PrionScan: an online database of predicted prion domains in complete proteomes

BMC Genomics

Database

Javier Sancho¹  Vladimir Espinosa Angarica¹  Salvador Ventura²  Alfonso Angulo³  Guillermo Losilla³  Arturo Giner³ 

[1]Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009, Zaragoza, Spain

[2]Institute for Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, Mariano Esquillor, Edificio I + D, 50018, Zaragoza, Spain

[3]Joint Unit BIFI-IQFR (CSIC), Serrano 119, 28006, Madrid, Spain

[4]Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain

[5]Departament de Bioquimica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain

[6]Institute for Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, Mariano Esquillor, Edificio I + D, 50018, Zaragoza, Spain

关键词: Prion domain;    Protein aggregation;    Amyloid fibrils;    Prion prediction;   

DOI  :  10.1186/1471-2164-15-102

 received in 2013-10-24, accepted in 2014-02-04,  发布年份 2014

来源: Springer

【 摘 要 】

BackgroundPrions are a particular type of amyloids related to a large variety of important processes in cells, but also responsible for serious diseases in mammals and humans. The number of experimentally characterized prions is still low and corresponds to a handful of examples in microorganisms and mammals. Prion aggregation is mediated by specific protein domains with a remarkable compositional bias towards glutamine/asparagine and against charged residues and prolines. These compositional features have been used to predict new prion proteins in the genomes of different organisms. Despite these efforts, there are only a few available data sources containing prion predictions at a genomic scale.DescriptionHere we present PrionScan, a new database of predicted prion-like domains in complete proteomes. We have previously developed a predictive methodology to identify and score prionogenic stretches in protein sequences. In the present work, we exploit this approach to scan all the protein sequences in public databases and compile a repository containing relevant information of proteins bearing prion-like domains. The database is updated regularly alongside UniprotKB and in its present version contains approximately 28000 predictions in proteins from different functional categories in more than 3200 organisms from all the taxonomic subdivisions. PrionScan can be used in two different ways: database query and analysis of protein sequences submitted by the users. In the first mode, simple queries allow to retrieve a detailed description of the properties of a defined protein. Queries can also be combined to generate more complex and specific searching patterns. In the second mode, users can submit and analyze their own sequences.ConclusionsIt is expected that this database would provide relevant insights on prion functions and regulation from a genome-wide perspective, allowing researches performing cross-species prion biology studies. Our database might also be useful for guiding experimentalists in the identification of new candidates for further experimental characterization.

【 授权许可】

CC BY   
© Espinosa Angarica et al.; licensee BioMed Central Ltd. 2014