Hierarchical core decomposition of RING structure as a method to capture novel functional residues within RING-type E3 ligases: a structural systems biology approach

Abstract

BackgroundIncreasing amounts of evidence strongly suggest that mutations located in RING (Really Interesting New Gene) domains of E3 ligases are involved in cancer development. Despite the existence of many experimentally defined E3 RING structures, there are still many RING mutations in the Catalog of Somatic Mutations in Cancer (COSMIC), with an unknown structural or functional significance, which are usually substitutions of amino acids with no conservation at the corresponding position. The core decomposition of networks has long been used in systems biology but never utilized in protein structure networks to identify a tolerant “core” to peripheral structure changes or failures, a region that is usually not easy to be determined with high accuracy through classical 3D protein structure analyses. MethodA new structure decomposition method that utilizes network analysis and computational thermodynamic measures of fold stability changes upon amino acids alterations is proposed. ResultsIn particular, by successively pruning the entire RING structure network of three cancer-associated E3s (BRCA1, MDM2, and cIAP2), a ‘‘core’’ for each RING domain is left. Interestingly, substitutions of ‘‘core’’ residues are associated with cancers according to COSMIC catalog. Unexpectedly, 80% of the residues located in the ‘‘core’’ RING subnetworks are non-conserved within E3 RING domains. To validate the predictions, the function of the identified RING ‘‘core’’ amino acids as well as the effects of their substitutions on E3 Ub ligase activity were mined from the literature and investigated by computational tools and in vitro Ub ligase assays. ConclusionsThis method could be widely applicable as a source of novel functional RING residues, non-conserved in E3s, for which substitutions could be deleterious.