title: PrionW: a server to identify proteins containing glutamine/asparagine rich prion-like domains and their amyloid cores.
abstract: Prions are a particular type of amyloids with the ability to self-perpetuate and propagate in vivo. Prion-like conversion underlies important biological processes but is also connected to human disease. Yeast prions are the best understood transmissible amyloids. In these proteins, prion formation from an initially soluble state involves a structural conversion, driven, in many cases, by specific domains enriched in glutamine/asparagine (Q/N) residues. Importantly, domains sharing this compositional bias are also present in the proteomes of higher organisms, thus suggesting that prion-like conversion might be an evolutionary conserved mechanism. We have recently shown that the identification and evaluation of the potency of amyloid nucleating sequences in putative prion domains allows discrimination of genuine prions. PrionW is a web application that exploits this principle to scan sequences in order to identify proteins containing Q/N enriched prion-like domains (PrLDs) in large datasets. When used to scan the complete yeast proteome, PrionW identifies previously experimentally validated prions with high accuracy. Users can analyze up to 10 000 sequences at a time, PrLD-containing proteins are identified and their putative PrLDs and amyloid nucleating cores visualized and scored. The output files can be downloaded for further analysis. PrionW server can be accessed at http://bioinf.uab.cat/prionw/.
authors.affiliation: Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.
authors.forename: Rafael
authors.initials: R
authors.lastname: Zambrano
authors.affiliation: Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.
authors.forename: Oscar
authors.initials: O
authors.lastname: Conchillo-Sole
authors.affiliation: Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.
authors.forename: Valentin
authors.initials: V
authors.lastname: Iglesias
authors.affiliation: Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.
authors.forename: Ricard
authors.initials: R
authors.lastname: Illa
authors.affiliation: VIB Switch Laboratory and Department for Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.
authors.forename: Frederic
authors.initials: F
authors.lastname: Rousseau
authors.affiliation: VIB Switch Laboratory and Department for Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.
authors.forename: Joost
authors.initials: J
authors.lastname: Schymkowitz
authors.affiliation: Institut de Nanociència i Nanotecnologia (INUB) and Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Spain.
authors.forename: Raimon
authors.initials: R
authors.lastname: Sabate
authors.affiliation: Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
authors.forename: Xavier
authors.initials: X
authors.lastname: Daura
authors.affiliation: Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain salvador.ventura@uab.es.
authors.forename: Salvador
authors.initials: S
authors.lastname: Ventura
mesh_terms: D000682:Amyloid / Q000737:chemistry*; D001216:Asparagine / Q000032:analysis*; D005656:Fungal Proteins / Q000737:chemistry; D005973:Glutamine / Q000032:analysis*; D020407:Internet; D011328:Prions / Q000737:chemistry*; D017434:Protein Structure, Tertiary; D040901:Proteomics / Q000379:methods; D020539:Sequence Analysis, Protein; D012984:Software
chemical_list: D000682:Amyloid; D005656:Fungal Proteins; D011328:Prions; D005973:Glutamine; D001216:Asparagine