengyuan Yang
- Department of Chemistry, Institutes of Biomedical Sciences and State Key Lab of Molecular Engineering of Polymers, Fudan University , Shanghai 200433, China
| | - Baohong Liu
- Department of Chemistry, Institutes of Biomedical Sciences and State Key Lab of Molecular Engineering of Polymers, Fudan University , Shanghai 200433, China
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24
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Zhang X. Less is More: Membrane Protein Digestion Beyond Urea-Trypsin Solution for Next-level Proteomics. Mol Cell Proteomics 2015; 14:2441-53. [PMID: 26081834 DOI: 10.1074/mcp.r114.042572] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Indexed: 12/13/2022] Open
Abstract
The goal of next-level bottom-up membrane proteomics is protein function investigation, via high-coverage high-throughput peptide-centric quantitation of expression, modifications and dynamic structures at systems scale. Yet efficient digestion of mammalian membrane proteins presents a daunting barrier, and prevalent day-long urea-trypsin in-solution digestion proved insufficient to reach this goal. Many efforts contributed incremental advances over past years, but involved protein denaturation that disconnected measurement from functional states. Beyond denaturation, the recent discovery of structure/proteomics omni-compatible detergent n-dodecyl-β-d-maltopyranoside, combined with pepsin and PNGase F columns, enabled breakthroughs in membrane protein digestion: a 2010 DDM-low-TCEP (DLT) method for H/D-exchange (HDX) using human G protein-coupled receptor, and a 2015 flow/detergent-facilitated protease and de-PTM digestions (FDD) for integrative deep sequencing and quantitation using full-length human ion channel complex. Distinguishing protein solubilization from denaturation, protease digestion reliability from theoretical specificity, and reduction from alkylation, these methods shifted day(s)-long paradigms into minutes, and afforded fully automatable (HDX)-protein-peptide-(tandem mass tag)-HPLC pipelines to instantly measure functional proteins at deep coverage, high peptide reproducibility, low artifacts and minimal leakage. Promoting-not destroying-structures and activities harnessed membrane proteins for the next-level streamlined functional proteomics. This review analyzes recent advances in membrane protein digestion methods and highlights critical discoveries for future proteomics.
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Affiliation(s)
- Xi Zhang
- From the ‡Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, Massachusetts; §Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
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25
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Golizeh M, Schneider C, Ohlund LB, Sleno L. Multidimensional LC–MS/MS analysis of liver proteins in rat, mouse and human microsomal and S9 fractions. EUPA OPEN PROTEOMICS 2015. [DOI: 10.1016/j.euprot.2015.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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26
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Habuka M, Fagerberg L, Hallström BM, Kampf C, Edlund K, Sivertsson Å, Yamamoto T, Pontén F, Uhlén M, Odeberg J. The kidney transcriptome and proteome defined by transcriptomics and antibody-based profiling. PLoS One 2014; 9:e116125. [PMID: 25551756 PMCID: PMC4281243 DOI: 10.1371/journal.pone.0116125] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 12/02/2014] [Indexed: 12/22/2022] Open
Abstract
To understand renal functions and disease, it is important to define the molecular constituents of the various compartments of the kidney. Here, we used comparative transcriptomic analysis of all major organs and tissues in the human body, in combination with kidney tissue micro array based immunohistochemistry, to generate a comprehensive description of the kidney-specific transcriptome and proteome. A special emphasis was placed on the identification of genes and proteins that were elevated in specific kidney subcompartments. Our analysis identified close to 400 genes that had elevated expression in the kidney, as compared to the other analysed tissues, and these were further subdivided, depending on expression levels, into tissue enriched, group enriched or tissue enhanced. Immunohistochemistry allowed us to identify proteins with distinct localisation to the glomeruli (n = 11), proximal tubules (n = 120), distal tubules (n = 9) or collecting ducts (n = 8). Among the identified kidney elevated transcripts, we found several proteins not previously characterised or identified as elevated in kidney. This description of the kidney specific transcriptome and proteome provides a resource for basic and clinical research to facilitate studies to understand kidney biology and disease.
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Affiliation(s)
- Masato Habuka
- School of Biotechnology, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
- Department of Structural Pathology, Institute of Nephrology, Medical and Dental School, Niigata University, Asahimachi-dori Niigata, Japan
| | - Linn Fagerberg
- School of Biotechnology, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Björn M. Hallström
- School of Biotechnology, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Caroline Kampf
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Karolina Edlund
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Åsa Sivertsson
- School of Biotechnology, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Tadashi Yamamoto
- Department of Structural Pathology, Institute of Nephrology, Medical and Dental School, Niigata University, Asahimachi-dori Niigata, Japan
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mathias Uhlén
- School of Biotechnology, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Jacob Odeberg
- School of Biotechnology, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
- Department of Medicine, Karolinska Institutet and Centre for Hematology, Karolinska University Hospital, Stockholm, Sweden
- * E-mail:
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27
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Artemenko K, Horáková J, Steinberger B, Besenfelder U, Brem G, Bergquist J, Mayrhofer C. A proteomic approach to monitor the dynamic response of the female oviductal epithelial cell surface to male gametes. J Proteomics 2014; 113:1-14. [PMID: 25281772 DOI: 10.1016/j.jprot.2014.09.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 09/18/2014] [Accepted: 09/22/2014] [Indexed: 12/11/2022]
Abstract
UNLABELLED Sophisticated strategies to analyze cell surface proteins are indispensable to study fundamental biological processes, such as the response of cells to environmental changes or cell-cell communication. Herein, we describe a refined mass spectrometry-based approach for the specific characterization and quantitation of cell surface proteins expressed in the female reproductive tract. The strategy is based on in situ biotinylation of rabbit oviducts, affinity enrichment of surface exposed biotin tagged proteins and dimethyl labeling of the obtained tryptic peptides followed by LC-MS/MS analysis. This approach proved to be sensitive enough to analyze small sample amounts (<1μg) and allowed further to trace the dynamic composition of the surface proteome of the oviductal epithelium in response to male gametes. The relative protein expression ratios of 175 proteins were quantified. Thirty-one of them were found to be altered over time, namely immediately, 1h and 2h after insemination compared to the time-matched control groups. Functional analysis demonstrated that structural reorganization of the oviductal epithelial cell surface was involved in the early response of the female organ to semen. In summary, this study outlines a workflow that is capable to monitor alterations in the female oviduct that are related to key reproductive processes in vivo. BIOLOGICAL SIGNIFICANCE The proper interaction between the female reproductive tract, in particular, the oviduct and the male gametes, is fundamental to fertilization and embryonic development under physiological conditions. Thereby the oviductal epithelial cell surface proteins play an important role. Besides their direct interaction with male gametes, these molecules participate in signal transduction and, thus, are involved in the mandatory cellular response of the oviductal epithelium. In this study we present a refined LC-MS/MS based workflow that is capable to quantitatively analyze the expression of oviductal epithelial cell surface proteins in response to insemination in vivo. A special focus was on the very early interaction between the female organ and the male gametes. At first, this study clearly revealed an immediate response of the surface proteome to semen, which was modulated over time. The described methodology can be applied for studies of further distinct biological events in the oviduct and therefore contribute to a deeper insight into the formation of new life.
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Affiliation(s)
- Konstantin Artemenko
- Institute of Analytical Chemistry, Department of Chemistry - Biomedical Center and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| | - Jana Horáková
- Institute of Analytical Chemistry, Department of Chemistry - Biomedical Center and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Birgit Steinberger
- Institute of Animal Breeding and Genetics, Department for Biomedical Sciences, University of Veterinary Medicine, Vienna, Austria; Institute of Biotechnology in Animal Production, Department for Agrobiotechnology (IFA Tulln), University of Natural Resources and Applied Life Sciences, Vienna, Tulln, Austria
| | - Urban Besenfelder
- Institute of Biotechnology in Animal Production, Department for Agrobiotechnology (IFA Tulln), University of Natural Resources and Applied Life Sciences, Vienna, Tulln, Austria
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, Department for Biomedical Sciences, University of Veterinary Medicine, Vienna, Austria
| | - Jonas Bergquist
- Institute of Analytical Chemistry, Department of Chemistry - Biomedical Center and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Corina Mayrhofer
- Institute of Animal Breeding and Genetics, Department for Biomedical Sciences, University of Veterinary Medicine, Vienna, Austria; Institute of Biotechnology in Animal Production, Department for Agrobiotechnology (IFA Tulln), University of Natural Resources and Applied Life Sciences, Vienna, Tulln, Austria
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Petrovská B, Jeřábková H, Chamrád I, Vrána J, Lenobel R, Uřinovská J, Šebela M, Doležel J. Proteomic Analysis of Barley Cell Nuclei Purified by Flow Sorting. Cytogenet Genome Res 2014; 143:78-86. [DOI: 10.1159/000365311] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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29
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Manikandan M, Nasser Abdelhamid H, Talib A, Wu HF. Facile synthesis of gold nanohexagons on graphene templates in Raman spectroscopy for biosensing cancer and cancer stem cells. Biosens Bioelectron 2014; 55:180-6. [DOI: 10.1016/j.bios.2013.11.037] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 11/08/2013] [Accepted: 11/11/2013] [Indexed: 02/07/2023]
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30
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Sun B, Hood L. Protein-centric N-glycoproteomics analysis of membrane and plasma membrane proteins. J Proteome Res 2014; 13:2705-14. [PMID: 24754784 PMCID: PMC4053080 DOI: 10.1021/pr500187g] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
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The advent of proteomics technology
has transformed our understanding
of biological membranes. The challenges for studying membrane proteins
have inspired the development of many analytical and bioanalytical
tools, and the techniques of glycoproteomics have emerged as an effective
means to enrich and characterize membrane and plasma-membrane proteomes.
This Review summarizes the development of various glycoproteomics
techniques to overcome the hurdles formed by the unique structures
and behaviors of membrane proteins with a focus on N-glycoproteomics.
Example contributions of N-glycoproteomics to the understanding of
membrane biology are provided, and the areas that require future technical
breakthroughs are discussed.
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Affiliation(s)
- Bingyun Sun
- Department of Chemistry, Simon Fraser University , 8888 University Drive, Burnaby, British Columbia V5A1S6, Canada
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31
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Battle KN, Uba FI, Soper SA. Microfluidics for the analysis of membrane proteins: How do we get there? Electrophoresis 2014; 35:2253-66. [DOI: 10.1002/elps.201300625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 02/16/2014] [Accepted: 02/17/2014] [Indexed: 01/22/2023]
Affiliation(s)
- Katrina N. Battle
- Department of Chemistry; Louisiana State University; Baton Rouge LA USA
| | - Franklin I. Uba
- Department of Chemistry; University of North Carolina; Chapel Hill NC USA
| | - Steven A. Soper
- Department of Chemistry; Louisiana State University; Baton Rouge LA USA
- Department of Chemistry; University of North Carolina; Chapel Hill NC USA
- Department of Biomedical Engineering; University of North Carolina; Chapel Hill NC USA
- BioFluidica, LLC, c/o Carolina Kick-Start; Chapel Hill NC USA
- School of Nano-Bioscience and Chemical Engineering; Ulsan National Institute of Science and Technology; Ulsan Korea
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32
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Chingin K, Liang J, Chen H. Direct analysis of in vitro grown microorganisms and mammalian cells by ambient mass spectrometry. RSC Adv 2014. [DOI: 10.1039/c3ra46327c] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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33
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Bendz M, Skwark M, Nilsson D, Granholm V, Cristobal S, Käll L, Elofsson A. Membrane protein shaving with thermolysin can be used to evaluate topology predictors. Proteomics 2013; 13:1467-80. [DOI: 10.1002/pmic.201200517] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 01/23/2013] [Accepted: 02/25/2013] [Indexed: 12/12/2022]
Affiliation(s)
- Maria Bendz
- Department of Biochemistry and Biophysics; Science for Life Laboratory, Center for Biomembrane Research, Stockholm University; Stockholm Sweden
| | - Marcin Skwark
- Department of Biochemistry and Biophysics; Science for Life Laboratory, Center for Biomembrane Research, Stockholm University; Stockholm Sweden
| | - Daniel Nilsson
- Department of Biochemistry and Biophysics; Science for Life Laboratory, Center for Biomembrane Research, Stockholm University; Stockholm Sweden
| | - Viktor Granholm
- Department of Biochemistry and Biophysics; Science for Life Laboratory, Center for Biomembrane Research, Stockholm University; Stockholm Sweden
| | - Susana Cristobal
- Department of Clinical and Experimental Medicine, Cell Biology; Faculty of Health Science, Linköping University; Linköping Sweden
- IKERBASQUE, Basque Foundation for Science; Department of Physiology, Basque Country Medical School; Bilbao Spain
| | - Lukas Käll
- Science for Life Laboratory, School of Biotechnology; Royal Institute of Technology (KTH); Solna Sweden
| | - Arne Elofsson
- Department of Biochemistry and Biophysics; Science for Life Laboratory, Center for Biomembrane Research, Stockholm University; Stockholm Sweden
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34
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Ryšlavá H, Doubnerová V, Kavan D, Vaněk O. Effect of posttranslational modifications on enzyme function and assembly. J Proteomics 2013; 92:80-109. [PMID: 23603109 DOI: 10.1016/j.jprot.2013.03.025] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Revised: 03/01/2013] [Accepted: 03/11/2013] [Indexed: 12/22/2022]
Abstract
The detailed examination of enzyme molecules by mass spectrometry and other techniques continues to identify hundreds of distinct PTMs. Recently, global analyses of enzymes using methods of contemporary proteomics revealed widespread distribution of PTMs on many key enzymes distributed in all cellular compartments. Critically, patterns of multiple enzymatic and nonenzymatic PTMs within a single enzyme are now functionally evaluated providing a holistic picture of a macromolecule interacting with low molecular mass compounds, some of them being substrates, enzyme regulators, or activated precursors for enzymatic and nonenzymatic PTMs. Multiple PTMs within a single enzyme molecule and their mutual interplays are critical for the regulation of catalytic activity. Full understanding of this regulation will require detailed structural investigation of enzymes, their structural analogs, and their complexes. Further, proteomics is now integrated with molecular genetics, transcriptomics, and other areas leading to systems biology strategies. These allow the functional interrogation of complex enzymatic networks in their natural environment. In the future, one might envisage the use of robust high throughput analytical techniques that will be able to detect multiple PTMs on a global scale of individual proteomes from a number of carefully selected cells and cellular compartments. This article is part of a Special Issue entitled: Posttranslational Protein modifications in biology and Medicine.
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Affiliation(s)
- Helena Ryšlavá
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12840 Prague 2, Czech Republic.
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35
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Optimized proteomic analysis of rat liver microsomes using dual enzyme digestion with 2D-LC–MS/MS. J Proteomics 2013; 82:166-78. [DOI: 10.1016/j.jprot.2013.02.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 01/24/2013] [Accepted: 02/08/2013] [Indexed: 12/23/2022]
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Abstract
The rapid technological developments following the Human Genome Project have made possible the availability of personalized genomes. As the focus now shifts from characterizing genomes to making personalized disease associations, in combination with the availability of other omics technologies, the next big push will be not only to obtain a personalized genome, but to quantitatively follow other omics. This will include transcriptomes, proteomes, metabolomes, antibodyomes, and new emerging technologies, enabling the profiling of thousands of molecular components in individuals. Furthermore, omics profiling performed longitudinally can probe the temporal patterns associated with both molecular changes and associated physiological health and disease states. Such data necessitates the development of computational methodology to not only handle and descriptively assess such data, but also construct quantitative biological models. Here we describe the availability of personal genomes and developing omics technologies that can be brought together for personalized implementations and how these novel integrated approaches may effectively provide a precise personalized medicine that focuses on not only characterization and treatment but ultimately the prevention of disease.
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37
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Trouillon R, Passarelli MK, Wang J, Kurczy ME, Ewing AG. Chemical Analysis of Single Cells. Anal Chem 2012; 85:522-42. [DOI: 10.1021/ac303290s] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Raphaël Trouillon
- University of Gothenburg, Department of Chemistry and Molecular
Biology, 41296 Gothenburg, Sweden
| | - Melissa K. Passarelli
- University of Gothenburg, Department of Chemistry and Molecular
Biology, 41296 Gothenburg, Sweden
| | - Jun Wang
- University of Gothenburg, Department of Chemistry and Molecular
Biology, 41296 Gothenburg, Sweden
| | - Michael E. Kurczy
- Chalmers University, Department of Chemistry
and Biological Engineering, 41296 Gothenburg, Sweden
| | - Andrew G. Ewing
- University of Gothenburg, Department of Chemistry and Molecular
Biology, 41296 Gothenburg, Sweden
- Chalmers University, Department of Chemistry
and Biological Engineering, 41296 Gothenburg, Sweden
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38
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Mass Spectrometry-based Proteomics and Peptidomics for Systems Biology and Biomarker Discovery. ACTA ACUST UNITED AC 2012; 7:313-335. [PMID: 24504115 DOI: 10.1007/s11515-012-1218-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The scientific community has shown great interest in the field of mass spectrometry-based proteomics and peptidomics for its applications in biology. Proteomics technologies have evolved to produce large datasets of proteins or peptides involved in various biological and disease progression processes producing testable hypothesis for complex biological questions. This review provides an introduction and insight to relevant topics in proteomics and peptidomics including biological material selection, sample preparation, separation techniques, peptide fragmentation, post-translation modifications, quantification, bioinformatics, and biomarker discovery and validation. In addition, current literature and remaining challenges and emerging technologies for proteomics and peptidomics are presented.
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39
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Guo T, Fan L, Ng WH, Zhu Y, Ho M, Wan WK, Lim KH, Ong WS, Lee SS, Huang S, Kon OL, Sze SK. Multidimensional Identification of Tissue Biomarkers of Gastric Cancer. J Proteome Res 2012; 11:3405-13. [DOI: 10.1021/pr300212g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Tiannan Guo
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive,
Singapore 637551
| | - Lingling Fan
- Center for Stem Cell Research & Application, Union Hospital, Huazhong University of Science and Technology, Wuhan, P.R. China 430022
| | | | - Yi Zhu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive,
Singapore 637551
| | | | - Wei Keat Wan
- Pathology Department, Singapore General Hospital, Outram Road, Singapore
169608
| | - Kiat Hon Lim
- Pathology Department, Singapore General Hospital, Outram Road, Singapore
169608
| | | | | | - Shiang Huang
- Center for Stem Cell Research & Application, Union Hospital, Huazhong University of Science and Technology, Wuhan, P.R. China 430022
| | | | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive,
Singapore 637551
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40
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Barrera NP, Robinson CV. Advances in the mass spectrometry of membrane proteins: from individual proteins to intact complexes. Annu Rev Biochem 2011; 80:247-71. [PMID: 21548785 DOI: 10.1146/annurev-biochem-062309-093307] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Rapid advances in structural genomics and in large-scale proteomic projects have yielded vast amounts of data on soluble proteins and their complexes. Despite these advances, progress in studying membrane proteins using mass spectrometry (MS) has been slow. This is due in part to the inherent solubility and dynamic properties of these proteins, but also to their low abundance and the absence of polar side chains in amino acid residues. Considerable progress in overcoming these challenges is, however, now being made for all levels of structural characterization. This progress includes MS studies of the primary structure of membrane proteins, wherein sophisticated enrichment and trapping procedures are allowing multiple posttranslational modifications to be defined through to the secondary structure level in which proteins and peptides have been probed using hydrogen exchange, covalent, or radiolytic labeling methods. Exciting possibilities now exist to go beyond primary and secondary structure to reveal the tertiary and quaternary interactions of soluble and membrane subunits within intact assemblies of more than 700 kDa.
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Affiliation(s)
- Nelson P Barrera
- Department of Physiology, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile.
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41
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Rucevic M, Hixson D, Josic D. Mammalian plasma membrane proteins as potential biomarkers and drug targets. Electrophoresis 2011; 32:1549-64. [PMID: 21706493 DOI: 10.1002/elps.201100212] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Defining the plasma membrane proteome is crucial to understand the role of plasma membrane in fundamental biological processes. Change in membrane proteins is one of the first events that take place under pathological conditions, making plasma membrane proteins a likely source of potential disease biomarkers with prognostic or diagnostic potential. Membrane proteins are also potential targets for monoclonal antibodies and other drugs that block receptors or inhibit enzymes essential to the disease progress. Despite several advanced methods recently developed for the analysis of hydrophobic proteins and proteins with posttranslational modifications, integral membrane proteins are still under-represented in plasma membrane proteome. Recent advances in proteomic investigation of plasma membrane proteins, defining their roles as diagnostic and prognostic disease biomarkers and as target molecules in disease treatment, are presented.
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Affiliation(s)
- Marijana Rucevic
- COBRE Center for Cancer Research Development, Rhode Island Hospital, Providence, RI, USA
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42
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Maddalo G, Chovanec P, Stenberg-Bruzell F, Nielsen HV, Jensen-Seaman MI, Ilag LL, Kline KA, Daley DO. A reference map of the membrane proteome of Enterococcus faecalis. Proteomics 2011; 11:3935-41. [PMID: 21800426 DOI: 10.1002/pmic.201100103] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Revised: 06/08/2011] [Accepted: 07/11/2011] [Indexed: 11/06/2022]
Abstract
Enterococcus faecalis is a gram-positive bacterium that is part of the indigenous microbiotica of humans and animals as well as an opportunistic pathogen. In this study, we have fractionated the membrane proteome of E. faecalis and identified many of its constituents by mass spectrometry. We present blue native-/SDS-PAGE reference maps that contain 102 proteins. These proteins are important for cellular homeostasis, virulence, and antibiotic intervention. Intriguingly, many proteins with no known function were also identified, indicating that there are substantial gaps in the knowledge of this organism's biology. On a more limited scale, we also provide insight into the composition of membrane protein complexes. This study is a first step toward elucidating the membrane proteome of E. faecalis, which is critical for a better understanding of how this bacterium interacts with a host and with the extracellular milieu.
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Affiliation(s)
- Gianluca Maddalo
- Department of Analytical Chemistry, Stockholm University, Stockholm, Sweden
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43
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Mass spectrometry accelerates membrane protein analysis. Trends Biochem Sci 2011; 36:388-96. [PMID: 21616670 DOI: 10.1016/j.tibs.2011.04.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Revised: 04/19/2011] [Accepted: 04/19/2011] [Indexed: 12/25/2022]
Abstract
Cellular membranes are composed of proteins and glyco- and phospholipids and play an indispensible role in maintaining cellular integrity and homeostasis, by physically restricting biochemical processes within cells and providing protection. Membrane proteins perform many essential functions, which include operating as transporters, adhesion-anchors, receptors, and enzymes. Recent advancements in proteomic mass spectrometry have resulted in substantial progress towards the determination of the plasma membrane (PM) proteome, resolution of membrane protein topology, establishment of numerous receptor protein complexes, identification of ligand-receptor pairs, and the elucidation of signaling networks originating at the PM. Here, we discuss the recent accelerated success of discovery-based proteomic pipelines for the establishment of a complete membrane proteome.
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