title: Identification of Extracellular Segments by Mass Spectrometry Improves Topology Prediction of Transmembrane Proteins.
abstract: Transmembrane proteins play crucial role in signaling, ion transport, nutrient uptake, as well as in maintaining the dynamic equilibrium between the internal and external environment of cells. Despite their important biological functions and abundance, less than 2% of all determined structures are transmembrane proteins. Given the persisting technical difficulties associated with high resolution structure determination of transmembrane proteins, additional methods, including computational and experimental techniques remain vital in promoting our understanding of their topologies, 3D structures, functions and interactions. Here we report a method for the high-throughput determination of extracellular segments of transmembrane proteins based on the identification of surface labeled and biotin captured peptide fragments by LC/MS/MS. We show that reliable identification of extracellular protein segments increases the accuracy and reliability of existing topology prediction algorithms. Using the experimental topology data as constraints, our improved prediction tool provides accurate and reliable topology models for hundreds of human transmembrane proteins.
authors.affiliation: Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok krt 2, Budapest, H-1117 Hungary.
authors.forename: Tamás
authors.initials: T
authors.lastname: Langó
authors.affiliation: Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok krt 2, Budapest, H-1117 Hungary.|Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Szent Gellért tér 4, Budapest, H-1111, Hungary.|Department of Biochemistry and Molecular Pharmacology, Perlmutter NYU Cancer Center, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA.
authors.forename: Gergely
authors.initials: G
authors.lastname: Róna
authors.affiliation: Laboratory of Proteomics Research, Biological Research Center of the Hungarian Academy of Sciences, Temesvari krt. 62, Szeged, H-6726, Hungary.
authors.forename: Éva
authors.initials: É
authors.lastname: Hunyadi-Gulyás
authors.affiliation: Institute of Organic Chemistry, RCNS, Hungarian Academy of Sciences, Magyar Tudósok krt 2, Budapest, H-1117 Hungary.
authors.forename: Lilla
authors.initials: L
authors.lastname: Turiák
authors.affiliation: Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok krt 2, Budapest, H-1117 Hungary.
authors.forename: Julia
authors.initials: J
authors.lastname: Varga
authors.affiliation: Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok krt 2, Budapest, H-1117 Hungary.
authors.forename: László
authors.initials: L
authors.lastname: Dobson
authors.affiliation: Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok krt 2, Budapest, H-1117 Hungary.
authors.forename: György
authors.initials: G
authors.lastname: Várady
authors.affiliation: Institute of Organic Chemistry, RCNS, Hungarian Academy of Sciences, Magyar Tudósok krt 2, Budapest, H-1117 Hungary.
authors.forename: László
authors.initials: L
authors.lastname: Drahos
authors.affiliation: Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok krt 2, Budapest, H-1117 Hungary.|Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Szent Gellért tér 4, Budapest, H-1111, Hungary.
authors.forename: Beáta G
authors.initials: BG
authors.lastname: Vértessy
authors.affiliation: Laboratory of Proteomics Research, Biological Research Center of the Hungarian Academy of Sciences, Temesvari krt. 62, Szeged, H-6726, Hungary.
authors.forename: Katalin F
authors.initials: KF
authors.lastname: Medzihradszky
authors.affiliation: Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok krt 2, Budapest, H-1117 Hungary.
authors.forename: Gergely
authors.initials: G
authors.lastname: Szakács
authors.affiliation: Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok krt 2, Budapest, H-1117 Hungary.
authors.forename: Gábor E
authors.initials: GE
authors.lastname: Tusnády
mesh_terms: D002853:Chromatography, Liquid; D006801:Humans; D008565:Membrane Proteins / Q000737:chemistry*; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry; D011487:Protein Conformation; D054730:Protein Interaction Domains and Motifs; D015203:Reproducibility of Results; D013329:Structure-Activity Relationship; D053719:Tandem Mass Spectrometry
chemical_list: D008565:Membrane Proteins; D010455:Peptides