Prediction of EF-hand calcium-binding proteins and analysis of bacterial EF-hand proteins

Author: Zhou, Y.; Yang, W.; Kirberger, M.; Lee, H.-W.; Ayalasomayajula, G.; Yang, J.J.

Description: The EF-hand protein with a helix-loop-helix Ca(2+) binding motif constitutes one of the largest protein families and is involved in numerous biological processes. To facilitate the understanding of the role of Ca(2+) in biological systems using genomic information, we report, herein, our improvement on the pattern search method for the identification of EF-hand and EF-like Ca(2+)-binding proteins. The canonical EF-hand patterns are modified to cater to different flanking structural elements. In addition, on the basis of the conserved sequence of both the N- and C-terminal EF-hands within S100 and S100-like proteins, a new signature profile has been established to allow for the identification of pseudo EF-hand and S100 proteins from genomic information. The new patterns have a positive predictive value of 99% and a sensitivity of 96% for pseudo EF-hands. Furthermore, using the developed patterns, we have identified zero pseudo EF-hand motif and 467 canonical EF-hand Ca(2+) binding motifs with diverse cellular functions in the bacteria genome. The prediction results imply that pseudo EF-hand motifs are phylogenetically younger than canonical EF-hand motifs. Our prediction of Ca(2+) binding motifs provides not only an insight into the role of Ca(2+) and Ca(2+)-binding proteins in bacterial systems, but also a way to explore and define the role of Ca(2+) in other biological systems (calciomics).

Subject headings: Amino Acid Motifs; Amino Acid Sequence; Animals; Bacterial Proteins/chemistry/metabolism; Calcium-Binding Proteins/chemistry; EF Hand Motifs/genetics; Evolution, Molecular; Humans; Models, Molecular; Molecular Sequence Data; Phylogeny; Sequence Alignment

Publication year: 2006

Journal or book title: Proteins

Volume: 65

Issue: 3

Pages: 643-655

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Type: Journal Article

Serial number: 415