1
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Hu J, Chang N, Hong C, Liu J, Zeng F, Gao H. A new method for studying the orientation of membrane proteins in plants based on the release of a fluorescent protein tag by TEV protease. PLANT COMMUNICATIONS 2023; 4:100602. [PMID: 37060178 PMCID: PMC10504556 DOI: 10.1016/j.xplc.2023.100602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/08/2023] [Accepted: 04/12/2023] [Indexed: 05/29/2023]
Affiliation(s)
- Jinglei Hu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Ning Chang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Conghao Hong
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Jia Liu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Fang Zeng
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Hongbo Gao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
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2
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Abstract
Is it possible to learn and create a first Hidden Markov Model (HMM) without programming skills or understanding the algorithms in detail? In this concise tutorial, we present the HMM through the 2 general questions it was initially developed to answer and describe its elements. The HMM elements include variables, hidden and observed parameters, the vector of initial probabilities, and the transition and emission probability matrices. Then, we suggest a set of ordered steps, for modeling the variables and illustrate them with a simple exercise of modeling and predicting transmembrane segments in a protein sequence. Finally, we show how to interpret the results of the algorithms for this particular problem. To guide the process of information input and explicit solution of the basic HMM algorithms that answer the HMM questions posed, we developed an educational webserver called HMMTeacher. Additional solved HMM modeling exercises can be found in the user’s manual and answers to frequently asked questions. HMMTeacher is available at https://hmmteacher.mobilomics.org, mirrored at https://hmmteacher1.mobilomics.org. A repository with the code of the tool and the webpage is available at https://gitlab.com/kmilo.f/hmmteacher.
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Affiliation(s)
- Camilo Fuentes-Beals
- PhD Program in Sciences Mention Modeling of Chemical and Biological Systems, School of Bioinformatics Engineering, Center for Bioinformatics, Simulation and Modeling, CBSM, Department of Bioinformatics, Faculty of Engineering, University of Talca, Campus Talca, Talca, Chile
| | - Alejandro Valdés-Jiménez
- Center for Bioinformatics, Simulation and Modeling, CBSM, Department of Bioinformatics, Faculty of Engineering, University of Talca, Campus Talca, Talca, Chile
| | - Gonzalo Riadi
- ANID–Millennium Science Initiative Program Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Center for Bioinformatics, Simulation and Modeling, CBSM, Department of Bioinformatics, Faculty of Engineering, University of Talca, Talca, Chile
- * E-mail:
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3
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Beeckmans S, Van Driessche E. Scrutinizing Coronaviruses Using Publicly Available Bioinformatic Tools: The Viral Structural Proteins as a Case Study. Front Mol Biosci 2021; 8:671923. [PMID: 34109214 PMCID: PMC8181738 DOI: 10.3389/fmolb.2021.671923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/15/2021] [Indexed: 01/18/2023] Open
Abstract
Since early 2020, the world suffers from a new beta-coronavirus, called SARS-CoV-2, that has devastating effects globally due to its associated disease, Covid-19. Until today, Covid-19, which not only causes life-threatening lung infections but also impairs various other organs and tissues, has killed hundreds of thousands of people and caused irreparable damage to many others. Since the very onset of the pandemic, huge efforts were made worldwide to fully understand this virus and numerous studies were, and still are, published. Many of these deal with structural analyses of the viral spike glycoprotein and with vaccine development, antibodies and antiviral molecules or immunomodulators that are assumed to become essential tools in the struggle against the virus. This paper summarizes knowledge on the properties of the four structural proteins (spike protein S, membrane protein M, envelope protein E and nucleocapsid protein N) of the SARS-CoV-2 virus and its relatives, SARS-CoV and MERS-CoV, that emerged few years earlier. Moreover, attention is paid to ways to analyze such proteins using freely available bioinformatic tools and, more importantly, to bring these proteins alive by looking at them on a computer/laptop screen with the easy-to-use but highly performant and interactive molecular graphics program DeepView. It is hoped that this paper will stimulate non-bioinformaticians and non-specialists in structural biology to scrutinize these and other macromolecules and as such will contribute to establishing procedures to fight these and maybe other forthcoming viruses.
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Affiliation(s)
- Sonia Beeckmans
- Research Unit Protein Chemistry, Vrije Universiteit Brussel, Brussels, Belgium
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4
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Klingler F, Mathias S, Schneider H, Buck T, Raab N, Zeh N, Shieh YW, Pfannstiel J, Otte K. Unveiling the CHO surfaceome: Identification of cell surface proteins reveals cell aggregation-relevant mechanisms. Biotechnol Bioeng 2021; 118:3015-3028. [PMID: 33951178 DOI: 10.1002/bit.27811] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/07/2021] [Accepted: 04/25/2021] [Indexed: 01/12/2023]
Abstract
Chinese hamster ovary (CHO) suspension cells are the main production hosts for biopharmaceuticals. For the improvement of production processes, it is essential to understand the interaction between CHO cells and their microenvironment. While the cellular membrane is the crucial surface barrier between the inner and outer cell compartments, the subgroup of cell surface proteins (surfaceome) is of particular interest due to its potential to react to external factors and initiate cell communication and interaction pathways. Therefore, the CHO surfaceome was explored for the first time by enriching exposed N-glycosylated membrane proteins before tandem mass spectrometry (MS/MS) analyses, identifying a total of 449 surface proteins, including 34 proteins specific for production cells. Functional annotation and classification located most proteins to the cell surface belonging mainly to the protein classes of receptors, enzymes, and transporters. In addition, adhesion molecules as cadherins, integrins, Ig superfamily and extracellular matrix (ECM) proteins as collagens, laminins, thrombospondin, fibronectin, and tenascin were significantly enriched, which are involved in mechanisms for the formation of cell junctions, cell-cell and cell-ECM adhesion as focal adhesions. As cell adhesion and aggregation counteracts scalable production of biopharmaceuticals, experimental validation confirmed differential expression of integrin β1 (ITGB1) and β3, CD44, laminin, and fibronectin on the surface of aggregation-prone CHO production cells. The subsequent modulation of the central interaction protein ITGB1 by small interfering RNA knockdown substantially counteracted cell aggregation pointing toward novel engineering routes for aggregation reduction in biopharmaceutical production cells and exemplifying the potential of the surfaceome for specified engineering strategies.
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Affiliation(s)
- Florian Klingler
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | - Sven Mathias
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany.,Early Stage Bioprocess Development, Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Helga Schneider
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | - Theresa Buck
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | - Nadja Raab
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | - Nikolas Zeh
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | - Yu-Wei Shieh
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | - Jens Pfannstiel
- Core Facility Mass Spectrometry, University of Hohenheim, Stuttgart, Germany
| | - Kerstin Otte
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
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5
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Halewa J, Marouillat S, Dixneuf M, Thépault RA, Ung DC, Chatron N, Gérard B, Ghoumid J, Lesca G, Till M, Smol T, Couque N, Ruaud L, Chune V, Grotto S, Verloes A, Vuillaume ML, Toutain A, Raynaud M, Laumonnier F. Novel missense mutations in PTCHD1 alter its plasma membrane subcellular localization and cause intellectual disability and autism spectrum disorder. Hum Mutat 2021; 42:848-861. [PMID: 33856728 PMCID: PMC8359977 DOI: 10.1002/humu.24208] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/29/2021] [Accepted: 04/08/2021] [Indexed: 12/22/2022]
Abstract
The X-linked PTCHD1 gene, encoding a synaptic membrane protein, has been involved in neurodevelopmental disorders with the description of deleterious genomic microdeletions or truncating coding mutations. Missense variants were also identified, however, without any functional evidence supporting their pathogenicity level. We investigated 13 missense variants of PTCHD1, including eight previously described (c.152G>A,p.(Ser51Asn); c.217C>T,p.(Leu73Phe); c.517A>G,p.(Ile173Val); c.542A>C,p.(Lys181Thr); c.583G>A,p.(Val195Ile); c.1076A>G,p.(His359Arg); c.1409C>A,p.(Ala470Asp); c.1436A>G,p.(Glu479Gly)), and five novel ones (c.95C>T,p.(Pro32Leu); c.95C>G,p.(Pro32Arg); c.638A>G,p.(Tyr213Cys); c.898G>C,p.(Gly300Arg); c.928G>C,p.(Ala310Pro)) identified in male patients with intellectual disability (ID) and/or autism spectrum disorder (ASD). Interestingly, several of these variants involve amino acids localized in structural domains such as transmembrane segments. To evaluate their potentially deleterious impact on PTCHD1 protein function, we performed in vitro overexpression experiments of the wild-type and mutated forms of PTCHD1-GFP in HEK 293T and in Neuro-2a cell lines as well as in mouse hippocampal primary neuronal cultures. We found that six variants impaired the expression level of the PTCHD1 protein, and were retained in the endoplasmic reticulum suggesting abnormal protein folding. Our functional analyses thus provided evidence of the pathogenic impact of missense variants in PTCHD1, which reinforces the involvement of the PTCHD1 gene in ID and in ASD.
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Affiliation(s)
- Judith Halewa
- UMR1253, iBrain, INSERM, University of Tours, Tours, France
| | | | - Manon Dixneuf
- UMR1253, iBrain, INSERM, University of Tours, Tours, France
| | | | - Dévina C Ung
- UMR1253, iBrain, INSERM, University of Tours, Tours, France
| | - Nicolas Chatron
- Department of Genetics, Hospices Civils de Lyon, Lyon, France.,Institut NeuroMyoGène, CNRS UMR-5310, INSERM U-1217, Univ Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Bénédicte Gérard
- Laboratoire de diagnostic génétique, Institut de Génétique Médicale d'Alsace, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Jamal Ghoumid
- EA7364 RADEME, Clinique de Génétique Guy Fontaine, Université de Lille, CHU de Lille, Lille, France
| | - Gaëtan Lesca
- Department of Genetics, Hospices Civils de Lyon, Lyon, France.,Institut NeuroMyoGène, CNRS UMR-5310, INSERM U-1217, Univ Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Marianne Till
- Department of Genetics, Hospices Civils de Lyon, Lyon, France
| | - Thomas Smol
- EA7364 RADEME, Institut de Génétique Médicale, Université de Lille, CHU de Lille, Lille, France
| | - Nathalie Couque
- Department of Genetics, APHP-Robert Debré University Hospital, Paris, France
| | - Lyse Ruaud
- Department of Genetics, APHP-Robert Debré University Hospital, Paris, France.,INSERM, UMR1141, Denis Diderot School of Medicine, Paris University, Paris, France
| | - Valérie Chune
- Department of Genetics, APHP-Robert Debré University Hospital, Paris, France
| | - Sarah Grotto
- Department of Genetics, APHP-Robert Debré University Hospital, Paris, France.,INSERM, UMR1141, Denis Diderot School of Medicine, Paris University, Paris, France
| | - Alain Verloes
- Department of Genetics, APHP-Robert Debré University Hospital, Paris, France.,INSERM, UMR1141, Denis Diderot School of Medicine, Paris University, Paris, France
| | - Marie-Laure Vuillaume
- UMR1253, iBrain, INSERM, University of Tours, Tours, France.,Service de Génétique, Centre hospitalier régional universitaire de Tours, Tours, France
| | - Annick Toutain
- UMR1253, iBrain, INSERM, University of Tours, Tours, France.,Service de Génétique, Centre hospitalier régional universitaire de Tours, Tours, France
| | - Martine Raynaud
- UMR1253, iBrain, INSERM, University of Tours, Tours, France.,Service de Génétique, Centre hospitalier régional universitaire de Tours, Tours, France
| | - Frédéric Laumonnier
- UMR1253, iBrain, INSERM, University of Tours, Tours, France.,Service de Génétique, Centre hospitalier régional universitaire de Tours, Tours, France
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6
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Sun F, Suttapitugsakul S, Wu R. Enzymatic Tagging of Glycoproteins on the Cell Surface for Their Global and Site-Specific Analysis with Mass Spectrometry. Anal Chem 2019; 91:4195-4203. [PMID: 30794380 PMCID: PMC6518397 DOI: 10.1021/acs.analchem.9b00441] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The cell surface is normally covered with sugars that are bound to lipids or proteins. Surface glycoproteins play critically important roles in many cellular events, including cell-cell communications, cell-matrix interactions, and response to environmental cues. Aberrant protein glycosylation on the cell surface is often a hallmark of human diseases such as cancer and infectious diseases. Global analysis of surface glycoproteins will result in a better understanding of glycoprotein functions and the molecular mechanisms of diseases and the discovery of surface glycoproteins as biomarkers and drug targets. Here, an enzyme is exploited to tag surface glycoproteins, generating a chemical handle for their selective enrichment prior to mass spectrometric (MS) analysis. The enzymatic reaction is very efficient, and the reaction conditions are mild, which are well-suited for surface glycoprotein tagging. For biologically triplicate experiments, on average 953 N-glycosylation sites on 393 surface glycoproteins per experiment were identified in MCF7 cells. Integrating chemical and enzymatic reactions with MS-based proteomics, the current method is highly effective to globally and site-specifically analyze glycoproteins only located on the cell surface. Considering the importance of surface glycoproteins, this method is expected to have extensive applications to advance glycoscience.
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Affiliation(s)
- Fangxu Sun
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Suttipong Suttapitugsakul
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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7
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Critchley WR, Pellet-Many C, Ringham-Terry B, Harrison MA, Zachary IC, Ponnambalam S. Receptor Tyrosine Kinase Ubiquitination and De-Ubiquitination in Signal Transduction and Receptor Trafficking. Cells 2018; 7:E22. [PMID: 29543760 PMCID: PMC5870354 DOI: 10.3390/cells7030022] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 03/09/2018] [Accepted: 03/13/2018] [Indexed: 12/13/2022] Open
Abstract
Receptor tyrosine kinases (RTKs) are membrane-based sensors that enable rapid communication between cells and their environment. Evidence is now emerging that interdependent regulatory mechanisms, such as membrane trafficking, ubiquitination, proteolysis and gene expression, have substantial effects on RTK signal transduction and cellular responses. Different RTKs exhibit both basal and ligand-stimulated ubiquitination, linked to trafficking through different intracellular compartments including the secretory pathway, plasma membrane, endosomes and lysosomes. The ubiquitin ligase superfamily comprising the E1, E2 and E3 enzymes are increasingly implicated in this post-translational modification by adding mono- and polyubiquitin tags to RTKs. Conversely, removal of these ubiquitin tags by proteases called de-ubiquitinases (DUBs) enables RTK recycling for another round of ligand sensing and signal transduction. The endocytosis of basal and activated RTKs from the plasma membrane is closely linked to controlled proteolysis after trafficking and delivery to late endosomes and lysosomes. Proteolytic RTK fragments can also have the capacity to move to compartments such as the nucleus and regulate gene expression. Such mechanistic diversity now provides new opportunities for modulating RTK-regulated cellular responses in health and disease states.
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Affiliation(s)
- William R Critchley
- Endothelial Cell Biology Unit, School of Molecular & Cellular Biology, University of Leeds, Leeds LS2 9JT, UK.
| | - Caroline Pellet-Many
- Centre for Cardiovascular Biology & Medicine, Rayne Building, University College London, London WC1E 6PT, UK.
| | - Benjamin Ringham-Terry
- Centre for Cardiovascular Biology & Medicine, Rayne Building, University College London, London WC1E 6PT, UK.
| | | | - Ian C Zachary
- Centre for Cardiovascular Biology & Medicine, Rayne Building, University College London, London WC1E 6PT, UK.
| | - Sreenivasan Ponnambalam
- Endothelial Cell Biology Unit, School of Molecular & Cellular Biology, University of Leeds, Leeds LS2 9JT, UK.
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8
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Evolution and adaptation of single-pass transmembrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:364-377. [DOI: 10.1016/j.bbamem.2017.11.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/29/2017] [Accepted: 11/07/2017] [Indexed: 12/19/2022]
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9
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Yu L, He H, Hu Z, Ma Z. Comprehensive quantification of N-glycoproteome in Fusarium graminearum reveals intensive glycosylation changes against fungicide. J Proteomics 2016; 142:82-90. [DOI: 10.1016/j.jprot.2016.05.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 04/10/2016] [Accepted: 05/09/2016] [Indexed: 11/28/2022]
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10
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Determining the N-terminal orientations of recombinant transmembrane proteins in the Escherichia coli plasma membrane. Sci Rep 2015; 5:15086. [PMID: 26462555 PMCID: PMC4604451 DOI: 10.1038/srep15086] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 09/11/2015] [Indexed: 11/08/2022] Open
Abstract
In silico algorithms have been the common approach for transmembrane (TM) protein topology prediction. However, computational tools may produce questionable results and experimental validation has proven difficult. Although biochemical strategies are available to determine the C-terminal orientation of TM proteins, experimental strategies to determine the N-terminal orientation are still limited but needed because the N-terminal end is essential for membrane targeting. Here, we describe a new and easy method to effectively determine the N-terminal orientation of the target TM proteins in Escherichia coli plasma membrane environment. D94N, the mutant of bacteriorhodopsin from Haloarcula marismortui, can be a fusion partner to increase the production of the target TM proteins if their N-termini are in cytoplasm (Nin orientation). To create a suitable linker for orientating the target TM proteins with the periplasmic N-termini (Nout orientation) correctly, we designed a three-TM-helix linker fused at the C-terminus of D94N fusion partner (termed D94N-3TM) and found that D94N-3TM can specifically improve the production of the Nout target TM proteins. In conclusion, D94N and D94N-3TM fusion partners can be applied to determine the N-terminal end of the target TM proteins oriented either Nin or Nout by evaluating the net expression of the fusion proteins.
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11
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Jun MH, Jun YW, Kim KH, Lee JA, Jang DJ. Characterization of the cellular localization of C4orf34 as a novel endoplasmic reticulum resident protein. BMB Rep 2015; 47:563-8. [PMID: 24499674 PMCID: PMC4261514 DOI: 10.5483/bmbrep.2014.47.10.252] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Indexed: 01/09/2023] Open
Abstract
Human genome projects have enabled whole genome mapping and improved our understanding of the genes in humans. However, many unknown genes remain to be functionally characterized. In this study, we characterized human chromosome 4 open reading frame 34 gene (hC4orf34). hC4orf34 was highly conserved from invertebrate to mammalian cells and ubiquitously expressed in the organs of mice, including the heart and brain. Interestingly, hC4orf34 is a novel ER-resident, type I transmembrane protein. Mutant analysis showed that the transmembrane domain (TMD) of hC4orf34 was involved in ER retention. Overall, our results indicate that hC4orf34 is an ER-resident type I transmembrane protein, and might play a role in ER functions including Ca2+ homeostasis and ER stress. [BMB Reports 2014; 47(10): 563-568]
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Affiliation(s)
- Mi-Hee Jun
- Department of Biotechnology, College of Life Science and Nano Technology, Hannam University, Daejeon 305-811, Korea
| | - Young-Wu Jun
- Department of Ecological Science, College of Ecology and Environment, Kyungpook National University, Sangju 742-711, Korea
| | - Kun-Hyung Kim
- Department of Ecological Science, College of Ecology and Environment, Kyungpook National University, Sangju 742-711, Korea
| | - Jin-A Lee
- Department of Biotechnology, College of Life Science and Nano Technology, Hannam University, Daejeon 305-811, Korea
| | - Deok-Jin Jang
- Department of Ecological Science, College of Ecology and Environment, Kyungpook National University, Sangju 742-711, Korea
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12
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Lin CH, Chen CY. Characterization of the Dual Subcellular Localization of Lilium LsGRP1, a Plant Class II Glycine-Rich Protein. PHYTOPATHOLOGY 2014; 104:1012-1020. [PMID: 25207480 DOI: 10.1094/phyto-01-14-0020-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The defense-related gene LsGRP1 exhibits an increased level of expression in Lilium spp. after being infected by Botrytis elliptica, the fungal pathogen of lily leaf blight. In this study, the expression profile of the LsGRP1 protein (a plant class II glycine-rich protein) was characterized biochemically and its subcellular localization in lily leaves was evaluated using immunohistochemistry, enhanced green fluorescent protein (EGFP) imaging, and protein extraction analysis. Using an LsGRP1-specific antibody, LsGRP1 was found to be most abundant in epidermal cells and phloem tissues. Leaves from lily plants at different growth stages demonstrated similar levels of 14- and 16-kDa LsGRP1 and a decreased amount of 23-kDa LsGRP1 at the senescence stage. LsGRP1-EGFP imaging and protein extraction assays revealed that 14-kDa LsGRP1 was located in the plasma membrane whereas 16- and 23-kDa LsGRP1 was weakly bound to the cell wall. The time course analyses of LsGRP1 expression in response to salicylic acid treatment or B. elliptica infection showed an increased accumulation of 14- and 23-kDa LsGRP1 over time. Because 23-kDa LsGRP1 could be detected by an ubiquitin antibody, conversion of 14-kDa to 23-kDa LsGRP1 via mono-ubiquitination was presumed, which is a phenomenon that has not been reported for a plant class II glycine-rich protein.
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13
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Zhu J, Sun Z, Cheng K, Chen R, Ye M, Xu B, Sun D, Wang L, Liu J, Wang F, Zou H. Comprehensive Mapping of Protein N-Glycosylation in Human Liver by Combining Hydrophilic Interaction Chromatography and Hydrazide Chemistry. J Proteome Res 2014; 13:1713-21. [DOI: 10.1021/pr401200h] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Jun Zhu
- Key
Lab of Separation Science for Analytical Chemistry, National Chromatographic
Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Zhen Sun
- Key
Lab of Separation Science for Analytical Chemistry, National Chromatographic
Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Kai Cheng
- Key
Lab of Separation Science for Analytical Chemistry, National Chromatographic
Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Rui Chen
- Key
Lab of Separation Science for Analytical Chemistry, National Chromatographic
Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Mingliang Ye
- Key
Lab of Separation Science for Analytical Chemistry, National Chromatographic
Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Bo Xu
- Key
Lab of Separation Science for Analytical Chemistry, National Chromatographic
Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Deguang Sun
- The Second Affiliated Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian 116027, China
| | - Liming Wang
- The Second Affiliated Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian 116027, China
| | - Jing Liu
- Key
Lab of Separation Science for Analytical Chemistry, National Chromatographic
Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Fangjun Wang
- Key
Lab of Separation Science for Analytical Chemistry, National Chromatographic
Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Hanfa Zou
- Key
Lab of Separation Science for Analytical Chemistry, National Chromatographic
Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
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14
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Su PC, Berger BW. A Novel Assay for Assessing Juxtamembrane and Transmembrane Domain Interactions Important for Receptor Heterodimerization. J Mol Biol 2013; 425:4652-8. [DOI: 10.1016/j.jmb.2013.07.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 07/12/2013] [Accepted: 07/15/2013] [Indexed: 10/26/2022]
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15
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Lin Y, Wang K, Yan Y, Lin H, Peng B, Liu Z. Evaluation of the combinative application of SDS and sodium deoxycholate to the LC-MS-based shotgun analysis of membrane proteomes. J Sep Sci 2013; 36:3026-34. [DOI: 10.1002/jssc.201300413] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Revised: 06/06/2013] [Accepted: 06/21/2013] [Indexed: 12/17/2022]
Affiliation(s)
- Yong Lin
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients; Hunan Agricultural University; Changsha P. R. China
- Key Laboratory of Tea Science of Ministry of Education; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P. R. China
| | - Kunbo Wang
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients; Hunan Agricultural University; Changsha P. R. China
- Key Laboratory of Tea Science of Ministry of Education; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P. R. China
| | - Yujun Yan
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients; Hunan Agricultural University; Changsha P. R. China
| | - Haiyan Lin
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients; Hunan Agricultural University; Changsha P. R. China
- Key Laboratory of Tea Science of Ministry of Education; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P. R. China
| | - Bin Peng
- Key Laboratory of Tea Science of Ministry of Education; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P. R. China
| | - Zhonghua Liu
- National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients; Hunan Agricultural University; Changsha P. R. China
- Key Laboratory of Tea Science of Ministry of Education; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P. R. China
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16
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Zhu G, Sun L, Keithley RB, Dovichi NJ. Capillary isoelectric focusing-tandem mass spectrometry and reversed-phase liquid chromatography-tandem mass spectrometry for quantitative proteomic analysis of differentiating PC12 cells by eight-plex isobaric tags for relative and absolute quantification. Anal Chem 2013; 85:7221-9. [PMID: 23822771 DOI: 10.1021/ac4009868] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We report the application of capillary isoelectric focusing for quantitative analysis of a complex proteome. Biological duplicates were generated from PC12 cells at days 0, 3, 7, and 12 following treatment with nerve growth factor. These biological duplicates were digested with trypsin, labeled using eight-plex isobaric tags for relative and absolute quantification (iTRAQ) chemistry, and pooled. The pooled peptides were separated into 25 fractions using reversed-phase liquid chromatography (RPLC). Technical duplicates of each fraction were separated by capillary isoelectric focusing (cIEF) using a set of amino acids as ampholytes. The cIEF column was interfaced to an Orbitrap Velos mass spectrometer with an electrokinetically pumped sheath-flow nanospray interface. This HPLC-cIEF-electrospray-tandem mass spectrometry (ESI-MS/MS) approach identified 835 protein groups and produced 2,329 unique peptides IDs. The biological duplicates were analyzed in parallel using conventional strong-cation exchange (SCX)-RPLC-ESI-MS/MS. The iTRAQ peptides were first separated into eight fractions using SCX. Each fraction was then analyzed by RPLC-ESI-MS/MS. The SCX-RPLC approach generated 1,369 protein groups and 3,494 unique peptide IDs. For protein quantitation, 96 and 198 differentially expressed proteins were obtained with RPLC-cIEF and SCX-RPLC, respectively. The combined set identified 231 proteins. Protein expression changes measured by RPLC-cEIF and SCX-RPLC were highly correlated.
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Affiliation(s)
- Guijie Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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17
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TMEM126A is a mitochondrial located mRNA (MLR) protein of the mitochondrial inner membrane. Biochim Biophys Acta Gen Subj 2013; 1830:3719-33. [DOI: 10.1016/j.bbagen.2013.02.025] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 02/13/2013] [Accepted: 02/26/2013] [Indexed: 12/22/2022]
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18
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Sodium laurate, a novel protease- and mass spectrometry-compatible detergent for mass spectrometry-based membrane proteomics. PLoS One 2013; 8:e59779. [PMID: 23555778 PMCID: PMC3610932 DOI: 10.1371/journal.pone.0059779] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 02/18/2013] [Indexed: 11/22/2022] Open
Abstract
The hydrophobic nature of most membrane proteins severely complicates their extraction, proteolysis and identification. Although detergents can be used to enhance the solubility of the membrane proteins, it is often difficult for a detergent not only to have a strong ability to extract membrane proteins, but also to be compatible with the subsequent proteolysis and mass spectrometric analysis. In this study, we made evaluation on a novel application of sodium laurate (SL) to the shotgun analysis of membrane proteomes. SL was found not only to lyse the membranes and solubilize membrane proteins as efficiently as SDS, but also to be well compatible with trypsin and chymotrypsin. Furthermore, SL could be efficiently removed by phase transfer method from samples after acidification, thus ensuring not to interfere with the subsequent CapLC-MS/MS analysis of the proteolytic peptides of proteins. When SL was applied to assist the digestion and identification of a standard protein mixture containing bacteriorhodoposin and the proteins in rat liver plasma membrane-enriched fractions, it was found that, compared with other two representative enzyme- and MS-compatible detergents RapiGest SF (RGS) and sodium deoxycholate (SDC), SL exhibited obvious superiority in the identification of membrane proteins particularly those with high hydrophobicity and/or multiple transmembrane domains.
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19
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Adaptation of low-resolution methods for the study of yeast microsomal polytopic membrane proteins: a methodological review. Biochem Soc Trans 2013; 41:35-42. [DOI: 10.1042/bst20120212] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Most integral membrane proteins of yeast with two or more membrane-spanning sequences have not yet been crystallized and for many of them the side on which the active sites or ligand-binding domains reside is unknown. Also, bioinformatic topology predictions are not yet fully reliable. However, so-called low-resolution biochemical methods can be used to locate hydrophilic loops or individual residues of polytopic membrane proteins at one or the other side of the membrane. The advantages and limitations of several such methods for topological studies with yeast ER integral membrane proteins are discussed. We also describe new tools that allow us to better control and validate results obtained with SCAM (substituted cysteine accessibility method), an approach that determines the position of individual residues with respect to the membrane plane, whereby only minimal changes in the primary sequence have to be introduced into the protein of interest.
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20
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Retraction. Protein domains, catalytic activity, and subcellular distribution of mouse NTE-related esterase. Mol Cell Biochem 2013; 371:233. [PMID: 23281490 DOI: 10.1007/s11010-009-0185-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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21
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Nixon A, Jia Y, White C, Bradbury NA. Determination of the membrane topology of lemur tyrosine kinase 2 (LMTK2) by fluorescence protease protection. Am J Physiol Cell Physiol 2012; 304:C164-9. [PMID: 23114966 DOI: 10.1152/ajpcell.00288.2012] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Lemur tyrosine kinase 2 (LMTK2) is a novel membrane-anchored kinase reported to be involved in several normal and pathophysiological conditions, including endosomal membrane recycling, prostate cancer, and neurodegeneration. In this study, we have investigated the topology and orientation of LMTK2 within cellular membranes utilizing fluorescence protease protection. Appending the green fluorescent protein to either the amino or carboxyl terminus of LMTK2, we were able to determine which side of intracellular membrane these regions were located. Our results indicate that LMTK2 is an integral membrane protein in which both the amino and carboxyl termini are exposed to the cytoplasm. Moreover, this topology places the kinase active site within the cytoplasm.
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Affiliation(s)
- Alexander Nixon
- Department of Physiology and Biophysics, Chicago Medical School, North Chicago, IL 60064, USA
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22
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Sun Z, Chen R, Cheng K, Liu H, Qin H, Ye M, Zou H. A new method for quantitative analysis of cell surface glycoproteome. Proteomics 2012; 12:3328-37. [DOI: 10.1002/pmic.201200150] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 07/10/2012] [Accepted: 09/10/2012] [Indexed: 12/22/2022]
Affiliation(s)
- Zhen Sun
- Key Laboratory of Separation Sciences for Analytical Chemistry; National Chromatographic R&A Center; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian China
| | - Rui Chen
- Key Laboratory of Separation Sciences for Analytical Chemistry; National Chromatographic R&A Center; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian China
| | - Kai Cheng
- Key Laboratory of Separation Sciences for Analytical Chemistry; National Chromatographic R&A Center; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian China
| | - Hongwei Liu
- Key Laboratory of Separation Sciences for Analytical Chemistry; National Chromatographic R&A Center; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian China
| | - Hongqiang Qin
- Key Laboratory of Separation Sciences for Analytical Chemistry; National Chromatographic R&A Center; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian China
| | - Mingliang Ye
- Key Laboratory of Separation Sciences for Analytical Chemistry; National Chromatographic R&A Center; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian China
| | - Hanfa Zou
- Key Laboratory of Separation Sciences for Analytical Chemistry; National Chromatographic R&A Center; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian China
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23
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Pagac M, Vazquez HM, Bochud A, Roubaty C, Knöpfli C, Vionnet C, Conzelmann A. Topology of the microsomal glycerol-3-phosphate acyltransferase Gpt2p/Gat1p ofSaccharomyces cerevisiae. Mol Microbiol 2012; 86:1156-66. [DOI: 10.1111/mmi.12047] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/18/2012] [Indexed: 02/06/2023]
Affiliation(s)
- Martin Pagac
- Department of Biology; University of Fribourg; CH-1700; Fribourg; Switzerland
| | - Hector M. Vazquez
- Department of Biology; University of Fribourg; CH-1700; Fribourg; Switzerland
| | - Arlette Bochud
- Department of Biology; University of Fribourg; CH-1700; Fribourg; Switzerland
| | - Carole Roubaty
- Department of Biology; University of Fribourg; CH-1700; Fribourg; Switzerland
| | - Cécile Knöpfli
- Department of Biology; University of Fribourg; CH-1700; Fribourg; Switzerland
| | - Christine Vionnet
- Department of Biology; University of Fribourg; CH-1700; Fribourg; Switzerland
| | - Andreas Conzelmann
- Department of Biology; University of Fribourg; CH-1700; Fribourg; Switzerland
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24
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Su PC, Berger BW. Identifying key juxtamembrane interactions in cell membranes using AraC-based transcriptional reporter assay (AraTM). J Biol Chem 2012; 287:31515-26. [PMID: 22822084 DOI: 10.1074/jbc.m112.396895] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Dimerization is a key regulatory mechanism in activation of transmembrane (TM) receptors during signal transduction. This process involves a coordinated interplay between extracellular (EX), TM, and cytoplasmic (CYTO) regions to form a specific interface required for both ligand binding and intracellular signaling to occur. While several transcriptional activator-based methods exist for investigating TM interactions in bacterial membranes, expression of TM chimera in these methods occurs in a reverse orientation, and are limited to only TM domains for proper membrane trafficking and integration. We therefore developed a new, AraC-based transcriptional reporter assay (AraTM) that expresses EX-TM-CYTO chimera in their native orientation, thereby enabling membrane trafficking to occur independent of the TM chimera used as well as permitting analysis of EX-TM-CYTO interactions in biological membranes. Using integrin α(IIb) TM-CYTO as a model, we observe a large increase in homodimerization for the constitutively active TM mutant L980A relative to wild-type in the TM-CYTO construct (A963-E1008). We also characterized the receptor for advanced glycation endproducts (RAGE), whose homooligomeric state is critical in ligand recognition, and find the specific juxtamembrane region within the CYTO (A375-P394) mediates homodimerization, and is dominant over effects observed when the extracellular C2 domain is included. Furthermore, we find good agreement between our AraTM measurements in bacterial membranes and BRET measurements made on corresponding RAGE constructs expressed in transfected HEK293 cells. Overall, the AraTM assay provides a new approach to identify specific interactions between receptor EX-TM-CYTO domains in biological membranes that are important in regulation of signal transduction.
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Affiliation(s)
- Pin-Chuan Su
- Department of Chemical Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, USA
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25
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Abstract
Integral membrane proteins of the cell surface and most intracellular compartments of eukaryotic cells are assembled at the endoplasmic reticulum. Two highly conserved and parallel pathways mediate membrane protein targeting to and insertion into this organelle. The classical cotranslational pathway, utilized by most membrane proteins, involves targeting by the signal recognition particle followed by insertion via the Sec61 translocon. A more specialized posttranslational pathway, employed by many tail-anchored membrane proteins, is composed of entirely different factors centered around a cytosolic ATPase termed TRC40 or Get3. Both of these pathways overcome the same biophysical challenges of ferrying hydrophobic cargo through an aqueous milieu, selectively delivering it to one among several intracellular membranes and asymmetrically integrating its transmembrane domain(s) into the lipid bilayer. Here, we review the conceptual and mechanistic themes underlying these core membrane protein insertion pathways, the complexities that challenge our understanding, and future directions to overcome these obstacles.
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Affiliation(s)
- Sichen Shao
- Cell Biology and Metabolism Program, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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26
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Lee JE, Kwon J, Baek MC. A combination method of chemical with enzyme reactions for identification of membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:397-404. [PMID: 21146638 DOI: 10.1016/j.bbapap.2010.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Revised: 11/30/2010] [Accepted: 12/02/2010] [Indexed: 11/29/2022]
Abstract
A simple method for effective analysis of various proteins has been developed, including membrane proteins, with LC-MS/MS, using CNBr and acetic acid cleavage in one reaction for the digestion of both the M/ and /D/ positions within the target proteins. This dual chemical reaction has been compared with traditional CNBr or an acid cleavage method using a rat kidney membrane fraction and it showed an advantage of the dual reaction with respect to a high number of peptides detected and a high protein recovery. Furthermore, when this dual chemical reaction was combined with trypsin digestion, the number of proteins surprisingly increased approximately 3.0 times more than in the cases with the trypsin digestion only. It was also 1.9 times more than in cases dealing with Tube-Gel trypsin digestion, which is one of the most efficient digestion methods. In addition, it was shown that this dual chemical reaction could be applied to an in-gel digestion. Using the combination of the chemical and enzyme reaction, 172 proteins including 95 membrane proteins were identified. This indicated that this method is one of the efficient systems in single MS/MS analysis. In particular, many membrane proteins identified in this study were detected by a new combination, but not by a traditional trypsin digestion method.
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Affiliation(s)
- Jeong-Eun Lee
- Dept. of Molecular Medicine, Kyungpook National University, Daegu, 700-422, Republic of Korea.
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27
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Sun L, Tao D, Han B, Ma J, Zhu G, Liang Z, Shan Y, Zhang L, Zhang Y. Ionic liquid 1-butyl-3-methyl imidazolium tetrafluoroborate for shotgun membrane proteomics. Anal Bioanal Chem 2010; 399:3387-97. [DOI: 10.1007/s00216-010-4381-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 10/11/2010] [Accepted: 10/24/2010] [Indexed: 12/25/2022]
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28
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Identification of topological determinants in the N-terminal domain of transcription factor Nrf1 that control its orientation in the endoplasmic reticulum membrane. Biochem J 2010; 430:497-510. [PMID: 20629635 DOI: 10.1042/bj20100471] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Nrf1 [NF-E2 (nuclear factor-erythroid 2)-related factor 1] is a CNC (cap'n'collar) bZIP (basic-region leucine zipper) transcription factor that is tethered to ER (endoplasmic reticulum) and nuclear envelope membranes through its N-terminal signal peptide (residues 1-30). Besides the signal peptide, amino acids 31-90 of Nrf1 also negatively regulate the CNC-bZIP factor. In the present study we have tested the hypothesis that amino acids 31-90 of Nrf1, and the overlapping NHB2 (N-terminal homology box 2; residues 82-106), inhibit Nrf1 because they control its topology within membranes. This region contains three amphipathic alpha-helical regions comprising amino acids 31-50 [called the SAS (signal peptide-associated sequence)], 55-82 [called the CRACs (cholesterol-recognition amino acid consensus sequences)] and 89-106 (part of NHB2). We present experimental data showing that the signal peptide of Nrf1 contains a TM1 (transmembrane 1) region (residues 7-24) that is orientated across the ER membrane in an N(cyt)/C(lum) fashion with its N-terminus facing the cytoplasm and its C-terminus positioned in the lumen of the ER. Once Nrf1 is anchored to the ER membrane through TM1, the remaining portion of the N-terminal domain (NTD, residues 1-124) is transiently translocated into the ER lumen. Thereafter, Nrf1 adopts a topology in which the SAS is inserted into the membrane, the CRACs are probably repartitioned to the cytoplasmic side of the ER membrane, and NHB2 may serve as an anchor switch, either lying on the luminal surface of the ER or traversing the membrane with an N(cyt)/C(lum) orientation. Thus Nrf1 can adopt several topologies within membranes that are determined by its NTD.
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29
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Domingo B, Gasset M, Durán-Prado M, Castaño JP, Serrano A, Fischer T, Llopis J. Discrimination between alternate membrane protein topologies in living cells using GFP/YFP tagging and pH exchange. Cell Mol Life Sci 2010; 67:3345-54. [PMID: 20454916 PMCID: PMC11115537 DOI: 10.1007/s00018-010-0386-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 03/30/2010] [Accepted: 04/22/2010] [Indexed: 02/05/2023]
Abstract
Membrane protein function is determined by the relative organization of the protein domains with respect to the membrane. We have experimentally verified the topology of a protein with diverse orientations arising from a single primary sequence (the cellular prion protein, PrP(C)), a novel somatostatin truncated receptor, and the Golgi-associated protein GPBP(91). Tagging with fluorescent proteins (FP) allows location of their expression at the plasma membrane or at endomembranes, but does not inform about their orientation. Exploiting the pH dependency of some FPs, we developed a pH exchange assay in which extracellularly exposed FPs are quenched by application of low pH buffer. We constructed standards to demonstrate and calibrate the assay, and the method was adapted for acidic organelle membrane proteins. This method can serve as a proof of concept, experimentally confirming and/or discriminating in living cells among theoretical topology predictions, providing the proportion of inside/outside orientation for proteins with multiple forms.
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Affiliation(s)
- Beatriz Domingo
- Centro Regional de Investigaciones Biomédicas y Facultad de Medicina, Universidad de Castilla-La Mancha, 02006 Albacete, Spain
| | - María Gasset
- Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Mario Durán-Prado
- Instituto de Parasitología y Biomedicina López-Neyra, CSIC, 18100 Granada, Spain
| | - Justo P. Castaño
- Departamento de Biología Celular, Fisiología e Inmunología, Universidad de Córdoba, Edificio Severo Ochoa, Planta 3. Campus de Rabanales, Córdoba, Spain
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn 06/03), Córdoba, Spain
| | | | | | - Juan Llopis
- Centro Regional de Investigaciones Biomédicas y Facultad de Medicina, Universidad de Castilla-La Mancha, 02006 Albacete, Spain
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Osmanbeyoglu HU, Wehner JA, Carbonell JG, Ganapathiraju MK. Active machine learning for transmembrane helix prediction. BMC Bioinformatics 2010; 11 Suppl 1:S58. [PMID: 20122233 PMCID: PMC3009531 DOI: 10.1186/1471-2105-11-s1-s58] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Background About 30% of genes code for membrane proteins, which are involved in a wide variety of crucial biological functions. Despite their importance, experimentally determined structures correspond to only about 1.7% of protein structures deposited in the Protein Data Bank due to the difficulty in crystallizing membrane proteins. Algorithms that can identify proteins whose high-resolution structure can aid in predicting the structure of many previously unresolved proteins are therefore of potentially high value. Active machine learning is a supervised machine learning approach which is suitable for this domain where there are a large number of sequences but only very few have known corresponding structures. In essence, active learning seeks to identify proteins whose structure, if revealed experimentally, is maximally predictive of others. Results An active learning approach is presented for selection of a minimal set of proteins whose structures can aid in the determination of transmembrane helices for the remaining proteins. TMpro, an algorithm for high accuracy TM helix prediction we previously developed, is coupled with active learning. We show that with a well-designed selection procedure, high accuracy can be achieved with only few proteins. TMpro, trained with a single protein achieved an F-score of 94% on benchmark evaluation and 91% on MPtopo dataset, which correspond to the state-of-the-art accuracies on TM helix prediction that are achieved usually by training with over 100 training proteins. Conclusion Active learning is suitable for bioinformatics applications, where manually characterized data are not a comprehensive representation of all possible data, and in fact can be a very sparse subset thereof. It aids in selection of data instances which when characterized experimentally can improve the accuracy of computational characterization of remaining raw data. The results presented here also demonstrate that the feature extraction method of TMpro is well designed, achieving a very good separation between TM and non TM segments.
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Affiliation(s)
- Hatice U Osmanbeyoglu
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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31
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Chang PA, Wang ZX, Long DX, Qin WZ, Wu YJ. Protein domains, catalytic activity, and subcellular distribution of mouse NTE-related esterase. Mol Cell Biochem 2010; 339:181-90. [PMID: 20058052 DOI: 10.1007/s11010-009-0382-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Accepted: 06/09/2009] [Indexed: 12/21/2022]
Abstract
A mammalian family of lipid hydrolases, designated "patatin-like phospholipase domain containing (PNPLA)" recently has attracted attention. NTE-related esterase (NRE) as a member of PNPLA is an insulin-regulated lysophospholipase with homology to neuropathy target esterase (NTE). Mouse NRE (mNRE) has a predicted amino-terminal transmembrane region (TM), a putative regulatory (R) domain, and a hydrophobic catalytic (C) domain. In the current study, we described the expression of green fluorescent protein (GFP)-tagged constructs of mNRE and mutant proteins lacking the specific protein domains. Esterase assays indicated that neither the TM nor R-domain was essential for mNRE esterase activity, but the TM significantly contributed to its activity. Subcellular distribution showed that mNRE was anchored in ER via its TM domain and that its C-domain was associated with ER. Furthermore, experiments involving proteinase treatment revealed that most of mNRE molecule was exposed on the cytoplasmic face of ER membranes. Collectively, our results for the first time revealed the protein domains, catalytic activity, and subcellular location of mNRE and a simplified model for mNRE was proposed.
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Affiliation(s)
- Ping-An Chang
- Key Laboratory of Molecular Biology, College of Bio-information, Chongqing University of Posts and Telecommunications, Nan'an District, 400065 Chongqing, People's Republic of China.
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Trusch M, Böhlick A, Hildebrand D, Lichtner B, Bertsch A, Kohlbacher O, Bachmann S, Schlüter H. Application of displacement chromatography for the analysis of a lipid raft proteome. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 878:309-14. [PMID: 20015709 DOI: 10.1016/j.jchromb.2009.11.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 10/16/2009] [Accepted: 11/20/2009] [Indexed: 10/20/2022]
Abstract
Defining membrane proteomes is fundamental to understand the role of membrane proteins in biological processes and to find new targets for drug development. Usually multidimensional chromatography using step or gradient elution is applied for the separation of tryptic peptides of membrane proteins prior to their mass spectrometric analysis. Displacement chromatography (DC) offers several advantages that are helpful for proteome analysis. However, DC has so far been applied for proteomic investigations only in few cases. In this study we therefore applied DC in a multidimensional LC-MS approach for the separation and identification of membrane proteins located in cholesterol-enriched membrane microdomains (lipid rafts) obtained from rat kidney by density gradient centrifugation. The tryptic peptides were separated on a cation-exchange column in the displacement mode with spermine used as displacer. Fractions obtained from DC were analyzed using an HPLC-chip system coupled to an electrospray-ionization ion-trap mass spectrometer. This procedure yielded more than 400 highly significant peptide spectrum matches and led to the identification of more than 140 reliable protein hits within an established rat kidney lipid raft proteome. The majority of identified proteins were membrane proteins. In sum, our results demonstrate that DC is a suitable alternative to gradient elution separations for the identification of proteins via a multidimensional LC-MS approach.
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Affiliation(s)
- Maria Trusch
- Department of Clinical Chemistry, University Medical Center Hamburg-Eppendorf, Campus Forschung, Martinistr. 52, D-20246 Hamburg, Germany.
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Doolittle MH, Neher SB, Ben-Zeev O, Ling-Liao J, Gallagher CM, Hosseini M, Yin F, Wong H, Walter P, Péterfy M. Lipase maturation factor LMF1, membrane topology and interaction with lipase proteins in the endoplasmic reticulum. J Biol Chem 2009; 284:33623-33. [PMID: 19783858 DOI: 10.1074/jbc.m109.049395] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Lipase maturation factor 1 (LMF1) is predicted to be a polytopic protein localized to the endoplasmic reticulum (ER) membrane. It functions in the post-translational attainment of enzyme activity for both lipoprotein lipase and hepatic lipase. By using transmembrane prediction methods in mouse and human orthologs, models of LMF1 topology were constructed and tested experimentally. Employing a tagging strategy that used insertion of ectopic glycan attachment sites and terminal fusions of green fluorescent protein, we established a five-transmembrane model, thus dividing LMF1 into six domains. Three domains were found to face the cytoplasm (the amino-terminal domain and loops B and D), and the other half was oriented to the ER lumen (loops A and C and the carboxyl-terminal domain). This representative model shows the arrangement of an evolutionarily conserved domain within LMF1 (DUF1222) that is essential to lipase maturation. DUF1222 comprises four of the six domains, with the two largest ones facing the ER lumen. We showed for the first time, using several naturally occurring variants featuring DUF1222 truncations, that Lmf1 interacts physically with lipoprotein lipase and hepatic lipase and localizes the lipase interaction site to loop C within DUF1222. We discuss the implication of our results with regard to lipase maturation and DUF1222 domain structure.
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Affiliation(s)
- Mark H Doolittle
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA.
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Velho AM, Jarvis SM. Topological studies of hSVCT1, the human sodium-dependent vitamin C transporter and the influence of N-glycosylation on its intracellular targeting. Exp Cell Res 2009; 315:2312-21. [PMID: 19379732 DOI: 10.1016/j.yexcr.2009.04.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Accepted: 04/12/2009] [Indexed: 10/20/2022]
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Blackler AR, Speers AE, Ladinsky MS, Wu CC. A shotgun proteomic method for the identification of membrane-embedded proteins and peptides. J Proteome Res 2008; 7:3028-34. [PMID: 18537282 DOI: 10.1021/pr700795f] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Integral membrane proteins perform crucial cellular functions and are the targets for the majority of pharmaceutical agents. However, the hydrophobic nature of their membrane-embedded domains makes them difficult to work with. Here, we describe a shotgun proteomic method for the high-throughput analysis of the membrane-embedded transmembrane domains of integral membrane proteins which extends the depth of coverage of the membrane proteome.
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Affiliation(s)
- Adele R Blackler
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
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36
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Ganapathiraju M, Balakrishnan N, Reddy R, Klein-Seetharaman J. Transmembrane helix prediction using amino acid property features and latent semantic analysis. BMC Bioinformatics 2008; 9 Suppl 1:S4. [PMID: 18315857 PMCID: PMC2259405 DOI: 10.1186/1471-2105-9-s1-s4] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background Prediction of transmembrane (TM) helices by statistical methods suffers from lack of sufficient training data. Current best methods use hundreds or even thousands of free parameters in their models which are tuned to fit the little data available for training. Further, they are often restricted to the generally accepted topology "cytoplasmic-transmembrane-extracellular" and cannot adapt to membrane proteins that do not conform to this topology. Recent crystal structures of channel proteins have revealed novel architectures showing that the above topology may not be as universal as previously believed. Thus, there is a need for methods that can better predict TM helices even in novel topologies and families. Results Here, we describe a new method "TMpro" to predict TM helices with high accuracy. To avoid overfitting to existing topologies, we have collapsed cytoplasmic and extracellular labels to a single state, non-TM. TMpro is a binary classifier which predicts TM or non-TM using multiple amino acid properties (charge, polarity, aromaticity, size and electronic properties) as features. The features are extracted from sequence information by applying the framework used for latent semantic analysis of text documents and are input to neural networks that learn the distinction between TM and non-TM segments. The model uses only 25 free parameters. In benchmark analysis TMpro achieves 95% segment F-score corresponding to 50% reduction in error rate compared to the best methods not requiring an evolutionary profile of a protein to be known. Performance is also improved when applied to more recent and larger high resolution datasets PDBTM and MPtopo. TMpro predictions in membrane proteins with unusual or disputed TM structure (K+ channel, aquaporin and HIV envelope glycoprotein) are discussed. Conclusion TMpro uses very few free parameters in modeling TM segments as opposed to the very large number of free parameters used in state-of-the-art membrane prediction methods, yet achieves very high segment accuracies. This is highly advantageous considering that high resolution transmembrane information is available only for very few proteins. The greatest impact of TMpro is therefore expected in the prediction of TM segments in proteins with novel topologies. Further, the paper introduces a novel method of extracting features from protein sequence, namely that of latent semantic analysis model. The success of this approach in the current context suggests that it can find potential applications in other sequence-based analysis problems. Availability and
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Affiliation(s)
- Madhavi Ganapathiraju
- Language Technologies Institute, Carnegie Mellon University, Pittsburgh, USA. madhavi+@cs.cmu.edu
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Kida Y, Morimoto F, Sakaguchi M. Two translocating hydrophilic segments of a nascent chain span the ER membrane during multispanning protein topogenesis. ACTA ACUST UNITED AC 2008; 179:1441-52. [PMID: 18166653 PMCID: PMC2373506 DOI: 10.1083/jcb.200707050] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
During protein integration into the endoplasmic reticulum, the N-terminal domain preceding the type I signal-anchor sequence is translocated through a translocon. By fusing a streptavidin-binding peptide tag to the N terminus, we created integration intermediates of multispanning membrane proteins. In a cell-free system, N-terminal domain (N-domain) translocation was arrested by streptavidin and resumed by biotin. Even when N-domain translocation was arrested, the second hydrophobic segment mediated translocation of the downstream hydrophilic segment. In one of the defined intermediates, two hydrophilic segments and two hydrophobic segments formed a transmembrane disposition in a productive state. Both of the translocating hydrophilic segments were crosslinked with a translocon subunit, Sec61α. We conclude that two translocating hydrophilic segment in a single membrane protein can span the membrane during multispanning topogenesis flanking the translocon. Furthermore, even after six successive hydrophobic segments entered the translocon, N-domain translocation could be induced to restart from an arrested state. These observations indicate the remarkably flexible nature of the translocon.
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Affiliation(s)
- Yuichiro Kida
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
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39
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Addressing membrane protein topology using the fluorescence protease protection (FPP) assay. Methods Mol Biol 2008; 440:227-33. [PMID: 18369949 DOI: 10.1007/978-1-59745-178-9_17] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Determining a protein's correct topological distribution within the cell is essential for understanding the proper functioning of many proteins. Here, we describe a fluorescence-based technique, termed FPP for fluorescence protease protection, to determine protein topology in living cells. The FPP assay uses the restricted proteolytic digestibility of green fluorescent protein-tagged membrane proteins to reveal their intramembrane orientation. Membrane protein topology can be assessed using this technique for proteins residing in organelles as diverse as the Golgi apparatus, the endoplasmic reticulum (ER), peroxisomes, mitochondria, and autophagosomes. To illustrate the technique, we describe its use for deciphering the topology of a membrane protein in the ER.
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40
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Matus S, Burgos PV, Bravo-Zehnder M, Kraft R, Porras OH, Farías P, Barros LF, Torrealba F, Massardo L, Jacobelli S, González A. Antiribosomal-P autoantibodies from psychiatric lupus target a novel neuronal surface protein causing calcium influx and apoptosis. ACTA ACUST UNITED AC 2007; 204:3221-34. [PMID: 18056288 PMCID: PMC2150977 DOI: 10.1084/jem.20071285] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The interesting observation was made 20 years ago that psychotic manifestations in patients with systemic lupus erythematosus are associated with the production of antiribosomal-P protein (anti-P) autoantibodies. Since then, the pathogenic role of anti-P antibodies has attracted considerable attention, giving rise to long-term controversies as evidence has either contradicted or confirmed their clinical association with lupus psychosis. Furthermore, a plausible mechanism supporting an anti-P-mediated neuronal dysfunction is still lacking. We show that anti-P antibodies recognize a new integral membrane protein of the neuronal cell surface. In the brain, this neuronal surface P antigen (NSPA) is preferentially distributed in areas involved in memory, cognition, and emotion. When added to brain cellular cultures, anti-P antibodies caused a rapid and sustained increase in calcium influx in neurons, resulting in apoptotic cell death. In contrast, astrocytes, which do not express NSPA, were not affected. Injection of anti-P antibodies into the brain of living rats also triggered neuronal death by apoptosis. These results demonstrate a neuropathogenic potential of anti-P antibodies and contribute a mechanistic basis for psychiatric lupus. They also provide a molecular target for future exploration of this and other psychiatric diseases.
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Affiliation(s)
- Soledad Matus
- Departamento de Inmunología Clínica y Reumatología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago 8330025, Chile
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41
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Xu X, Lu J, Lu Q, Zhong H, Weng S, He J. Characterization of a membrane protein (VP001L) from infectious spleen and kidney necrosis virus (ISKNV). Virus Genes 2007; 36:157-67. [DOI: 10.1007/s11262-007-0177-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2007] [Accepted: 11/07/2007] [Indexed: 10/22/2022]
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Forrest KL, Bhave M. The PIP and TIP aquaporins in wheat form a large and diverse family with unique gene structures and functionally important features. Funct Integr Genomics 2007; 8:115-33. [PMID: 18030508 DOI: 10.1007/s10142-007-0065-4] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2007] [Revised: 10/12/2007] [Accepted: 10/14/2007] [Indexed: 11/27/2022]
Abstract
Aquaporins, members of major intrinsic proteins (MIPs), transport water across cellular membranes and play vital roles in all organisms. Adversities such as drought, salinity, or chilling affect water uptake and transport, and numerous plant MIPs are reported to be differentially regulated under such stresses. However, MIP genes have been not yet been characterized in wheat, the largest cereal crop. We have identified 24 PIP and 11 TIP aquaporin genes from wheat by gene isolation and database searches. They vary extensively in lengths, numbers, and sequences of exons and introns, and sequences and cellular locations of predicted proteins, but the intron positions (if present) are characteristic. The putative PIP proteins show a high degree of conservation of signature sequences or residues for membrane integration, water transport, and regulation. The TIPs are more diverse, some with potential for water transport and others with various selectivity filters including a new combination. Most genes appear to be expressed as expressed sequence tags, while two are likely pseudogenes. Many of the genes are highly identical to rice but some are unique, and many correspond to genes that show differential expression under salinity and/or drought. The results provide extensive information for functional studies and developing markers for stress tolerance.
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Affiliation(s)
- Kerrie L Forrest
- Environment and Biotechnology Centre, Faculty of Life and Social Sciences, Swinburne University of Technology, PO Box 218, John St, Hawthorn, Victoria 3122, Australia
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43
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Wijeyesakere SJ, Richardson RJ, Stuckey JA. Modeling the tertiary structure of the patatin domain of neuropathy target esterase. Protein J 2007; 26:165-72. [PMID: 17216363 PMCID: PMC6643263 DOI: 10.1007/s10930-006-9058-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Neuropathy target esterase (NTE) is a transmembrane protein of unknown function whose specific chemical modification by certain organophosphorus (OP) compounds leads to distal axonopathy. Therefore, solving the 3D structure of NTE would advance the understanding of its pathogenic and physiologic roles. In this study, the tertiary structures of the patatin (catalytic) domain and the N-terminal transmembrane domain of NTE were modeled using the crystal structures of patatin (PDB ID 1oxw) and moricin (PDB ID 1kv4) as templates. Sequence alignments and secondary structure predictions were obtained from the INUB server (Buffalo, NY). O and PyMol were used to build the PNTE and NTE TMD chains from these sequence alignments. The PNTE model was refined in the presence of water using the crystallography and NMR system, while the NTE TMD model was refined in vacuo using the GROMOS implementation in the Swiss PDB viewer. The modeled active site of NTE was found to consist of a Ser966-Asp1086 catalytic dyad, which is characteristic of phospholipase A2 enzymes. The Ser966 Ogamma was located 2.93 A from the Odelta2 of Asp1086. In addition, our NTE model was found to contain a single N-terminal transmembrane domain. This modeling effort provided structural and mechanistic predictions about the catalytic domain of NTE that are being verified via experimental techniques.
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Affiliation(s)
- Sanjeeva J. Wijeyesakere
- Toxicology Program, Department of Environmental Health Sciences, The University of Michigan, Ann Arbor, Michigan
| | - Rudy J. Richardson
- Toxicology Program, Department of Environmental Health Sciences, The University of Michigan, Ann Arbor, Michigan
- Neurology Department, The University of Michigan, Ann Arbor, Michigan
| | - Jeanne A. Stuckey
- Department of Biological Chemistry, University of Michigan School of Medicine and Life Sciences Institute, University of Michigan, Ann Arbor, Michigan
- Address correspondence to Dr. Jeanne A. Stuckey, Life Sciences Institute, The University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216, USA. Tel: (734) 647-7535; Fax: (734) 763-6492; .
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Affiliation(s)
- Anna E Speers
- Department of Pharmacology, University of Colorado School of Medicine, P.O. Box 6511, MS 8303, Aurora, Colorado 80045, USA
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45
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Xu BB, Li JN, Zhang XK, Wang R, Xie LL, Chai YR. Cloning and molecular characterization of a functional flavonoid 3'-hydroxylase gene from Brassica napus. JOURNAL OF PLANT PHYSIOLOGY 2007; 164:350-63. [PMID: 16618519 DOI: 10.1016/j.jplph.2006.03.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2006] [Accepted: 03/07/2006] [Indexed: 05/08/2023]
Abstract
A flavonoid 3'-hydroxylase (F3'H) gene, denoted BnF3'H-1, was cloned from oilseed rape (Brassica napus). The gene of 3038 base pairs (bp) contains 3 introns. The complementary DNA (cDNA) consists of 1820bp and has an open reading frame of 1536bp encoding a polypeptide of 511 amino acids with a molecular weight of 56.62kDa and an isoelectric point of 7.08. BnF3'H-1 shows high homology to known F3'H genes, especially F3'H from Arabidopsis thaliana. Untranslated regions (UTRs) may play important roles in regulating the expression of BnF3'H-1. Besides containing a Kozak sequence, the first 77-bp region is C-rich but G-poor, and the 26-bp 5'-UTR contains 3 sites of ACCACT-like sequences. Alternative polyadenylation in the 3'-UTR is adopted by this gene to generate heterogeneous transcripts. Conserved domain search and motif characterization identified BnF3'H-1 as a cytochrome P450. All F3'H-featured motifs, VVVAAS, GGEK and VDVKG, are unchanged in BnF3'H-1. The N-terminal signal peptide/anchor and 3 transmembrane helices were predicted in BnF3'H-1, and its subcellular localization is most probably at the endoplasmic reticulum. Since 16 phosphorylation sites could be predicted, phosphorylation may be a necessary post-translational modification of BnF3'H-1. The secondary structure is dominated by alpha-helices and random coils. Most helices are located in the middle region, while extended strands mainly intersperse in terminal regions. DNA gel blot analysis indicated that 2 different F3'H genes might exist in B. napus. Semi-quantitative reverse transcription-polymerase chain reaction (RT-PCR) and RNA gel blot analysis showed that flowers have the highest F3'H expression, followed by pericarp and seed, and lower levels in some other organs. This species-featured expression pattern is in obedience to multiple functional roles that F3'H gene(s) play(s) in various organs of B. napus. The BnF3'H-1 coding region was expressed in Escherichia coli, and enzyme activity of the His-tagged protein was demonstrated by monitoring the conversion of the substrate naringenin using high-performance liquid chromatography (HPLC), suggesting that BnF3'H-1 is catalytically functional. RT-PCR analysis suggests that transcription level of the F3'H gene(s) is not the reason for the different seed colorations found in near-isogenic lines (black-seeded L1 and yellow-seeded L2) of B. napus.
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Affiliation(s)
- Ben-Bo Xu
- Chongqing Rapeseed Technology Research Center, Chongqing Key Laboratory of Crop Quality Improvement, Beibei, Chongqing, PR China
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Ott CM, Akhavan A, Lingappa VR. Specific features of the prion protein transmembrane domain regulate nascent chain orientation. J Biol Chem 2007; 282:11163-71. [PMID: 17276986 DOI: 10.1074/jbc.m607660200] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The sequence of a transmembrane (TM) domain and the adjacent regions are important for recognition, orientation, and integration at the translocon during membrane protein biosynthesis. However, the sequences of individual TM domains vary considerably. Although some general effects of electrostatic and hydrophobic interactions have been observed, it is still not clear what features of diverse sequences influence TM domain orientation. Here we utilized the ability of the prion protein (PrP) to be synthesized in multiple topological forms to assay the effects of substitutions and mutations on TM domain orientation. Several of the TM domains we tested appear to contain no inherent information regulating orientation. In contrast, we found that the middle region of the PrP TM domain significantly reduces the ability of the chain to invert its orientation in the translocon. We also observed that the C-terminal region of the PrP TM domain influences orientation, and we characterized the orientation differences between two forms of a physiologically relevant polymorphism in this region. Specifically, we found that the identity of a single amino acid, that at position 129, can significantly alter PrP TM domain orientation. Because position 129 is the location of the disease-associated Met/Val polymorphism, we discuss both how this small change may affect TMD orientation and the larger biological implications of these results.
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Affiliation(s)
- Carolyn M Ott
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143, USA
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Agnihothram SS, York J, Trahey M, Nunberg JH. Bitopic membrane topology of the stable signal peptide in the tripartite Junín virus GP-C envelope glycoprotein complex. J Virol 2007; 81:4331-7. [PMID: 17267481 PMCID: PMC1866146 DOI: 10.1128/jvi.02779-06] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The stable signal peptide (SSP) of the GP-C envelope glycoprotein of the Junín arenavirus plays a critical role in trafficking of the GP-C complex to the cell surface and in its membrane fusion activity. SSP therefore may function on both sides of the lipid membrane. In this study, we have investigated the membrane topology of SSP by confocal microscopy of cells treated with the detergent digitonin to selectively permeabilize the plasma membrane. By using an affinity tag to mark the termini of SSP in the properly assembled GP-C complex, we find that both the N and C termini reside in the cytosol. Thus, SSP adopts a bitopic topology in which the C terminus is translocated from the lumen of the endoplasmic reticulum to the cytoplasm. This model is supported by (i) the presence of two conserved hydrophobic regions in SSP (hphi1 and hphi2) and (ii) our previous demonstration that lysine-33 in the ectodomain loop is essential for pH-dependent membrane fusion. Moreover, we demonstrate that the introduction of a charged side chain or single amino acid deletion in the membrane-spanning hphi2 region significantly diminishes SSP association in the GP-C complex and abolishes membrane fusion activity. Taken together, our results suggest that bitopic membrane insertion of SSP is centrally important in the assembly and function of the tripartite GP-C complex.
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Affiliation(s)
- Sudhakar S Agnihothram
- Montana Biotechnology Center, The University of Montana, Science Complex, Room 221, Missoula, MT 59812, USA
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Zhang G, Sanfaçon H. Characterization of membrane association domains within the Tomato ringspot nepovirus X2 protein, an endoplasmic reticulum-targeted polytopic membrane protein. J Virol 2006; 80:10847-57. [PMID: 16928745 PMCID: PMC1641798 DOI: 10.1128/jvi.00789-06] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2006] [Accepted: 08/09/2006] [Indexed: 12/19/2022] Open
Abstract
Replication of nepoviruses (family Comoviridae) occurs in association with endoplasmic reticulum (ER)-derived membranes. We have previously shown that the putative nucleoside triphosphate-binding protein (NTB) of Tomato ringspot nepovirus is an integral membrane protein with two ER-targeting sequences and have suggested that it anchors the viral replication complex (VRC) to the membranes. A second highly hydrophobic protein domain (X2) is located immediately upstream of the NTB domain in the RNA1-encoded polyprotein. X2 shares conserved sequence motifs with the comovirus 32-kDa protein, an ER-targeted protein implicated in VRC assembly. In this study, we examined the ability of X2 to associate with intracellular membranes. The X2 protein was fused to the green fluorescent protein and expressed in Nicotiana benthamiana by agroinfiltration. Confocal microscopy and membrane flotation experiments suggested that X2 is targeted to ER membranes. Mutagenesis studies revealed that X2 contains multiple ER-targeting domains, including two C-terminal transmembrane helices and a less-well-defined domain further upstream. To investigate the topology of the protein in the membrane, in vitro glycosylation assays were conducted using X2 derivatives that contained N-glycosylation sites introduced at the N or C termini of the protein. The results led us to propose a topological model for X2 in which the protein traverses the membrane three times, with the N terminus oriented in the lumen and the C terminus exposed to the cytoplasmic face. Taken together, our results indicate that X2 is an ER-targeted polytopic membrane protein and raises the possibility that it acts as a second membrane anchor for the VRC.
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Affiliation(s)
- Guangzhi Zhang
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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49
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Lorenz H, Hailey DW, Wunder C, Lippincott-Schwartz J. The fluorescence protease protection (FPP) assay to determine protein localization and membrane topology. Nat Protoc 2006; 1:276-9. [PMID: 17406244 DOI: 10.1038/nprot.2006.42] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Correct localization and topology are crucial for the cellular function of a protein. To determine the topology of membrane proteins, a new technique, called the fluorescence protease protection (FPP) assay, can be applied. This assay uses the restricted proteolytic digestibility of GFP-tagged transmembrane proteins to indicate their intramembrane orientation. The sole requirements for FPP are the expression of GFP fusion proteins and the selective permeabilization of the plasma membrane, which permits a wide range of cell types and organelles to be investigated. The FPP assay can be carried out in a straightforward manner to obtain reliable results within minutes. Here we provide a step-by-step protocol for the assay. As an example, we use FPP to determine which terminus of an endoplasmic reticulum (ER) transmembrane protein is lumenal and which one is facing the cytosol.
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Affiliation(s)
- Holger Lorenz
- Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health, Building 18T Library Drive, Bethesda, Maryland 20892, USA.
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Chun YHP, Yamakoshi Y, Kim JW, Iwata T, Hu JCC, Simmer JP. Porcine SPARC: isolation from dentin, cDNA sequence, and computer model. Eur J Oral Sci 2006; 114 Suppl 1:78-85; discussion 93-5, 379-80. [PMID: 16674666 DOI: 10.1111/j.1600-0722.2006.00280.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Genes encoding the major enamel matrix proteins and non-collagenous proteins of bone and dentin are members of the secretory calcium-binding phosphoprotein (SCPP) family, which originated from ancestral SPARC (secreted protein, acidic and rich in cysteine; BM-40/osteonectin). To better understand the role of SPARC in mineralizing systems, we isolated SPARC from developing pig teeth, deduced its primary structure from the cDNA sequence, and determined its quaternary structure by homology modelling with reference to human SPARC crystal structures. The guanidine/EDTA extract from porcine dentin was fractionated by anion-exchange and size-exclusion chromatography. Stains-all positive bands at 38 and 35 kDa gave the N-terminal sequences APQQEALPDETEV and DFEKNYNMYIFPV, which corresponded to the SPARC N terminus and an internal region of the protein. Porcine SPARC contains 300 amino acids, including the 17-amino acid signal peptide, and shares 96.2% amino acid sequence identity with human SPARC. Without post-translational modifications, the 283-amino acid secreted protein has a molecular mass of 32.3 kDa. The three-dimensional model revealed that porcine SPARC contains a single N-linked glycosylation at N113, seven intramolecular disulfide bridges, and assembles into dimers. SPARC is composed of three structural/functional domains: an acidic Ca2+-binding, a follistatin-like, and an extracellular calcium-binding domain.
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Affiliation(s)
- Yong-Hee P Chun
- University of Michigan Dental Research Laboratory, Ann Arbor, MI 48108, USA
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