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A novel uracil-DNA degrading protein factor (termed UDE) was identified inDrosophila melanogaster with no significant structural and functional homologyto other uracil-DNA binding or processing factors. Determination of the 3Dstructure of UDE will be a true breakthrough in description of the molecularmechanism of action of UDE catalysis, as well as in general uracil-recognitionand nuclease action. The revolutionary ESPRIT technology was applied to thenovel protein UDE to overcome problems in identifying soluble expressingconstructs given the absence of precise information on domain content andarrangement. Nine specimen from the created numerous truncated constructs ofUDE were choosen to dechiper structural and functional relationships. VUVCDwith neural network was performed to define the secondary structure content andlocation of UDE and its truncated variants. The quantitative analysisdemonstrated exclusive {\alpha}-helical content for the full-length protein,which is preserved in the truncated constructs. Partition of {\alpha}-helicalboundles comparison with the truncated protein segments denoted new domainboundaries which differ from the conserved motifs determined by sequence-basedalignment of UDE homologues in pupating insects. Here we demonstrate thatcombination of ESPRIT and VUVCD with NN provided significant structuraldescription of UDE and resulted useful truncated constructs for furtherdetailed functional studies.

Secondary structure prediction of protein constructs using random incremental truncation and vacuum-ultraviolet CD spectroscopy