title: Experimentally based topology models for E. coli inner membrane proteins.
abstract: Membrane protein topology predictions can be markedly improved by the inclusion of even very limited experimental information. We have recently introduced an approach for the production of reliable topology models based on a combination of experimental determination of the location (cytoplasmic or periplasmic) of a protein's C terminus and topology prediction. Here, we show that determination of the location of a protein's C terminus, rather than some internal loop, is the best strategy for large-scale topology mapping studies. We further report experimentally based topology models for 31 Escherichia coli inner membrane proteins, using methodology suitable for genome-scale studies.
authors.affiliation: Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden.
authors.forename: Mikaela
authors.initials: M
authors.lastname: Rapp
authors.forename: David
authors.initials: D
authors.lastname: Drew
authors.forename: Daniel O
authors.initials: DO
authors.lastname: Daley
authors.forename: Johan
authors.initials: J
authors.lastname: Nilsson
authors.forename: Tiago
authors.initials: T
authors.lastname: Carvalho
authors.forename: Karin
authors.initials: K
authors.lastname: Melén
authors.forename: Jan-Willem
authors.initials: JW
authors.lastname: De Gier
authors.forename: Gunnar
authors.initials: G
authors.lastname: Von Heijne
mesh_terms: D000469:Alkaline Phosphatase; D002462:Cell Membrane / Q000737:chemistry* / Q000235:genetics; D019295:Computational Biology; D018844:Cyclin-Dependent Kinases / Q000737:chemistry* / Q000235:genetics; D004926:Escherichia coli / Q000737:chemistry* / Q000235:genetics; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000235:genetics; D015870:Gene Expression; D049452:Green Fluorescent Proteins; D008164:Luminescent Proteins; D011993:Recombinant Fusion Proteins / Q000737:chemistry* / Q000235:genetics; D012984:Software
chemical_list: D029968:Escherichia coli Proteins; D008164:Luminescent Proteins; D011993:Recombinant Fusion Proteins; D049452:Green Fluorescent Proteins; D018844:Cyclin-Dependent Kinases; D000469:Alkaline Phosphatase; C114089:phoA protein, E coli