期刊
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
卷 65, 期 3, 页码 643-655出版社
WILEY
DOI: 10.1002/prot.21139
关键词
EF-hand; S100; pattern search; bacterial genomes; prediction; evolution
资金
- NIGMS NIH HHS [GM070555, R01 GM062999, GM62999] Funding Source: Medline
The EF-hand protein with a helix-loop-helix Ca2+ binding motif constitutes one of the largest protein families and is involved in numerous biological processes. To facilitate the understanding of the role of Ca2+ 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 Ca2+-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 Ca2+ 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 Ca2+ binding motifs provides not only an insight into the role of Ca2+ and Ca2+-binding proteins in bacterial systems, but also a way to explore and define the role of Ca2+ in other biological systems (calciomics).
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