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Online Journal of Bioinformatics ©
Murthy BSN, Pandit MW, Singh L.
Centre
for Cellular and Molecular Biology,
ABSTRACT
Murthy BSN Pandit MW, Singh L, Prediction
of the putative function of mouse WDR13 protein,
Online Journal of Bioinformatics, 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
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