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Online Journal of Bioinformatics ©
Murthy BSN, Pandit MW, Singh L.
Centre for Cellular and Molecular Biology,
Murthy BSN, Pandit MW, Singh L., Prediction of the putative function of mouse WDR13 protein, Onl J Bioinform., 9 (1): 60-77, 2008. Literature reports large number of WD-repeat proteins involved in variety of functions, although only few of them are characterized for their true physiological roles. As these proteins function in multi-protein complexes, it is rather difficult to individually express, purify, fold and functionally characterize these proteins. Thus, novel approaches are imperative in assessing their putative physiological functions. Evolutionary conservation of the protein sequence-structure and function is well known. Realizing that WDR13 is an unstable protein and expecting that protein instability could be an evolutionarily conserved property, we have analyzed a set of WD-repeat proteins for their Protein Instability Index and sequence motifs present in them, employing bioinformatics, and using this information predicted the physiological functions of WDR13. Nearly 65% of WD-repeat proteins are unstable and they apparently form functional clusters according to PII. N-terminal of WDR13 possesses novel nuclear localization signal and SOCS-homologous sequence, which suggested that WDR13 putatively participates in E3 ubiquitin ligase ECS complex known to associate with the Ubiquitin Proteasome System. BLAST of the Database of Interacting Proteins revealing sequence homology of WDR13 with Fbw7 (product of hCDC4), another component of E3 ubiquitin ligase (SCF) complex, on one side and Eukaryotic Linear Motif analysis identifying presence of functional domains necessary for participation in ubiquitin ligase on the other, strongly suggests that WDR13 is the ECS component, functionally complimentary to Fbw7, which participated in the SCF complex. Above results suggest a new dimension of relation between primary sequences of proteins influencing their own fate as well as of the cells. Supplementary Data (Table S): Stable and unstable WD-repeat proteins available in the literature are shown in Table SA and SB along with their calculated Protein Instability Index (PII) values, identified / reported function, accession number and the organism.
Key words: WD-repeat protein; Memory related protein; Suppressor of cytokine signaling; SOCS; Elongin A; VHL protein; ECS Complex; SCF Complex; Ubiquitin ligase; Ubiquitin Proteasome System