The folding space for all the protein sequences is limited. Therefore it was observed that many proteins, whose sequences are not related, have similar fold characteristics. The fold databases like SCOP and CATH have classified various protein folds. However, in-depth analysis of the functional features of these folds was not done. We analyzed about twenty unique SH3-like folded proteins in their structural environment and functional characteristics. From our analysis it is apparent that the SH3-like folds could carry out various functions by modulation of loops and the functional region is restricted to one side of a particular sheet helped by two or three loops. The functions vary from oligonucleotide-binding to peptide-binding and other ligand binding. Although certain degree of sequence similarity was observed among the SH3-fold proteins, the similarity was restricted to the β-strand regions of the proteins.
Keywords: src homology, motif binding, tim-barrel fold, dna-binding (hid) domain, hidden, markov model (hmm), dihydrofolate reductase (dhfr)
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Published on: 01 March, 2012
Page: [143 - 150]