title: Intrinsically disordered proteins (IDPs) in trypanosomatids.
abstract: BACKGROUND
  Proteins are composed of one or more amino acid chains and exhibit several structure levels. IDPs (intrinsically disordered proteins) represent a class of proteins that do not fold into any particular conformation and exist as dynamic ensembles in their native state. Due to their intrinsic adaptability, IDPs participate in many regulatory biological processes, including parasite immune escape. Using the information from trypanosomatids proteomes, we developed a pipeline for the identification, characterization and analysis of IDPs. The pipeline employs six disorder prediction methodologies and integrates structural and functional annotation information, subcellular location prediction and physicochemical properties. At the core of the IDP pipeline, there is a relational database that describes the protein disorder knowledge in a logically consistent manner.
  
  
  RESULTS
  The results obtained from the IDP pipeline showed that Leishmania and Trypanosoma species have approximately 70% and 55% IDPs, respectively. Our results indicate that IDPs in trypanosomatids contain disorder-promoting amino acids and order-promoting amino acids. The functional annotation analysis demonstrated enrichment of selected Gene Ontology terms. A relevant association was observed between the disordered residue numbers within predicted IDPs and their subcellular location, lack of transmembrane domains and lack of predicted function. We validated our computational findings with 2D electrophoresis designed for IDP identification and found that 100% of the identified protein spots were predicted in silico.
  
  
  CONCLUSIONS
  Because there is no pipeline or database addressing IDPs in trypanosomatids, the pipeline described here represents the first attempt to establish possible correlations between protein function and structural disorder in these eukaryotes. Interestingly, all significant associations detected in the contingency analysis were observed when the protein disorder content reached approximately 40%. The exploratory data analysis allowed us to develop hypotheses regarding the IDPs' association with key biological features of these parasites, including transcription and transcriptional regulation, RNA processing and splicing, and cytoskeleton.
authors.forename: Patrícia
authors.initials: P
authors.lastname: de Cássia Ruy
authors.forename: Raul
authors.initials: R
authors.lastname: Torrieri
authors.forename: Juliano Simões
authors.initials: JS
authors.lastname: Toledo
authors.forename: Viviane
authors.initials: V
authors.lastname: de Souza Alves
authors.forename: Angela Kaysel
authors.initials: AK
authors.lastname: Cruz
authors.affiliation: Informática de Biossistemas, Centro de Pesquisas René Rachou - Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, MG, Brasil. jeronimo@cpqrr.fiocruz.br.
authors.forename: Jeronimo Conceição
authors.initials: JC
authors.lastname: Ruiz
mesh_terms: D016384:Consensus Sequence; D064267:Intrinsically Disordered Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D040901:Proteomics; D015800:Protozoan Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D014351:Trypanosomatina / Q000235:genetics* / Q000378:metabolism*
chemical_list: D064267:Intrinsically Disordered Proteins; D015800:Protozoan Proteins