Bioinformatics Vol. 18 no. 6 2002
Pages 880-883
© 2002 Oxford University Press
Discovery Note |
Global analysis of tandem aromatic octapeptide repeats: The significance of the aromatic–glycine motif
Department of Molecular Microbiology and Biotechnology, Tel-Aviv University, Tel-Aviv, 69978, Israel
Received on July 2, 2001
; revised on October 12, 2001
; accepted on January 8, 2002
Motivation: Tandem peptide repeats play a key role in self-assembly and aggregation processes. A notable example is the occurrence of tandem peptide repeats in prionic proteins and their role in the aggregation process that leads to the formation of the prion. One of the structural characteristics that is evident from the comparison of mammalian and yeast prion proteins is the presence of aromatic residues in their tandem repeats. These residues are accompanied by glycine residues before and/or after the aromatic amino acid. Such aromatic–glycine conjugates are also present in the tandem repeats of the large family of the bacterial ice nucleation proteins. To study the significance of such aromatic–glycine occurrences, a global analysis of all the aromatic octapeptide repeats in the Swiss-Prot and TrEMBL databases was conducted. The search pattern was formulated to compare the number of conjugates of each of the 20 natural amino acids before or after the different aromatic residues.
Results: The presence of aromatic-glycine conjugates appears to be significantly higher than aromatic conjugates to any other amino acid. Furthermore, all the six various combination of glycine occurrences before or after the three aromatic residues are present. No such pattern was observed for any other amino acid. The significance of the findings is being discussed in the context of the physicochemical properties of aromatic–glycine conjugates and its possible role in the facilitation of aggregates formation.
Contact: ehudg{at}post.tau.ac.il
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