ABSTRACT
IDEAL (Intrinsically Disordered proteins with Extensive Annotations and Literature, http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/) is a collection of intrinsically disordered proteins (IDPs) that cannot adopt stable globular structures under physiological conditions. Since its previous publication in 2012, the number of entries in IDEAL has almost tripled (120 to 340). In addition to the increase in quantity, the quality of IDEAL has been significantly improved. The new IDEAL incorporates the interactions of IDPs and their binding partners more explicitly, and illustrates the protein-protein interaction (PPI) networks and the structures of protein complexes. Redundant experimental data are arranged based on the clustering of Protein Data Bank entries, and similar sequences with the same binding mode are grouped. As a result, the new IDEAL presents more concise and informative experimental data. Nuclear magnetic resonance (NMR) disorder is annotated in a systematic manner, by identifying the regions with large deviations among the NMR models. The ordered/disordered and new domain predictions by DICHOT are available, as well as the domain assignments by HMMER. Some examples of the PPI networks and the highly deviated regions derived from NMR models will be described, together with other advances. These enhancements will facilitate deeper understanding of IDPs, in terms of their flexibility, plasticity and promiscuity.
Subject(s)
Databases, Protein , Intrinsically Disordered Proteins/chemistry , Intrinsically Disordered Proteins/metabolism , Protein Interaction Maps , Internet , Nuclear Magnetic Resonance, BiomolecularABSTRACT
IDEAL, Intrinsically Disordered proteins with Extensive Annotations and Literature (http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/), is a collection of knowledge on experimentally verified intrinsically disordered proteins. IDEAL contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments. In particular, IDEAL explicitly describes protean segments that can be transformed from a disordered state to an ordered state. Since in most cases they can act as molecular recognition elements upon binding of partner proteins, IDEAL provides a data resource for functional regions of intrinsically disordered proteins. The information in IDEAL is provided on a user-friendly graphical view and in a computer-friendly XML format.
Subject(s)
Databases, Protein , Protein Conformation , Molecular Sequence Annotation , Protein Processing, Post-Translational , Proteins/chemistry , User-Computer InterfaceABSTRACT
Large-scale expressed sequence tags (EST) analysis was used to demonstrate a number of dynamic changes in the global gene expression profile of the basal chordate Ciona intestinalis over the course of its development. The fertilized egg was found to store a great variety of maternal transcripts and, as development proceeds, the organism expresses a progressively smaller repertoire of genes. In addition, a significant portion of genes involved in embryogenesis were observed to be downregulated during metamorphosis, at which point the adult appears to utilize a different set of genes to form its body. At least 25% of the genes involved in development were found to be used multiple times. This kind of information is essential to form a comprehensive understanding of the overarching expression-control plan by which the basic chordate body is formed.
