Partial proteolysis improves the identification of the extracellular segments of transmembrane proteins by surface biotinylation

[1]  Jing Yang,et al.  Topology prediction improvement of α-helical transmembrane proteins through helix-tail modeling and multiscale deep learning fusion. , 2019, Journal of molecular biology.

[2]  G. Tusnády,et al.  Covalently modified carboxyl side chains on cell surface leads to a novel method toward topology analysis of transmembrane proteins , 2019, Scientific Reports.

[3]  Michael R. Shortreed,et al.  Improved Protein Inference from Multiple Protease Bottom-Up Mass Spectrometry Data. , 2019, Journal of proteome research.

[4]  G. Tusnády,et al.  Structural Principles Governing Disease-Causing Germline Mutations. , 2018, Journal of molecular biology.

[5]  M. Fransen,et al.  Membrane topologies of PEX13 and PEX14 provide new insights on the mechanism of protein import into peroxisomes , 2018, The FEBS journal.

[6]  Jiahong Wang,et al.  Membrane topology of rat sodium-coupled neutral amino acid transporter 2 (SNAT2). , 2018, Biochimica et biophysica acta. Biomembranes.

[7]  Dmitrij Frishman,et al.  MutHTP: mutations in human transmembrane proteins , 2018, Bioinform..

[8]  C. Gati,et al.  Cryo-EM structure of the human neutral amino acid transporter ASCT2 , 2018, Nature Structural & Molecular Biology.

[9]  J. Beckwith,et al.  Aeropyrum pernix membrane topology of protein VKOR promotes protein disulfide bond formation in two subcellular compartments. , 2017, Microbiology.

[10]  R. Schneiter,et al.  Chemical crosslinking and mass spectrometry to elucidate the topology of integral membrane proteins , 2017, PloS one.

[11]  M. Jackson,et al.  Green Fluorescent Protein as a protein localization and topological reporter in mycobacteria. , 2017, Tuberculosis.

[12]  G. Szakács,et al.  Identification of Extracellular Segments by Mass Spectrometry Improves Topology Prediction of Transmembrane Proteins , 2017, Scientific Reports.

[13]  István Reményi,et al.  TSTMP: target selection for structural genomics of human transmembrane proteins , 2016, Nucleic Acids Res..

[14]  Jaime Prilusky,et al.  Interplay between hydrophobicity and the positive-inside rule in determining membrane-protein topology , 2016, Proceedings of the National Academy of Sciences.

[15]  G. Szakács,et al.  Characterization of Disease-Associated Mutations in Human Transmembrane Proteins , 2016, PloS one.

[16]  Alexey I Nesvizhskii,et al.  Effective Leveraging of Targeted Search Spaces for Improving Peptide Identification in Tandem Mass Spectrometry Based Proteomics. , 2015, Journal of proteome research.

[17]  L. Fliegel,et al.  Topological analysis of the Na+/H+ exchanger. , 2015, Biochimica et biophysica acta.

[18]  István Reményi,et al.  The human transmembrane proteome , 2015, Biology Direct.

[19]  Arne Elofsson,et al.  The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides , 2015, Nucleic Acids Res..

[20]  István Reményi,et al.  CCTOP: a Consensus Constrained TOPology prediction web server , 2015, Nucleic Acids Res..

[21]  G. von Heijne,et al.  Tissue-based map of the human proteome , 2015, Science.

[22]  István Reményi,et al.  Expediting topology data gathering for the TOPDB database , 2014, Nucleic Acids Res..

[23]  Tao Zhou,et al.  Mapping of the N-linked glycoproteome of human spermatozoa. , 2013, Journal of proteome research.

[24]  Marcin J. Skwark,et al.  Membrane protein shaving with thermolysin can be used to evaluate topology predictors , 2013, Proteomics.

[25]  Dániel Kozma,et al.  PDBTM: Protein Data Bank of transmembrane proteins after 8 years , 2012, Nucleic Acids Res..

[26]  B. Garcia,et al.  Discovery of lysine post-translational modifications through mass spectrometric detection. , 2012, Essays in biochemistry.

[27]  Derek P. Ng,et al.  Membrane protein misassembly in disease. , 2012, Biochimica et biophysica acta.

[28]  Martin R Larsen,et al.  Chemical deamidation: a common pitfall in large-scale N-linked glycoproteomic mass spectrometry-based analyses. , 2012, Journal of proteome research.

[29]  Hyeon Joo,et al.  OPM database and PPM web server: resources for positioning of proteins in membranes , 2011, Nucleic Acids Res..

[30]  Piliang Hao,et al.  Detection, Evaluation and Minimization of Nonenzymatic Deamidation in Proteomic Sample Preparation* , 2011, Molecular & Cellular Proteomics.

[31]  J. Yates,et al.  Mass spectrometry accelerates membrane protein analysis. , 2011, Trends in biochemical sciences.

[32]  Stavros J. Hamodrakas,et al.  ExTopoDB: a database of experimentally derived topological models of transmembrane proteins , 2010, Bioinform..

[33]  M. Larsen,et al.  Improved accuracy of cell surface shaving proteomics in Staphylococcus aureus using a false‐positive control , 2010, Proteomics.

[34]  S. Botchway,et al.  Five Arabidopsis Reticulon Isoforms Share Endoplasmic Reticulum Location, Topology, and Membrane-Shaping Properties[W] , 2010, Plant Cell.

[35]  R. Vachet,et al.  Probing protein structure by amino acid-specific covalent labeling and mass spectrometry. , 2009, Mass spectrometry reviews.

[36]  David T. Jones,et al.  Transmembrane protein topology prediction using support vector machines , 2009, BMC Bioinformatics.

[37]  Ruedi Aebersold,et al.  Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins , 2009, Nature Biotechnology.

[38]  Xinning Jiang,et al.  Glycoproteomics analysis of human liver tissue by combination of multiple enzyme digestion and hydrazide chemistry. , 2009, Journal of proteome research.

[39]  Honggang Wang,et al.  Membrane topology of the human breast cancer resistance protein (BCRP/ABCG2) determined by epitope insertion and immunofluorescence. , 2008, Biochemistry.

[40]  Arne Elofsson,et al.  OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar , 2008, Bioinform..

[41]  Byungkook Lee,et al.  Topology of NGEP, a prostate-specific cell:cell junction protein widely expressed in many cancers of different grade level. , 2008, Cancer research.

[42]  D. Stuart,et al.  Paired receptor specificity explained by structures of signal regulatory proteins alone and complexed with CD47. , 2008, Molecular cell.

[43]  Y. Kano,et al.  The Membrane Topology of ALMT1, an Aluminum-Activated Malate Transport Protein in Wheat (Triticum aestivum) , 2007, Plant signaling & behavior.

[44]  István Simon,et al.  TOPDB: topology data bank of transmembrane proteins , 2007, Nucleic Acids Res..

[45]  Jianjie Ma,et al.  Determination of the external loops and the cellular orientation of the N- and the C-termini of the human organic anion transporter hOAT1. , 2007, The Biochemical journal.

[46]  B. Barquera,et al.  Membrane Topology Mapping of the Na+-Pumping NADH: Quinone Oxidoreductase from Vibrio cholerae by PhoA- Green Fluorescent Protein Fusion Analysis , 2006, Journal of bacteriology.

[47]  P. Swaan,et al.  Membrane topology of human ASBT (SLC10A2) determined by dual label epitope insertion scanning mutagenesis. New evidence for seven transmembrane domains. , 2006, Biochemistry.

[48]  Fanfan Zhou,et al.  The Role of N-Linked Glycosylation in Protein Folding, Membrane Targeting, and Substrate Binding of Human Organic Anion Transporter hOAT4 , 2005, Molecular Pharmacology.

[49]  J. Goldstein,et al.  Membrane Topology of Human Insig-1, a Protein Regulator of Lipid Synthesis* , 2004, Journal of Biological Chemistry.

[50]  L. Matherly,et al.  Analysis of membrane topology of the human reduced folate carrier protein by hemagglutinin epitope insertion and scanning glycosylation insertion mutagenesis. , 2002, Biochimica et biophysica acta.

[51]  Johan Nilsson,et al.  Rapid topology mapping of Escherichia coli inner-membrane proteins by prediction and PhoA/GFP fusion analysis , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[52]  István Simon,et al.  The HMMTOP transmembrane topology prediction server , 2001, Bioinform..

[53]  A. Krogh,et al.  Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. , 2001, Journal of molecular biology.

[54]  J. Lolkema,et al.  Membrane Topology and Insertion of Membrane Proteins: Search for Topogenic Signals , 2000, Microbiology and Molecular Biology Reviews.

[55]  G. Heijne,et al.  Genome‐wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms , 1998, Protein science : a publication of the Protein Society.

[56]  Oliver H. Lowry,et al.  Protein measurement with the Folin phenol reagent. , 1951, The Journal of biological chemistry.

[57]  M. Valvano,et al.  Sulfhydryl Labeling as a Tool to Investigate the Topology of Membrane Proteins Involved in Lipopolysaccharide Biosynthesis. , 2019, Methods in molecular biology.

[58]  R. Wysocki,et al.  Transmembrane topology of the arsenite permease Acr3 from Saccharomyces cerevisiae. , 2017, Biochimica et biophysica acta. Biomembranes.

[59]  Bernd Wollscheid,et al.  Cell surface capturing technologies for the surfaceome discovery of hepatocytes. , 2012, Methods in molecular biology.